Starting phenix.real_space_refine on Fri Mar 6 13:01:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mbv_23748/03_2026/7mbv_23748.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mbv_23748/03_2026/7mbv_23748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mbv_23748/03_2026/7mbv_23748.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mbv_23748/03_2026/7mbv_23748.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mbv_23748/03_2026/7mbv_23748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mbv_23748/03_2026/7mbv_23748.map" } resolution = 2.8 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= 0.002 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 20228 2.51 5 N 5180 2.21 5 O 5212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30804 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7570 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 138} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 952} Chain breaks: 4 Unresolved non-hydrogen bonds: 474 Unresolved non-hydrogen angles: 586 Unresolved non-hydrogen dihedrals: 370 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'ASP:plan': 28, 'ARG:plan': 9, 'GLU:plan': 29, 'GLN:plan1': 13, 'HIS:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 325 Chain: "B" Number of atoms: 7570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7570 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 138} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 952} Chain breaks: 4 Unresolved non-hydrogen bonds: 474 Unresolved non-hydrogen angles: 586 Unresolved non-hydrogen dihedrals: 370 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'ASP:plan': 28, 'ARG:plan': 9, 'GLU:plan': 29, 'GLN:plan1': 13, 'HIS:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 325 Chain: "C" Number of atoms: 7570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7570 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 138} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 952} Chain breaks: 4 Unresolved non-hydrogen bonds: 474 Unresolved non-hydrogen angles: 586 Unresolved non-hydrogen dihedrals: 370 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'ASP:plan': 28, 'ARG:plan': 9, 'GLU:plan': 29, 'GLN:plan1': 13, 'HIS:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 325 Chain: "D" Number of atoms: 7570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7570 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 138} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 952} Chain breaks: 4 Unresolved non-hydrogen bonds: 474 Unresolved non-hydrogen angles: 586 Unresolved non-hydrogen dihedrals: 370 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'ASP:plan': 28, 'ARG:plan': 9, 'GLU:plan': 29, 'GLN:plan1': 13, 'HIS:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 325 Chain: "A" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 131 Unusual residues: {' CA': 2, 'NAG': 1, 'YUS': 1, 'YUV': 1, 'YUY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 131 Unusual residues: {' CA': 2, 'NAG': 1, 'YUS': 1, 'YUV': 1, 'YUY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 131 Unusual residues: {' CA': 2, 'NAG': 1, 'YUS': 1, 'YUV': 1, 'YUY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 131 Unusual residues: {' CA': 2, 'NAG': 1, 'YUS': 1, 'YUV': 1, 'YUY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2187 SG CYS A 324 74.973 108.199 30.106 1.00 38.87 S ATOM 9757 SG CYS B 324 35.523 74.978 30.112 1.00 38.87 S ATOM 17327 SG CYS C 324 68.755 35.522 30.118 1.00 38.87 S ATOM 24897 SG CYS D 324 108.205 68.756 30.106 1.00 38.87 S Time building chain proxies: 8.03, per 1000 atoms: 0.26 Number of scatterers: 30804 At special positions: 0 Unit cell: (144.55, 144.55, 155.288, 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 5212 8.00 N 5180 7.00 C 20228 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: 2.57 Conformation dependent library (CDL) restraints added in 1.3 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: 196 helices and 12 sheets defined 70.3% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 40 through 51 removed outlier: 3.750A pdb=" N ILE A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 90 removed outlier: 3.922A pdb=" N SER A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 119 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: 3.786A 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 330 through 333 removed outlier: 3.740A pdb=" N ASP A 333 " --> pdb=" O GLU A 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 330 through 333' Processing helix chain 'A' and resid 334 through 344 Processing helix chain 'A' and resid 346 through 354 Processing helix chain 'A' and resid 362 through 376 removed outlier: 3.569A pdb=" N LEU A 366 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLU A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) 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: 3.686A pdb=" N THR A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 462 removed outlier: 3.661A pdb=" N VAL A 454 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 510 Processing helix chain 'A' and resid 513 through 523 Processing helix chain 'A' and resid 526 through 545 removed outlier: 4.109A pdb=" N HIS A 543 " --> pdb=" O LYS A 539 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU A 544 " --> pdb=" O GLU A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 556 Processing helix chain 'A' and resid 558 through 574 removed outlier: 3.638A pdb=" N PHE A 562 " --> pdb=" O LYS A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 584 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 644 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 790 Processing helix chain 'A' and resid 791 through 812 Processing helix chain 'A' and resid 816 through 839 removed outlier: 4.043A pdb=" N ILE A 836 " --> pdb=" O THR A 832 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N HIS A 837 " --> pdb=" O LEU A 833 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A 839 " --> pdb=" O LEU A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 842 No H-bonds generated for 'chain 'A' and resid 840 through 842' Processing helix chain 'A' and resid 845 through 882 removed outlier: 4.818A pdb=" N LYS A 857 " --> pdb=" O GLU A 853 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ASP A 858 " --> pdb=" O ARG A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 902 removed outlier: 4.920A pdb=" N ARG A 898 " --> pdb=" O ARG A 894 " (cutoff:3.500A) Proline residue: A 899 - end of helix Processing helix chain 'A' and resid 903 through 905 No H-bonds generated for 'chain 'A' and resid 903 through 905' 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 931 Processing helix chain 'A' and resid 942 through 994 removed outlier: 3.760A pdb=" N VAL A 946 " --> pdb=" O ALA A 942 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 961 " --> pdb=" O THR A 957 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LEU A 962 " --> pdb=" O ASN A 958 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N GLU A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ASN A 979 " --> pdb=" O VAL A 975 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN A 990 " --> pdb=" O PHE A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1020 removed outlier: 3.902A 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 Processing helix chain 'B' and resid 40 through 51 removed outlier: 3.751A pdb=" N ILE B 44 " --> pdb=" O ASP B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 90 removed outlier: 3.922A pdb=" N SER B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 119 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: 3.786A 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 330 through 333 removed outlier: 3.740A pdb=" N ASP B 333 " --> pdb=" O GLU B 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 330 through 333' Processing helix chain 'B' and resid 334 through 344 Processing helix chain 'B' and resid 346 through 354 Processing helix chain 'B' and resid 362 through 376 removed outlier: 3.569A pdb=" N LEU B 366 " --> pdb=" O SER B 362 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU B 368 " --> pdb=" O GLN B 364 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL B 369 " --> pdb=" O ASP B 365 " (cutoff:3.500A) 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: 3.685A pdb=" N THR B 416 " --> pdb=" O ASN B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 462 removed outlier: 3.661A pdb=" N VAL B 454 " --> pdb=" O THR B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 510 Processing helix chain 'B' and resid 513 through 523 Processing helix chain 'B' and resid 526 through 545 removed outlier: 4.109A pdb=" N HIS B 543 " --> pdb=" O LYS B 539 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU B 544 " --> pdb=" O GLU B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 556 Processing helix chain 'B' and resid 558 through 574 removed outlier: 3.638A pdb=" N PHE B 562 " --> pdb=" O LYS B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 584 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 644 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 790 Processing helix chain 'B' and resid 791 through 812 Processing helix chain 'B' and resid 816 through 839 removed outlier: 4.042A pdb=" N ILE B 836 " --> pdb=" O THR B 832 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N HIS B 837 " --> pdb=" O LEU B 833 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE B 839 " --> pdb=" O LEU B 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 842 No H-bonds generated for 'chain 'B' and resid 840 through 842' Processing helix chain 'B' and resid 845 through 882 removed outlier: 4.817A pdb=" N LYS B 857 " --> pdb=" O GLU B 853 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ASP B 858 " --> pdb=" O ARG B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 902 removed outlier: 4.919A pdb=" N ARG B 898 " --> pdb=" O ARG B 894 " (cutoff:3.500A) Proline residue: B 899 - end of helix Processing helix chain 'B' and resid 903 through 905 No H-bonds generated for 'chain 'B' and resid 903 through 905' 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 931 Processing helix chain 'B' and resid 942 through 994 removed outlier: 3.760A pdb=" N VAL B 946 " --> pdb=" O ALA B 942 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU B 961 " --> pdb=" O THR B 957 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LEU B 962 " --> pdb=" O ASN B 958 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N GLU B 978 " --> pdb=" O GLN B 974 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ASN B 979 " --> pdb=" O VAL B 975 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN B 990 " --> pdb=" O PHE B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 1005 through 1020 removed outlier: 3.902A 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 Processing helix chain 'C' and resid 40 through 51 removed outlier: 3.750A pdb=" N ILE C 44 " --> pdb=" O ASP C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 90 removed outlier: 3.922A pdb=" N SER C 90 " --> pdb=" O LYS C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 119 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: 3.786A 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 330 through 333 removed outlier: 3.740A pdb=" N ASP C 333 " --> pdb=" O GLU C 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 330 through 333' Processing helix chain 'C' and resid 334 through 344 Processing helix chain 'C' and resid 346 through 354 Processing helix chain 'C' and resid 362 through 376 removed outlier: 3.569A pdb=" N LEU C 366 " --> pdb=" O SER C 362 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU C 368 " --> pdb=" O GLN C 364 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL C 369 " --> pdb=" O ASP C 365 " (cutoff:3.500A) 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: 3.686A pdb=" N THR C 416 " --> pdb=" O ASN C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 462 removed outlier: 3.661A pdb=" N VAL C 454 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 510 Processing helix chain 'C' and resid 513 through 523 Processing helix chain 'C' and resid 526 through 545 removed outlier: 4.109A pdb=" N HIS C 543 " --> pdb=" O LYS C 539 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU C 544 " --> pdb=" O GLU C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 556 Processing helix chain 'C' and resid 558 through 574 removed outlier: 3.638A pdb=" N PHE C 562 " --> pdb=" O LYS C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 584 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 644 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 790 Processing helix chain 'C' and resid 791 through 812 Processing helix chain 'C' and resid 816 through 839 removed outlier: 4.043A pdb=" N ILE C 836 " --> pdb=" O THR C 832 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N HIS C 837 " --> pdb=" O LEU C 833 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE C 839 " --> pdb=" O LEU C 835 " (cutoff:3.500A) Processing helix chain 'C' and resid 840 through 842 No H-bonds generated for 'chain 'C' and resid 840 through 842' Processing helix chain 'C' and resid 845 through 882 removed outlier: 4.817A pdb=" N LYS C 857 " --> pdb=" O GLU C 853 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ASP C 858 " --> pdb=" O ARG C 854 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 902 removed outlier: 4.920A pdb=" N ARG C 898 " --> pdb=" O ARG C 894 " (cutoff:3.500A) Proline residue: C 899 - end of helix Processing helix chain 'C' and resid 903 through 905 No H-bonds generated for 'chain 'C' and resid 903 through 905' 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 931 Processing helix chain 'C' and resid 942 through 994 removed outlier: 3.760A pdb=" N VAL C 946 " --> pdb=" O ALA C 942 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C 961 " --> pdb=" O THR C 957 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LEU C 962 " --> pdb=" O ASN C 958 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N GLU C 978 " --> pdb=" O GLN C 974 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ASN C 979 " --> pdb=" O VAL C 975 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN C 990 " --> pdb=" O PHE C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1020 removed outlier: 3.903A 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 Processing helix chain 'D' and resid 40 through 51 removed outlier: 3.750A pdb=" N ILE D 44 " --> pdb=" O ASP D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 90 removed outlier: 3.922A pdb=" N SER D 90 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 119 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: 3.786A 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 330 through 333 removed outlier: 3.740A pdb=" N ASP D 333 " --> pdb=" O GLU D 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 330 through 333' Processing helix chain 'D' and resid 334 through 344 Processing helix chain 'D' and resid 346 through 354 Processing helix chain 'D' and resid 362 through 376 removed outlier: 3.569A pdb=" N LEU D 366 " --> pdb=" O SER D 362 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU D 368 " --> pdb=" O GLN D 364 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL D 369 " --> pdb=" O ASP D 365 " (cutoff:3.500A) 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: 3.686A pdb=" N THR D 416 " --> pdb=" O ASN D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 462 removed outlier: 3.661A pdb=" N VAL D 454 " --> pdb=" O THR D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 510 Processing helix chain 'D' and resid 513 through 523 Processing helix chain 'D' and resid 526 through 545 removed outlier: 4.109A pdb=" N HIS D 543 " --> pdb=" O LYS D 539 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU D 544 " --> pdb=" O GLU D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 556 Processing helix chain 'D' and resid 558 through 574 removed outlier: 3.638A pdb=" N PHE D 562 " --> pdb=" O LYS D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 584 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 644 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 790 Processing helix chain 'D' and resid 791 through 812 Processing helix chain 'D' and resid 816 through 839 removed outlier: 4.043A pdb=" N ILE D 836 " --> pdb=" O THR D 832 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N HIS D 837 " --> pdb=" O LEU D 833 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE D 839 " --> pdb=" O LEU D 835 " (cutoff:3.500A) Processing helix chain 'D' and resid 840 through 842 No H-bonds generated for 'chain 'D' and resid 840 through 842' Processing helix chain 'D' and resid 845 through 882 removed outlier: 4.817A pdb=" N LYS D 857 " --> pdb=" O GLU D 853 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ASP D 858 " --> pdb=" O ARG D 854 " (cutoff:3.500A) Processing helix chain 'D' and resid 887 through 902 removed outlier: 4.921A pdb=" N ARG D 898 " --> pdb=" O ARG D 894 " (cutoff:3.500A) Proline residue: D 899 - end of helix Processing helix chain 'D' and resid 903 through 905 No H-bonds generated for 'chain 'D' and resid 903 through 905' 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 931 Processing helix chain 'D' and resid 942 through 994 removed outlier: 3.760A pdb=" N VAL D 946 " --> pdb=" O ALA D 942 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU D 961 " --> pdb=" O THR D 957 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N LEU D 962 " --> pdb=" O ASN D 958 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N GLU D 978 " --> pdb=" O GLN D 974 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ASN D 979 " --> pdb=" O VAL D 975 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN D 990 " --> pdb=" O PHE D 986 " (cutoff:3.500A) Processing helix chain 'D' and resid 1005 through 1020 removed outlier: 3.902A 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 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 32 removed outlier: 3.604A pdb=" N THR A 28 " --> pdb=" O PHE A 22 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE A 32 " --> pdb=" O GLY A 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 36 removed outlier: 8.789A pdb=" N HIS A 173 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA A 128 " --> pdb=" O HIS A 173 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE A 175 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLY A 130 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N VAL A 177 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA A 132 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA A 93 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ILE A 129 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ILE A 95 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE A 131 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR A 97 " --> pdb=" O ILE A 131 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N LEU A 241 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N CYS A 217 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LEU A 243 " --> pdb=" O CYS A 217 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU A 219 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TRP A 240 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N HIS A 304 " --> pdb=" O TRP A 240 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ILE A 242 " --> pdb=" O HIS A 304 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 202 through 204 Processing sheet with id=AA4, first strand: chain 'B' and resid 28 through 32 removed outlier: 3.605A pdb=" N THR B 28 " --> pdb=" O PHE B 22 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE B 32 " --> pdb=" O GLY B 18 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 34 through 36 removed outlier: 8.790A pdb=" N HIS B 173 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA B 128 " --> pdb=" O HIS B 173 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE B 175 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLY B 130 " --> pdb=" O ILE B 175 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL B 177 " --> pdb=" O GLY B 130 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA B 132 " --> pdb=" O VAL B 177 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA B 93 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILE B 129 " --> pdb=" O ALA B 93 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ILE B 95 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE B 131 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR B 97 " --> pdb=" O ILE B 131 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N LEU B 241 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N CYS B 217 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LEU B 243 " --> pdb=" O CYS B 217 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU B 219 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TRP B 240 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N HIS B 304 " --> pdb=" O TRP B 240 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ILE B 242 " --> pdb=" O HIS B 304 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 202 through 204 Processing sheet with id=AA7, first strand: chain 'C' and resid 28 through 32 removed outlier: 3.605A pdb=" N THR C 28 " --> pdb=" O PHE C 22 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE C 32 " --> pdb=" O GLY C 18 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 34 through 36 removed outlier: 8.790A pdb=" N HIS C 173 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA C 128 " --> pdb=" O HIS C 173 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ILE C 175 " --> pdb=" O ALA C 128 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLY C 130 " --> pdb=" O ILE C 175 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N VAL C 177 " --> pdb=" O GLY C 130 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA C 132 " --> pdb=" O VAL C 177 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA C 93 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILE C 129 " --> pdb=" O ALA C 93 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ILE C 95 " --> pdb=" O ILE C 129 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE C 131 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR C 97 " --> pdb=" O ILE C 131 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N LEU C 241 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N CYS C 217 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LEU C 243 " --> pdb=" O CYS C 217 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU C 219 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TRP C 240 " --> pdb=" O THR C 302 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N HIS C 304 " --> pdb=" O TRP C 240 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ILE C 242 " --> pdb=" O HIS C 304 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 202 through 204 Processing sheet with id=AB1, first strand: chain 'D' and resid 28 through 32 removed outlier: 3.604A pdb=" N THR D 28 " --> pdb=" O PHE D 22 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE D 32 " --> pdb=" O GLY D 18 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 34 through 36 removed outlier: 8.790A pdb=" N HIS D 173 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA D 128 " --> pdb=" O HIS D 173 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ILE D 175 " --> pdb=" O ALA D 128 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLY D 130 " --> pdb=" O ILE D 175 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL D 177 " --> pdb=" O GLY D 130 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA D 132 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA D 93 " --> pdb=" O VAL D 127 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ILE D 129 " --> pdb=" O ALA D 93 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ILE D 95 " --> pdb=" O ILE D 129 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE D 131 " --> pdb=" O ILE D 95 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR D 97 " --> pdb=" O ILE D 131 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N LEU D 241 " --> pdb=" O VAL D 215 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N CYS D 217 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LEU D 243 " --> pdb=" O CYS D 217 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU D 219 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TRP D 240 " --> pdb=" O THR D 302 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N HIS D 304 " --> pdb=" O TRP D 240 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ILE D 242 " --> pdb=" O HIS D 304 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 202 through 204 2020 hydrogen bonds defined for protein. 5964 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: 7.25 Time building geometry restraints manager: 3.26 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: 9501 1.34 - 1.46: 4859 1.46 - 1.57: 16956 1.57 - 1.69: 4 1.69 - 1.81: 292 Bond restraints: 31612 Sorted by residual: bond pdb=" CB PRO A 746 " pdb=" CG PRO A 746 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.03e+00 bond pdb=" CB PRO B 746 " pdb=" CG PRO B 746 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.02e+00 bond pdb=" CB PRO D 746 " pdb=" CG PRO D 746 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.02e+00 bond pdb=" CB PRO C 746 " pdb=" CG PRO C 746 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.02e+00 bond pdb=" N YUS A1504 " pdb=" N1 YUS A1504 " ideal model delta sigma weight residual 1.342 1.376 -0.034 2.00e-02 2.50e+03 2.92e+00 ... (remaining 31607 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 41933 1.48 - 2.96: 1035 2.96 - 4.44: 188 4.44 - 5.93: 40 5.93 - 7.41: 16 Bond angle restraints: 43212 Sorted by residual: angle pdb=" CA PRO A 746 " pdb=" N PRO A 746 " pdb=" CD PRO A 746 " ideal model delta sigma weight residual 112.00 104.59 7.41 1.40e+00 5.10e-01 2.80e+01 angle pdb=" CA PRO C 746 " pdb=" N PRO C 746 " pdb=" CD PRO C 746 " ideal model delta sigma weight residual 112.00 104.63 7.37 1.40e+00 5.10e-01 2.78e+01 angle pdb=" CA PRO D 746 " pdb=" N PRO D 746 " pdb=" CD PRO D 746 " ideal model delta sigma weight residual 112.00 104.63 7.37 1.40e+00 5.10e-01 2.78e+01 angle pdb=" CA PRO B 746 " pdb=" N PRO B 746 " pdb=" CD PRO B 746 " ideal model delta sigma weight residual 112.00 104.63 7.37 1.40e+00 5.10e-01 2.78e+01 angle pdb=" C ASP C 463 " pdb=" CA ASP C 463 " pdb=" CB ASP C 463 " ideal model delta sigma weight residual 110.92 116.07 -5.15 1.59e+00 3.96e-01 1.05e+01 ... (remaining 43207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 17693 16.93 - 33.85: 1290 33.85 - 50.78: 221 50.78 - 67.71: 44 67.71 - 84.63: 24 Dihedral angle restraints: 19272 sinusoidal: 7592 harmonic: 11680 Sorted by residual: dihedral pdb=" CA ASP A 610 " pdb=" CB ASP A 610 " pdb=" CG ASP A 610 " pdb=" OD1 ASP A 610 " ideal model delta sinusoidal sigma weight residual -30.00 -89.40 59.40 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASP C 610 " pdb=" CB ASP C 610 " pdb=" CG ASP C 610 " pdb=" OD1 ASP C 610 " ideal model delta sinusoidal sigma weight residual -30.00 -89.36 59.36 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASP D 610 " pdb=" CB ASP D 610 " pdb=" CG ASP D 610 " pdb=" OD1 ASP D 610 " ideal model delta sinusoidal sigma weight residual -30.00 -89.36 59.36 1 2.00e+01 2.50e-03 1.18e+01 ... (remaining 19269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 5029 0.100 - 0.200: 91 0.200 - 0.300: 4 0.300 - 0.401: 0 0.401 - 0.501: 4 Chirality restraints: 5128 Sorted by residual: chirality pdb=" C1 NAG B1501 " pdb=" ND2 ASN B 921 " pdb=" C2 NAG B1501 " pdb=" O5 NAG B1501 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.27e+00 chirality pdb=" C1 NAG A1501 " pdb=" ND2 ASN A 921 " pdb=" C2 NAG A1501 " pdb=" O5 NAG A1501 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.27e+00 chirality pdb=" C1 NAG C1501 " pdb=" ND2 ASN C 921 " pdb=" C2 NAG C1501 " pdb=" O5 NAG C1501 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.27e+00 ... (remaining 5125 not shown) Planarity restraints: 5288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1501 " 0.338 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C7 NAG B1501 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG B1501 " 0.136 2.00e-02 2.50e+03 pdb=" N2 NAG B1501 " -0.522 2.00e-02 2.50e+03 pdb=" O7 NAG B1501 " 0.128 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1501 " 0.338 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C7 NAG C1501 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG C1501 " 0.136 2.00e-02 2.50e+03 pdb=" N2 NAG C1501 " -0.521 2.00e-02 2.50e+03 pdb=" O7 NAG C1501 " 0.128 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D3002 " 0.338 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C7 NAG D3002 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG D3002 " 0.136 2.00e-02 2.50e+03 pdb=" N2 NAG D3002 " -0.521 2.00e-02 2.50e+03 pdb=" O7 NAG D3002 " 0.128 2.00e-02 2.50e+03 ... (remaining 5285 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 7733 2.80 - 3.33: 30559 3.33 - 3.85: 53168 3.85 - 4.38: 60817 4.38 - 4.90: 103372 Nonbonded interactions: 255649 Sorted by model distance: nonbonded pdb=" O GLY D 524 " pdb=" NZ LYS D1049 " model vdw 2.280 3.120 nonbonded pdb=" O GLY A 524 " pdb=" NZ LYS A1049 " model vdw 2.280 3.120 nonbonded pdb=" O GLY C 524 " pdb=" NZ LYS C1049 " model vdw 2.280 3.120 nonbonded pdb=" O GLY B 524 " pdb=" NZ LYS B1049 " model vdw 2.280 3.120 nonbonded pdb=" OD1 ASP A 463 " pdb=" N ASP A 464 " model vdw 2.301 3.120 ... (remaining 255644 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: 0.08 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: 3.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 29.460 Find NCS groups from input model: 1.020 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: 0.010 Load rotamer database and sin/cos tables:7.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 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 0.087 31616 Z= 0.158 Angle : 0.605 14.094 43224 Z= 0.320 Chirality : 0.041 0.501 5128 Planarity : 0.010 0.292 5284 Dihedral : 12.274 84.632 11672 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: 1.48 (0.14), residues: 3944 helix: 1.56 (0.10), residues: 2620 sheet: 0.72 (0.32), residues: 252 loop : -0.30 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 448 TYR 0.012 0.001 TYR D 231 PHE 0.021 0.001 PHE A 734 TRP 0.070 0.002 TRP A 760 HIS 0.003 0.001 HIS B1060 Details of bonding type rmsd covalent geometry : bond 0.00332 (31612) covalent geometry : angle 0.58510 (43212) hydrogen bonds : bond 0.11715 ( 2020) hydrogen bonds : angle 5.04213 ( 5964) link_NAG-ASN : bond 0.01517 ( 4) link_NAG-ASN : angle 9.34044 ( 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 302 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 1.050 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.7258 time to fit residues: 254.6270 Evaluate side-chains 159 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.190 ------------------------------------------------------------------------------- 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: 6.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.6980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 ASN A 236 ASN A 304 HIS A 792 ASN A 943 ASN A1076 GLN B 233 ASN B 236 ASN B 304 HIS B 792 ASN B 943 ASN B1076 GLN C 233 ASN C 236 ASN C 792 ASN C 943 ASN C1076 GLN D 233 ASN D 236 ASN D 304 HIS D 792 ASN D 943 ASN D1076 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.089180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.060675 restraints weight = 66361.379| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 2.46 r_work: 0.2694 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 31616 Z= 0.197 Angle : 0.589 11.613 43224 Z= 0.297 Chirality : 0.040 0.253 5128 Planarity : 0.005 0.068 5284 Dihedral : 5.809 62.235 5276 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.38 % Allowed : 7.99 % Favored : 90.63 % 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: 1.84 (0.14), residues: 3944 helix: 1.88 (0.10), residues: 2604 sheet: 0.69 (0.31), residues: 256 loop : -0.21 (0.20), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1061 TYR 0.011 0.001 TYR A 559 PHE 0.018 0.001 PHE D 734 TRP 0.032 0.002 TRP C 760 HIS 0.004 0.001 HIS B1060 Details of bonding type rmsd covalent geometry : bond 0.00449 (31612) covalent geometry : angle 0.57145 (43212) hydrogen bonds : bond 0.05028 ( 2020) hydrogen bonds : angle 4.27608 ( 5964) link_NAG-ASN : bond 0.00559 ( 4) link_NAG-ASN : angle 8.68011 ( 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 240 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 199 time to evaluate : 1.177 Fit side-chains REVERT: A 31 LYS cc_start: 0.8524 (mttt) cc_final: 0.8160 (mtmp) REVERT: A 471 GLN cc_start: 0.8327 (mm110) cc_final: 0.8045 (pp30) REVERT: A 492 ASP cc_start: 0.8096 (m-30) cc_final: 0.7616 (t0) REVERT: A 785 MET cc_start: 0.8354 (mtp) cc_final: 0.8065 (mtp) REVERT: A 1028 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8309 (mp) REVERT: A 1078 LEU cc_start: 0.8682 (tp) cc_final: 0.8460 (tt) REVERT: B 31 LYS cc_start: 0.8535 (mttt) cc_final: 0.8168 (mtmp) REVERT: B 471 GLN cc_start: 0.8319 (mm110) cc_final: 0.8032 (pp30) REVERT: B 492 ASP cc_start: 0.8064 (m-30) cc_final: 0.7604 (t0) REVERT: B 1028 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8302 (mp) REVERT: C 31 LYS cc_start: 0.8535 (mttt) cc_final: 0.8164 (mtmp) REVERT: C 471 GLN cc_start: 0.8324 (mm110) cc_final: 0.8035 (pp30) REVERT: C 492 ASP cc_start: 0.8056 (m-30) cc_final: 0.7605 (t0) REVERT: C 1028 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8307 (mp) REVERT: C 1078 LEU cc_start: 0.8681 (tp) cc_final: 0.8473 (tt) REVERT: D 31 LYS cc_start: 0.8559 (mttt) cc_final: 0.8187 (mtmp) REVERT: D 471 GLN cc_start: 0.8320 (mm110) cc_final: 0.8042 (pp30) REVERT: D 492 ASP cc_start: 0.8087 (m-30) cc_final: 0.7602 (t0) REVERT: D 785 MET cc_start: 0.8354 (mtp) cc_final: 0.8062 (mtp) REVERT: D 1028 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8306 (mp) outliers start: 41 outliers final: 12 residues processed: 227 average time/residue: 0.7077 time to fit residues: 187.5172 Evaluate side-chains 177 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 1028 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 354 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 chunk 381 optimal weight: 0.1980 chunk 310 optimal weight: 30.0000 chunk 14 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 chunk 306 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 379 optimal weight: 0.0050 chunk 6 optimal weight: 2.9990 chunk 321 optimal weight: 9.9990 overall best weight: 2.2400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 ASN A 943 ASN B 376 ASN B 943 ASN C 376 ASN C 943 ASN D 376 ASN D 943 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.088355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.060125 restraints weight = 66625.477| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.46 r_work: 0.2686 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31616 Z= 0.172 Angle : 0.533 7.649 43224 Z= 0.274 Chirality : 0.039 0.171 5128 Planarity : 0.005 0.060 5284 Dihedral : 5.666 56.958 5276 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.62 % Allowed : 9.06 % Favored : 89.32 % 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: 2.02 (0.14), residues: 3944 helix: 2.05 (0.10), residues: 2612 sheet: 0.57 (0.30), residues: 256 loop : -0.17 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1080 TYR 0.009 0.001 TYR A 559 PHE 0.014 0.001 PHE B 828 TRP 0.018 0.001 TRP C 984 HIS 0.003 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00395 (31612) covalent geometry : angle 0.52480 (43212) hydrogen bonds : bond 0.04868 ( 2020) hydrogen bonds : angle 4.14821 ( 5964) link_NAG-ASN : bond 0.00037 ( 4) link_NAG-ASN : angle 5.64463 ( 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 225 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 177 time to evaluate : 1.144 Fit side-chains REVERT: A 31 LYS cc_start: 0.8436 (mttt) cc_final: 0.8018 (mtmp) REVERT: A 471 GLN cc_start: 0.8265 (mm110) cc_final: 0.7988 (pp30) REVERT: A 492 ASP cc_start: 0.8139 (m-30) cc_final: 0.7707 (t0) REVERT: A 1028 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8273 (mp) REVERT: B 31 LYS cc_start: 0.8447 (mttt) cc_final: 0.8029 (mtmp) REVERT: B 471 GLN cc_start: 0.8264 (mm110) cc_final: 0.7968 (pp30) REVERT: B 492 ASP cc_start: 0.8143 (m-30) cc_final: 0.7716 (t0) REVERT: B 1028 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8273 (mp) REVERT: C 31 LYS cc_start: 0.8447 (mttt) cc_final: 0.8028 (mtmp) REVERT: C 471 GLN cc_start: 0.8265 (mm110) cc_final: 0.7980 (pp30) REVERT: C 492 ASP cc_start: 0.8137 (m-30) cc_final: 0.7714 (t0) REVERT: C 1028 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8283 (mp) REVERT: D 31 LYS cc_start: 0.8437 (mttt) cc_final: 0.8021 (mtmp) REVERT: D 471 GLN cc_start: 0.8249 (mm110) cc_final: 0.7984 (pp30) REVERT: D 492 ASP cc_start: 0.8132 (m-30) cc_final: 0.7692 (t0) outliers start: 48 outliers final: 23 residues processed: 211 average time/residue: 0.6632 time to fit residues: 165.7690 Evaluate side-chains 182 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 943 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 943 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 943 ASN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 943 ASN Chi-restraints excluded: chain D residue 976 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 70 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 266 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 136 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 99 optimal weight: 20.0000 chunk 383 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 181 optimal weight: 0.9980 chunk 165 optimal weight: 0.4980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 943 ASN A1076 GLN B 943 ASN B1076 GLN C 943 ASN C1076 GLN D 943 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.088109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.059832 restraints weight = 66016.871| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 2.46 r_work: 0.2682 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2552 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31616 Z= 0.164 Angle : 0.529 8.535 43224 Z= 0.268 Chirality : 0.038 0.146 5128 Planarity : 0.005 0.058 5284 Dihedral : 5.246 47.821 5276 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.42 % Allowed : 10.88 % Favored : 87.70 % 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: 2.11 (0.14), residues: 3944 helix: 2.14 (0.10), residues: 2612 sheet: 0.50 (0.30), residues: 256 loop : -0.20 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1080 TYR 0.009 0.001 TYR C 45 PHE 0.013 0.001 PHE D 828 TRP 0.018 0.001 TRP C 984 HIS 0.002 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00378 (31612) covalent geometry : angle 0.52175 (43212) hydrogen bonds : bond 0.04765 ( 2020) hydrogen bonds : angle 4.09076 ( 5964) link_NAG-ASN : bond 0.00120 ( 4) link_NAG-ASN : angle 5.12759 ( 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 207 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 165 time to evaluate : 1.039 Fit side-chains REVERT: A 31 LYS cc_start: 0.8432 (mttt) cc_final: 0.8019 (mtmp) REVERT: A 270 LEU cc_start: 0.8540 (mm) cc_final: 0.8322 (mt) REVERT: A 471 GLN cc_start: 0.8234 (mm110) cc_final: 0.8017 (pp30) REVERT: A 492 ASP cc_start: 0.8196 (m-30) cc_final: 0.7960 (m-30) REVERT: A 779 MET cc_start: 0.8524 (tpt) cc_final: 0.7985 (ttt) REVERT: A 1028 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8258 (mp) REVERT: B 31 LYS cc_start: 0.8445 (mttt) cc_final: 0.8031 (mtmp) REVERT: B 270 LEU cc_start: 0.8550 (mm) cc_final: 0.8330 (mt) REVERT: B 471 GLN cc_start: 0.8235 (mm110) cc_final: 0.8004 (pp30) REVERT: B 492 ASP cc_start: 0.8204 (m-30) cc_final: 0.7769 (t0) REVERT: B 779 MET cc_start: 0.8510 (tpt) cc_final: 0.7948 (ttt) REVERT: B 1028 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8252 (mp) REVERT: C 31 LYS cc_start: 0.8438 (mttt) cc_final: 0.8017 (mtmp) REVERT: C 270 LEU cc_start: 0.8540 (mm) cc_final: 0.8316 (mt) REVERT: C 471 GLN cc_start: 0.8238 (mm110) cc_final: 0.8008 (pp30) REVERT: C 492 ASP cc_start: 0.8197 (m-30) cc_final: 0.7788 (t0) REVERT: C 779 MET cc_start: 0.8522 (tpt) cc_final: 0.7985 (ttt) REVERT: C 1028 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8259 (mp) REVERT: D 31 LYS cc_start: 0.8434 (mttt) cc_final: 0.8021 (mtmp) REVERT: D 47 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8455 (pp) REVERT: D 270 LEU cc_start: 0.8540 (mm) cc_final: 0.8320 (mt) REVERT: D 471 GLN cc_start: 0.8227 (mm110) cc_final: 0.8017 (pp30) REVERT: D 492 ASP cc_start: 0.8191 (m-30) cc_final: 0.7758 (t0) REVERT: D 779 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.8020 (tpt) outliers start: 42 outliers final: 16 residues processed: 197 average time/residue: 0.6960 time to fit residues: 162.6449 Evaluate side-chains 181 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 779 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 194 optimal weight: 4.9990 chunk 163 optimal weight: 0.9990 chunk 187 optimal weight: 0.8980 chunk 190 optimal weight: 0.1980 chunk 286 optimal weight: 2.9990 chunk 295 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 268 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 134 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 943 ASN B 943 ASN C 943 ASN D 882 HIS D 943 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.090240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.062383 restraints weight = 65885.209| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.45 r_work: 0.2742 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 31616 Z= 0.109 Angle : 0.491 9.415 43224 Z= 0.249 Chirality : 0.037 0.138 5128 Planarity : 0.004 0.055 5284 Dihedral : 4.714 40.063 5276 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.26 % Allowed : 10.95 % Favored : 86.79 % 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: 2.29 (0.14), residues: 3944 helix: 2.33 (0.10), residues: 2612 sheet: 0.28 (0.28), residues: 260 loop : -0.18 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1080 TYR 0.012 0.001 TYR C 45 PHE 0.011 0.001 PHE C 828 TRP 0.017 0.001 TRP C 984 HIS 0.002 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00229 (31612) covalent geometry : angle 0.48651 (43212) hydrogen bonds : bond 0.04044 ( 2020) hydrogen bonds : angle 3.92073 ( 5964) link_NAG-ASN : bond 0.00386 ( 4) link_NAG-ASN : angle 3.92509 ( 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 252 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 185 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 GLN cc_start: 0.8202 (mm110) cc_final: 0.7995 (pp30) REVERT: A 492 ASP cc_start: 0.8303 (m-30) cc_final: 0.8063 (m-30) REVERT: A 645 THR cc_start: 0.8858 (OUTLIER) cc_final: 0.8602 (p) REVERT: A 1028 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8241 (mp) REVERT: B 471 GLN cc_start: 0.8204 (mm110) cc_final: 0.7977 (pp30) REVERT: B 492 ASP cc_start: 0.8317 (m-30) cc_final: 0.8068 (m-30) REVERT: B 645 THR cc_start: 0.8900 (OUTLIER) cc_final: 0.8648 (p) REVERT: B 779 MET cc_start: 0.8558 (tpt) cc_final: 0.8076 (ttt) REVERT: B 1028 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8240 (mp) REVERT: C 31 LYS cc_start: 0.8431 (mttt) cc_final: 0.8069 (mtpt) REVERT: C 471 GLN cc_start: 0.8208 (mm110) cc_final: 0.7986 (pp30) REVERT: C 492 ASP cc_start: 0.8303 (m-30) cc_final: 0.8056 (m-30) REVERT: C 645 THR cc_start: 0.8898 (OUTLIER) cc_final: 0.8648 (p) REVERT: C 785 MET cc_start: 0.8321 (mtp) cc_final: 0.8105 (mtt) REVERT: C 1028 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8243 (mp) REVERT: D 47 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8445 (pp) REVERT: D 471 GLN cc_start: 0.8198 (mm110) cc_final: 0.7993 (pp30) REVERT: D 492 ASP cc_start: 0.8307 (m-30) cc_final: 0.8069 (m-30) REVERT: D 645 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8604 (p) REVERT: D 779 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.7998 (tpt) outliers start: 67 outliers final: 10 residues processed: 234 average time/residue: 0.5901 time to fit residues: 166.0784 Evaluate side-chains 186 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 779 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 247 optimal weight: 0.9990 chunk 10 optimal weight: 20.0000 chunk 267 optimal weight: 0.0970 chunk 328 optimal weight: 9.9990 chunk 154 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 264 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 182 optimal weight: 5.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 943 ASN B 943 ASN C 943 ASN D 943 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.088707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.060599 restraints weight = 66126.186| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.44 r_work: 0.2701 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31616 Z= 0.140 Angle : 0.510 10.021 43224 Z= 0.256 Chirality : 0.037 0.139 5128 Planarity : 0.004 0.056 5284 Dihedral : 4.499 40.586 5276 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.68 % Allowed : 12.30 % Favored : 86.02 % 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: 2.38 (0.14), residues: 3944 helix: 2.40 (0.10), residues: 2612 sheet: 0.25 (0.28), residues: 260 loop : -0.13 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1080 TYR 0.018 0.001 TYR C 45 PHE 0.012 0.001 PHE B 567 TRP 0.016 0.001 TRP B 984 HIS 0.002 0.001 HIS B1060 Details of bonding type rmsd covalent geometry : bond 0.00319 (31612) covalent geometry : angle 0.50550 (43212) hydrogen bonds : bond 0.04401 ( 2020) hydrogen bonds : angle 3.92963 ( 5964) link_NAG-ASN : bond 0.00273 ( 4) link_NAG-ASN : angle 4.00344 ( 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 225 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 175 time to evaluate : 1.242 Fit side-chains REVERT: A 31 LYS cc_start: 0.8417 (mttt) cc_final: 0.8028 (mtmt) REVERT: A 270 LEU cc_start: 0.8597 (mm) cc_final: 0.8387 (mt) REVERT: A 471 GLN cc_start: 0.8220 (mm110) cc_final: 0.7969 (pp30) REVERT: A 492 ASP cc_start: 0.8376 (m-30) cc_final: 0.8117 (m-30) REVERT: A 645 THR cc_start: 0.8868 (OUTLIER) cc_final: 0.8554 (p) REVERT: A 1028 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8209 (mp) REVERT: B 31 LYS cc_start: 0.8414 (mttt) cc_final: 0.8023 (mtmt) REVERT: B 86 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8536 (mppt) REVERT: B 270 LEU cc_start: 0.8593 (mm) cc_final: 0.8381 (mt) REVERT: B 471 GLN cc_start: 0.8205 (mm110) cc_final: 0.7961 (pp30) REVERT: B 492 ASP cc_start: 0.8269 (m-30) cc_final: 0.8041 (m-30) REVERT: B 645 THR cc_start: 0.8894 (OUTLIER) cc_final: 0.8571 (p) REVERT: B 1028 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8209 (mp) REVERT: C 31 LYS cc_start: 0.8436 (mttt) cc_final: 0.8045 (mtmt) REVERT: C 270 LEU cc_start: 0.8600 (mm) cc_final: 0.8380 (mt) REVERT: C 471 GLN cc_start: 0.8229 (mm110) cc_final: 0.7980 (pp30) REVERT: C 492 ASP cc_start: 0.8351 (m-30) cc_final: 0.8096 (m-30) REVERT: C 645 THR cc_start: 0.8894 (OUTLIER) cc_final: 0.8576 (p) REVERT: C 785 MET cc_start: 0.8399 (mtp) cc_final: 0.8170 (mtt) REVERT: C 1028 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8212 (mp) REVERT: D 31 LYS cc_start: 0.8440 (mttt) cc_final: 0.8057 (mtmt) REVERT: D 47 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8446 (pp) REVERT: D 270 LEU cc_start: 0.8602 (mm) cc_final: 0.8390 (mt) REVERT: D 471 GLN cc_start: 0.8211 (mm110) cc_final: 0.7961 (pp30) REVERT: D 492 ASP cc_start: 0.8270 (m-30) cc_final: 0.8042 (m-30) REVERT: D 645 THR cc_start: 0.8868 (OUTLIER) cc_final: 0.8551 (p) outliers start: 50 outliers final: 24 residues processed: 210 average time/residue: 0.6706 time to fit residues: 166.7377 Evaluate side-chains 200 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 943 ASN Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain B residue 943 ASN Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 838 ILE Chi-restraints excluded: chain C residue 943 ASN Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 838 ILE Chi-restraints excluded: chain D residue 943 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 32 optimal weight: 10.0000 chunk 185 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 20.0000 chunk 316 optimal weight: 20.0000 chunk 54 optimal weight: 0.9980 chunk 262 optimal weight: 1.9990 chunk 376 optimal weight: 1.9990 chunk 263 optimal weight: 0.9980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 943 ASN B 943 ASN B1076 GLN C 943 ASN C1076 GLN D 943 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.087738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.059549 restraints weight = 66425.345| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 2.44 r_work: 0.2676 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2545 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 31616 Z= 0.175 Angle : 0.528 10.808 43224 Z= 0.266 Chirality : 0.038 0.137 5128 Planarity : 0.004 0.057 5284 Dihedral : 4.420 41.472 5276 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.82 % Allowed : 12.63 % Favored : 85.55 % 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: 2.36 (0.14), residues: 3944 helix: 2.38 (0.10), residues: 2608 sheet: 0.19 (0.29), residues: 260 loop : -0.10 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1080 TYR 0.011 0.001 TYR C 45 PHE 0.013 0.001 PHE B 567 TRP 0.016 0.001 TRP D 984 HIS 0.002 0.001 HIS B1060 Details of bonding type rmsd covalent geometry : bond 0.00405 (31612) covalent geometry : angle 0.52445 (43212) hydrogen bonds : bond 0.04641 ( 2020) hydrogen bonds : angle 3.98145 ( 5964) link_NAG-ASN : bond 0.00277 ( 4) link_NAG-ASN : angle 3.77361 ( 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 226 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 172 time to evaluate : 1.130 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8423 (mttt) cc_final: 0.8035 (mtmt) REVERT: A 270 LEU cc_start: 0.8622 (mm) cc_final: 0.8418 (mt) REVERT: A 471 GLN cc_start: 0.8214 (mm110) cc_final: 0.7967 (pp30) REVERT: A 492 ASP cc_start: 0.8306 (m-30) cc_final: 0.8078 (m-30) REVERT: A 645 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8596 (p) REVERT: A 785 MET cc_start: 0.8372 (mtp) cc_final: 0.8167 (mtt) REVERT: A 1028 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8247 (mp) REVERT: B 31 LYS cc_start: 0.8421 (mttt) cc_final: 0.8032 (mtmt) REVERT: B 270 LEU cc_start: 0.8611 (mm) cc_final: 0.8406 (mt) REVERT: B 471 GLN cc_start: 0.8206 (mm110) cc_final: 0.7941 (pp30) REVERT: B 492 ASP cc_start: 0.8282 (m-30) cc_final: 0.8055 (m-30) REVERT: B 645 THR cc_start: 0.8897 (OUTLIER) cc_final: 0.8581 (p) REVERT: B 1028 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8237 (mp) REVERT: C 270 LEU cc_start: 0.8613 (mm) cc_final: 0.8404 (mt) REVERT: C 471 GLN cc_start: 0.8213 (mm110) cc_final: 0.7963 (pp30) REVERT: C 492 ASP cc_start: 0.8291 (m-30) cc_final: 0.8060 (m-30) REVERT: C 645 THR cc_start: 0.8896 (OUTLIER) cc_final: 0.8581 (p) REVERT: C 1028 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8238 (mp) REVERT: D 31 LYS cc_start: 0.8432 (mttt) cc_final: 0.8041 (mtmt) REVERT: D 47 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8428 (pp) REVERT: D 270 LEU cc_start: 0.8622 (mm) cc_final: 0.8420 (mt) REVERT: D 471 GLN cc_start: 0.8205 (mm110) cc_final: 0.7961 (pp30) REVERT: D 492 ASP cc_start: 0.8279 (m-30) cc_final: 0.8064 (m-30) REVERT: D 645 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8592 (p) REVERT: D 779 MET cc_start: 0.8704 (tpt) cc_final: 0.8268 (ttt) outliers start: 54 outliers final: 29 residues processed: 209 average time/residue: 0.6517 time to fit residues: 161.9031 Evaluate side-chains 208 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 171 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain B residue 867 SER Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 838 ILE Chi-restraints excluded: chain C residue 867 SER Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 838 ILE Chi-restraints excluded: chain D residue 867 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 361 optimal weight: 0.6980 chunk 287 optimal weight: 0.9990 chunk 254 optimal weight: 0.8980 chunk 368 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 128 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 376 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 943 ASN B 943 ASN C 943 ASN D 943 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.088692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.060526 restraints weight = 66269.103| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 2.44 r_work: 0.2711 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 31616 Z= 0.126 Angle : 0.497 11.500 43224 Z= 0.250 Chirality : 0.037 0.135 5128 Planarity : 0.004 0.057 5284 Dihedral : 4.244 41.081 5276 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.65 % Allowed : 13.14 % Favored : 85.21 % 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: 2.43 (0.14), residues: 3944 helix: 2.44 (0.10), residues: 2612 sheet: 0.18 (0.29), residues: 260 loop : -0.10 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1080 TYR 0.011 0.001 TYR C 45 PHE 0.011 0.001 PHE B 828 TRP 0.017 0.001 TRP D 984 HIS 0.002 0.000 HIS C 221 Details of bonding type rmsd covalent geometry : bond 0.00283 (31612) covalent geometry : angle 0.49407 (43212) hydrogen bonds : bond 0.04238 ( 2020) hydrogen bonds : angle 3.90174 ( 5964) link_NAG-ASN : bond 0.00305 ( 4) link_NAG-ASN : angle 3.36004 ( 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 218 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 169 time to evaluate : 1.131 Fit side-chains REVERT: A 31 LYS cc_start: 0.8425 (mttt) cc_final: 0.8035 (mtmt) REVERT: A 270 LEU cc_start: 0.8639 (mm) cc_final: 0.8432 (mt) REVERT: A 492 ASP cc_start: 0.8331 (m-30) cc_final: 0.8099 (m-30) REVERT: A 645 THR cc_start: 0.8932 (OUTLIER) cc_final: 0.8641 (p) REVERT: A 785 MET cc_start: 0.8357 (mtp) cc_final: 0.8144 (mtt) REVERT: A 1028 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8241 (mp) REVERT: A 1081 MET cc_start: 0.8017 (ppp) cc_final: 0.7810 (ppp) REVERT: B 31 LYS cc_start: 0.8434 (mttt) cc_final: 0.8049 (mtmt) REVERT: B 86 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8537 (mppt) REVERT: B 270 LEU cc_start: 0.8639 (mm) cc_final: 0.8432 (mt) REVERT: B 471 GLN cc_start: 0.8190 (mm110) cc_final: 0.7983 (pp30) REVERT: B 492 ASP cc_start: 0.8288 (m-30) cc_final: 0.8083 (m-30) REVERT: B 645 THR cc_start: 0.8938 (OUTLIER) cc_final: 0.8647 (p) REVERT: B 1028 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8240 (mp) REVERT: C 31 LYS cc_start: 0.8434 (mttt) cc_final: 0.8032 (mtmt) REVERT: C 270 LEU cc_start: 0.8647 (mm) cc_final: 0.8432 (mt) REVERT: C 492 ASP cc_start: 0.8331 (m-30) cc_final: 0.8097 (m-30) REVERT: C 645 THR cc_start: 0.8940 (OUTLIER) cc_final: 0.8651 (p) REVERT: C 1028 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8240 (mp) REVERT: D 31 LYS cc_start: 0.8442 (mttt) cc_final: 0.8050 (mtmt) REVERT: D 47 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8437 (pp) REVERT: D 270 LEU cc_start: 0.8641 (mm) cc_final: 0.8437 (mt) REVERT: D 645 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8644 (p) outliers start: 49 outliers final: 25 residues processed: 204 average time/residue: 0.7051 time to fit residues: 170.2107 Evaluate side-chains 202 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 168 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 838 ILE Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 838 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 194 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 360 optimal weight: 4.9990 chunk 339 optimal weight: 7.9990 chunk 344 optimal weight: 0.5980 chunk 356 optimal weight: 4.9990 chunk 395 optimal weight: 0.9980 chunk 342 optimal weight: 0.9980 chunk 226 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 338 optimal weight: 8.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 943 ASN B 943 ASN ** C 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 943 ASN ** D 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 943 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.086886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.058591 restraints weight = 66367.136| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 2.43 r_work: 0.2666 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2537 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 31616 Z= 0.181 Angle : 0.535 12.566 43224 Z= 0.270 Chirality : 0.038 0.137 5128 Planarity : 0.005 0.059 5284 Dihedral : 4.252 42.119 5276 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.58 % Allowed : 13.58 % Favored : 84.84 % 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: 2.38 (0.14), residues: 3944 helix: 2.40 (0.10), residues: 2608 sheet: 0.20 (0.29), residues: 260 loop : -0.09 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1080 TYR 0.010 0.001 TYR C 989 PHE 0.014 0.001 PHE B 567 TRP 0.016 0.001 TRP A 984 HIS 0.002 0.001 HIS A1060 Details of bonding type rmsd covalent geometry : bond 0.00420 (31612) covalent geometry : angle 0.53271 (43212) hydrogen bonds : bond 0.04794 ( 2020) hydrogen bonds : angle 3.99536 ( 5964) link_NAG-ASN : bond 0.00233 ( 4) link_NAG-ASN : angle 3.10900 ( 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 212 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 165 time to evaluate : 1.163 Fit side-chains REVERT: A 31 LYS cc_start: 0.8421 (mttt) cc_final: 0.8037 (mtmt) REVERT: A 492 ASP cc_start: 0.8323 (m-30) cc_final: 0.8112 (m-30) REVERT: A 645 THR cc_start: 0.8948 (OUTLIER) cc_final: 0.8664 (p) REVERT: A 785 MET cc_start: 0.8384 (mtp) cc_final: 0.8166 (mtt) REVERT: A 1028 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8285 (mp) REVERT: A 1081 MET cc_start: 0.7982 (ppp) cc_final: 0.7775 (ppp) REVERT: B 31 LYS cc_start: 0.8421 (mttt) cc_final: 0.8036 (mtmt) REVERT: B 645 THR cc_start: 0.8961 (OUTLIER) cc_final: 0.8648 (p) REVERT: B 779 MET cc_start: 0.8687 (tpt) cc_final: 0.8337 (ttt) REVERT: B 1028 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8279 (mp) REVERT: C 31 LYS cc_start: 0.8429 (mttt) cc_final: 0.8039 (mtmt) REVERT: C 47 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8648 (pp) REVERT: C 270 LEU cc_start: 0.8731 (mm) cc_final: 0.8527 (mt) REVERT: C 492 ASP cc_start: 0.8317 (m-30) cc_final: 0.8104 (m-30) REVERT: C 645 THR cc_start: 0.8959 (OUTLIER) cc_final: 0.8649 (p) REVERT: C 1028 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8283 (mp) REVERT: D 31 LYS cc_start: 0.8433 (mttt) cc_final: 0.8048 (mtmt) REVERT: D 47 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8440 (pp) REVERT: D 645 THR cc_start: 0.8945 (OUTLIER) cc_final: 0.8658 (p) outliers start: 47 outliers final: 29 residues processed: 201 average time/residue: 0.6725 time to fit residues: 160.1071 Evaluate side-chains 199 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 161 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 943 ASN Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 867 SER Chi-restraints excluded: chain B residue 943 ASN Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 867 SER Chi-restraints excluded: chain C residue 943 ASN Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 867 SER Chi-restraints excluded: chain D residue 943 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 164 optimal weight: 2.9990 chunk 253 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 222 optimal weight: 20.0000 chunk 51 optimal weight: 0.9980 chunk 260 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 chunk 111 optimal weight: 10.0000 chunk 331 optimal weight: 5.9990 chunk 277 optimal weight: 7.9990 chunk 251 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 943 ASN ** B 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 943 ASN C 943 ASN D 943 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.086976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.058637 restraints weight = 66221.563| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 2.45 r_work: 0.2665 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2535 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 31616 Z= 0.207 Angle : 0.897 59.192 43224 Z= 0.519 Chirality : 0.041 0.554 5128 Planarity : 0.005 0.073 5284 Dihedral : 4.266 42.123 5276 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.15 % Allowed : 13.92 % Favored : 84.94 % Cbeta Deviations : 0.11 % 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: 2.38 (0.14), residues: 3944 helix: 2.40 (0.10), residues: 2608 sheet: 0.20 (0.29), residues: 260 loop : -0.10 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1080 TYR 0.009 0.001 TYR B 989 PHE 0.014 0.001 PHE B 567 TRP 0.016 0.001 TRP C 984 HIS 0.002 0.001 HIS A1060 Details of bonding type rmsd covalent geometry : bond 0.00447 (31612) covalent geometry : angle 0.89599 (43212) hydrogen bonds : bond 0.04778 ( 2020) hydrogen bonds : angle 4.00206 ( 5964) link_NAG-ASN : bond 0.00238 ( 4) link_NAG-ASN : angle 3.10076 ( 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 195 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 1.225 Fit side-chains REVERT: A 31 LYS cc_start: 0.8432 (mttt) cc_final: 0.8048 (mtmt) REVERT: A 492 ASP cc_start: 0.8333 (m-30) cc_final: 0.8112 (m-30) REVERT: A 645 THR cc_start: 0.8957 (OUTLIER) cc_final: 0.8674 (p) REVERT: A 785 MET cc_start: 0.8391 (mtp) cc_final: 0.8173 (mtt) REVERT: A 1028 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8282 (mp) REVERT: A 1081 MET cc_start: 0.7993 (ppp) cc_final: 0.7782 (ppp) REVERT: B 31 LYS cc_start: 0.8431 (mttt) cc_final: 0.8046 (mtmt) REVERT: B 645 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8659 (p) REVERT: B 779 MET cc_start: 0.8689 (tpt) cc_final: 0.8341 (ttt) REVERT: B 1028 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8283 (mp) REVERT: C 31 LYS cc_start: 0.8445 (mttt) cc_final: 0.8056 (mtmt) REVERT: C 47 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8640 (pp) REVERT: C 270 LEU cc_start: 0.8736 (mm) cc_final: 0.8531 (mt) REVERT: C 492 ASP cc_start: 0.8322 (m-30) cc_final: 0.8097 (m-30) REVERT: C 645 THR cc_start: 0.8966 (OUTLIER) cc_final: 0.8660 (p) REVERT: C 1028 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8284 (mp) REVERT: D 31 LYS cc_start: 0.8448 (mttt) cc_final: 0.8063 (mtmt) REVERT: D 47 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8435 (pp) REVERT: D 645 THR cc_start: 0.8956 (OUTLIER) cc_final: 0.8669 (p) outliers start: 34 outliers final: 25 residues processed: 189 average time/residue: 0.6958 time to fit residues: 154.9391 Evaluate side-chains 195 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 867 SER Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 867 SER Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 867 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 58 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 192 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 382 optimal weight: 9.9990 chunk 386 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 393 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 235 optimal weight: 8.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 943 ASN ** B 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 943 ASN C 943 ASN D 943 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.086811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.058551 restraints weight = 66629.952| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 2.46 r_work: 0.2657 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2527 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 31616 Z= 0.212 Angle : 0.886 55.967 43224 Z= 0.506 Chirality : 0.039 0.138 5128 Planarity : 0.005 0.059 5284 Dihedral : 4.258 42.117 5276 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.25 % Allowed : 13.92 % Favored : 84.84 % 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: 2.35 (0.14), residues: 3944 helix: 2.37 (0.10), residues: 2608 sheet: 0.20 (0.29), residues: 260 loop : -0.10 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1080 TYR 0.009 0.001 TYR B 989 PHE 0.013 0.001 PHE B 567 TRP 0.015 0.001 TRP C 984 HIS 0.002 0.001 HIS D1060 Details of bonding type rmsd covalent geometry : bond 0.00501 (31612) covalent geometry : angle 0.88505 (43212) hydrogen bonds : bond 0.04844 ( 2020) hydrogen bonds : angle 3.99535 ( 5964) link_NAG-ASN : bond 0.00226 ( 4) link_NAG-ASN : angle 3.09172 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9748.52 seconds wall clock time: 166 minutes 44.95 seconds (10004.95 seconds total)