Starting phenix.real_space_refine on Thu Nov 20 06:14:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mbp_23740/11_2025/7mbp_23740.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mbp_23740/11_2025/7mbp_23740.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/7mbp_23740/11_2025/7mbp_23740.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mbp_23740/11_2025/7mbp_23740.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mbp_23740/11_2025/7mbp_23740.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mbp_23740/11_2025/7mbp_23740.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= 0.004 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: 4 Type Number sf(0) Gaussians S 176 5.16 5 C 20168 2.51 5 N 5188 2.21 5 O 5176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30708 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7574 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 137} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 952} Chain breaks: 4 Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 585 Unresolved non-hydrogen dihedrals: 368 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ASP:plan': 30, 'ARG:plan': 8, 'GLU:plan': 29, 'GLN:plan1': 13, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 333 Chain: "A" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 103 Unusual residues: {'NAG': 1, 'YUV': 1, 'YUY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 103 Unusual residues: {'NAG': 1, 'YUV': 1, 'YUY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 103 Unusual residues: {'NAG': 1, 'YUV': 1, 'YUY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 103 Unusual residues: {'NAG': 1, 'YUV': 1, 'YUY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, D Time building chain proxies: 9.28, per 1000 atoms: 0.30 Number of scatterers: 30708 At special positions: 0 Unit cell: (144.838, 144.838, 156.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 176 16.00 O 5176 8.00 N 5188 7.00 C 20168 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: 3.04 Conformation dependent library (CDL) restraints added in 1.4 seconds 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7600 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 8 sheets defined 70.4% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 40 through 51 removed outlier: 3.876A pdb=" N ILE A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 89 Processing helix chain 'A' and resid 102 through 119 removed outlier: 3.652A pdb=" N ASN A 107 " --> pdb=" O GLY A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 139 through 145 removed outlier: 3.795A pdb=" N LEU A 143 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 199 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 removed outlier: 3.543A pdb=" N ILE A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 275 Processing helix chain 'A' and resid 280 through 298 removed outlier: 3.773A pdb=" N HIS A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY A 298 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 328 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: 4.762A pdb=" N GLU A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 387 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: 3.534A pdb=" N THR A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 462 removed outlier: 3.618A pdb=" N VAL A 454 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 511 removed outlier: 3.758A pdb=" N GLN A 511 " --> pdb=" O TRP A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 522 Processing helix chain 'A' and resid 526 through 545 removed outlier: 3.533A pdb=" N ALA A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N HIS A 543 " --> pdb=" O LYS A 539 " (cutoff:3.500A) removed outlier: 4.051A 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 Processing helix chain 'A' and resid 576 through 584 removed outlier: 3.848A pdb=" N SER A 580 " --> pdb=" O ASP A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 602 Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 609 through 622 Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 640 through 645 Processing helix chain 'A' and resid 699 through 714 Processing helix chain 'A' and resid 715 through 740 Processing helix chain 'A' and resid 751 through 774 Processing helix chain 'A' and resid 780 through 791 removed outlier: 3.967A pdb=" N ASP A 791 " --> pdb=" O LEU A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 813 removed outlier: 3.594A pdb=" N ALA A 813 " --> pdb=" O SER A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 840 removed outlier: 3.545A pdb=" N MET A 829 " --> pdb=" O ALA A 825 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE A 836 " --> pdb=" O THR A 832 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS A 837 " --> pdb=" O LEU A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 882 removed outlier: 4.838A pdb=" N LYS A 857 " --> pdb=" O GLU A 853 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASP A 858 " --> pdb=" O ARG A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 902 removed outlier: 5.057A 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 932 Processing helix chain 'A' and resid 942 through 998 removed outlier: 3.712A pdb=" N VAL A 946 " --> pdb=" O ALA A 942 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 961 " --> pdb=" O THR A 957 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU A 962 " --> pdb=" O ASN A 958 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N GLU A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ASN A 979 " --> pdb=" O VAL A 975 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE A 982 " --> pdb=" O GLU A 978 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN A 990 " --> pdb=" O PHE A 986 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER A 997 " --> pdb=" O VAL A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1020 removed outlier: 4.121A 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: 3.876A pdb=" N ILE B 44 " --> pdb=" O ASP B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 89 Processing helix chain 'B' and resid 102 through 119 removed outlier: 3.651A pdb=" N ASN B 107 " --> pdb=" O GLY B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 139 through 145 removed outlier: 3.797A pdb=" N LEU B 143 " --> pdb=" O ASN B 139 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER B 145 " --> pdb=" O ASP B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 199 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 removed outlier: 3.543A pdb=" N ILE B 252 " --> pdb=" O GLY B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 275 Processing helix chain 'B' and resid 280 through 298 removed outlier: 3.772A pdb=" N HIS B 297 " --> pdb=" O ARG B 293 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY B 298 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 328 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: 4.762A pdb=" N GLU B 368 " --> pdb=" O GLN B 364 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL B 369 " --> pdb=" O ASP B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 387 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: 3.536A pdb=" N THR B 416 " --> pdb=" O ASN B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 462 removed outlier: 3.619A pdb=" N VAL B 454 " --> pdb=" O THR B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 511 removed outlier: 3.758A pdb=" N GLN B 511 " --> pdb=" O TRP B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 524 Processing helix chain 'B' and resid 526 through 545 removed outlier: 3.533A pdb=" N ALA B 530 " --> pdb=" O GLU B 526 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N HIS B 543 " --> pdb=" O LYS B 539 " (cutoff:3.500A) removed outlier: 4.051A 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 Processing helix chain 'B' and resid 576 through 584 removed outlier: 3.847A pdb=" N SER B 580 " --> pdb=" O ASP B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 602 Processing helix chain 'B' and resid 603 through 608 Processing helix chain 'B' and resid 609 through 622 Processing helix chain 'B' and resid 629 through 639 Processing helix chain 'B' and resid 640 through 645 Processing helix chain 'B' and resid 699 through 714 Processing helix chain 'B' and resid 715 through 740 Processing helix chain 'B' and resid 751 through 774 Processing helix chain 'B' and resid 780 through 791 removed outlier: 3.968A pdb=" N ASP B 791 " --> pdb=" O LEU B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 813 removed outlier: 3.594A pdb=" N ALA B 813 " --> pdb=" O SER B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 840 removed outlier: 3.545A pdb=" N MET B 829 " --> pdb=" O ALA B 825 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE B 836 " --> pdb=" O THR B 832 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N HIS B 837 " --> pdb=" O LEU B 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 882 removed outlier: 4.839A pdb=" N LYS B 857 " --> pdb=" O GLU B 853 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASP B 858 " --> pdb=" O ARG B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 902 removed outlier: 5.059A 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 932 Processing helix chain 'B' and resid 942 through 998 removed outlier: 3.713A pdb=" N VAL B 946 " --> pdb=" O ALA B 942 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU B 961 " --> pdb=" O THR B 957 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LEU B 962 " --> pdb=" O ASN B 958 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N GLU B 978 " --> pdb=" O GLN B 974 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ASN B 979 " --> pdb=" O VAL B 975 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE B 982 " --> pdb=" O GLU B 978 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN B 990 " --> pdb=" O PHE B 986 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER B 997 " --> pdb=" O VAL B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1005 through 1020 removed outlier: 4.118A 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: 3.876A pdb=" N ILE C 44 " --> pdb=" O ASP C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 89 Processing helix chain 'C' and resid 102 through 119 removed outlier: 3.651A pdb=" N ASN C 107 " --> pdb=" O GLY C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 137 No H-bonds generated for 'chain 'C' and resid 135 through 137' Processing helix chain 'C' and resid 139 through 145 removed outlier: 3.795A pdb=" N LEU C 143 " --> pdb=" O ASN C 139 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER C 145 " --> pdb=" O ASP C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 199 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 removed outlier: 3.544A pdb=" N ILE C 252 " --> pdb=" O GLY C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 275 Processing helix chain 'C' and resid 280 through 298 removed outlier: 3.773A pdb=" N HIS C 297 " --> pdb=" O ARG C 293 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY C 298 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 328 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: 4.761A pdb=" N GLU C 368 " --> pdb=" O GLN C 364 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL C 369 " --> pdb=" O ASP C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 387 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: 3.536A pdb=" N THR C 416 " --> pdb=" O ASN C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 462 removed outlier: 3.619A pdb=" N VAL C 454 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 511 removed outlier: 3.757A pdb=" N GLN C 511 " --> pdb=" O TRP C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 524 Processing helix chain 'C' and resid 526 through 545 removed outlier: 3.533A pdb=" N ALA C 530 " --> pdb=" O GLU C 526 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N HIS C 543 " --> pdb=" O LYS C 539 " (cutoff:3.500A) removed outlier: 4.051A 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 Processing helix chain 'C' and resid 576 through 584 removed outlier: 3.848A pdb=" N SER C 580 " --> pdb=" O ASP C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 602 Processing helix chain 'C' and resid 603 through 608 Processing helix chain 'C' and resid 609 through 622 Processing helix chain 'C' and resid 629 through 639 Processing helix chain 'C' and resid 640 through 645 Processing helix chain 'C' and resid 699 through 714 Processing helix chain 'C' and resid 715 through 740 Processing helix chain 'C' and resid 751 through 774 Processing helix chain 'C' and resid 780 through 791 removed outlier: 3.968A pdb=" N ASP C 791 " --> pdb=" O LEU C 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 791 through 813 removed outlier: 3.594A pdb=" N ALA C 813 " --> pdb=" O SER C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 840 removed outlier: 3.545A pdb=" N MET C 829 " --> pdb=" O ALA C 825 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE C 836 " --> pdb=" O THR C 832 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N HIS C 837 " --> pdb=" O LEU C 833 " (cutoff:3.500A) Processing helix chain 'C' and resid 845 through 882 removed outlier: 4.838A pdb=" N LYS C 857 " --> pdb=" O GLU C 853 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASP C 858 " --> pdb=" O ARG C 854 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 902 removed outlier: 5.058A 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 932 Processing helix chain 'C' and resid 942 through 998 removed outlier: 3.713A pdb=" N VAL C 946 " --> pdb=" O ALA C 942 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C 961 " --> pdb=" O THR C 957 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N LEU C 962 " --> pdb=" O ASN C 958 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N GLU C 978 " --> pdb=" O GLN C 974 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ASN C 979 " --> pdb=" O VAL C 975 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE C 982 " --> pdb=" O GLU C 978 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN C 990 " --> pdb=" O PHE C 986 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER C 997 " --> pdb=" O VAL C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1020 removed outlier: 4.119A 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: 3.876A pdb=" N ILE D 44 " --> pdb=" O ASP D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 89 Processing helix chain 'D' and resid 102 through 119 removed outlier: 3.651A pdb=" N ASN D 107 " --> pdb=" O GLY D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 137 No H-bonds generated for 'chain 'D' and resid 135 through 137' Processing helix chain 'D' and resid 139 through 145 removed outlier: 3.796A pdb=" N LEU D 143 " --> pdb=" O ASN D 139 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER D 145 " --> pdb=" O ASP D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 199 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 removed outlier: 3.544A pdb=" N ILE D 252 " --> pdb=" O GLY D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 275 Processing helix chain 'D' and resid 280 through 298 removed outlier: 3.775A pdb=" N HIS D 297 " --> pdb=" O ARG D 293 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY D 298 " --> pdb=" O ILE D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 328 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: 4.761A pdb=" N GLU D 368 " --> pdb=" O GLN D 364 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N VAL D 369 " --> pdb=" O ASP D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 387 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: 3.535A pdb=" N THR D 416 " --> pdb=" O ASN D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 462 removed outlier: 3.617A pdb=" N VAL D 454 " --> pdb=" O THR D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 511 removed outlier: 3.758A pdb=" N GLN D 511 " --> pdb=" O TRP D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 524 Processing helix chain 'D' and resid 526 through 545 removed outlier: 3.533A pdb=" N ALA D 530 " --> pdb=" O GLU D 526 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N HIS D 543 " --> pdb=" O LYS D 539 " (cutoff:3.500A) removed outlier: 4.050A 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 Processing helix chain 'D' and resid 576 through 584 removed outlier: 3.848A pdb=" N SER D 580 " --> pdb=" O ASP D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 602 Processing helix chain 'D' and resid 603 through 608 Processing helix chain 'D' and resid 609 through 622 Processing helix chain 'D' and resid 629 through 639 Processing helix chain 'D' and resid 640 through 645 Processing helix chain 'D' and resid 699 through 714 Processing helix chain 'D' and resid 715 through 740 Processing helix chain 'D' and resid 751 through 774 Processing helix chain 'D' and resid 780 through 791 removed outlier: 3.968A pdb=" N ASP D 791 " --> pdb=" O LEU D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 791 through 813 removed outlier: 3.595A pdb=" N ALA D 813 " --> pdb=" O SER D 809 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 840 removed outlier: 3.545A pdb=" N MET D 829 " --> pdb=" O ALA D 825 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE D 836 " --> pdb=" O THR D 832 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS D 837 " --> pdb=" O LEU D 833 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 882 removed outlier: 4.837A pdb=" N LYS D 857 " --> pdb=" O GLU D 853 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASP D 858 " --> pdb=" O ARG D 854 " (cutoff:3.500A) Processing helix chain 'D' and resid 887 through 902 removed outlier: 5.058A 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 932 Processing helix chain 'D' and resid 942 through 998 removed outlier: 3.712A pdb=" N VAL D 946 " --> pdb=" O ALA D 942 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 961 " --> pdb=" O THR D 957 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LEU D 962 " --> pdb=" O ASN D 958 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N GLU D 978 " --> pdb=" O GLN D 974 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ASN D 979 " --> pdb=" O VAL D 975 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE D 982 " --> pdb=" O GLU D 978 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN D 990 " --> pdb=" O PHE D 986 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER D 997 " --> pdb=" O VAL D 993 " (cutoff:3.500A) Processing helix chain 'D' and resid 1005 through 1020 removed outlier: 4.119A 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 152 through 155 removed outlier: 3.628A pdb=" N TYR A 154 " --> pdb=" O ASP A 21 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA A 128 " --> pdb=" O HIS A 173 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ILE A 175 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLY A 130 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL A 177 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA A 132 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N VAL A 60 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU A 218 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ALA A 62 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 243 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N TRP A 240 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N HIS A 304 " --> pdb=" O TRP A 240 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ILE A 242 " --> pdb=" O HIS A 304 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 585 through 586 removed outlier: 3.811A pdb=" N ALA A 592 " --> pdb=" O THR A 586 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 152 through 155 removed outlier: 3.629A pdb=" N TYR B 154 " --> pdb=" O ASP B 21 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA B 128 " --> pdb=" O HIS B 173 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE B 175 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLY B 130 " --> pdb=" O ILE B 175 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL B 177 " --> pdb=" O GLY B 130 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA B 132 " --> pdb=" O VAL B 177 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL B 60 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU B 218 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ALA B 62 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 243 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TRP B 240 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N HIS B 304 " --> pdb=" O TRP B 240 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ILE B 242 " --> pdb=" O HIS B 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 585 through 586 removed outlier: 3.811A pdb=" N ALA B 592 " --> pdb=" O THR B 586 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 152 through 155 removed outlier: 3.627A pdb=" N TYR C 154 " --> pdb=" O ASP C 21 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA C 128 " --> pdb=" O HIS C 173 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ILE C 175 " --> pdb=" O ALA C 128 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLY C 130 " --> pdb=" O ILE C 175 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL C 177 " --> pdb=" O GLY C 130 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA C 132 " --> pdb=" O VAL C 177 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL C 60 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU C 218 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ALA C 62 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU C 243 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N TRP C 240 " --> pdb=" O THR C 302 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N HIS C 304 " --> pdb=" O TRP C 240 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ILE C 242 " --> pdb=" O HIS C 304 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 585 through 586 removed outlier: 3.811A pdb=" N ALA C 592 " --> pdb=" O THR C 586 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 152 through 155 removed outlier: 3.628A pdb=" N TYR D 154 " --> pdb=" O ASP D 21 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA D 128 " --> pdb=" O HIS D 173 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE D 175 " --> pdb=" O ALA D 128 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLY D 130 " --> pdb=" O ILE D 175 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL D 177 " --> pdb=" O GLY D 130 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA D 132 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N VAL D 60 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU D 218 " --> pdb=" O VAL D 60 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA D 62 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU D 243 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N TRP D 240 " --> pdb=" O THR D 302 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N HIS D 304 " --> pdb=" O TRP D 240 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ILE D 242 " --> pdb=" O HIS D 304 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 585 through 586 removed outlier: 3.810A pdb=" N ALA D 592 " --> pdb=" O THR D 586 " (cutoff:3.500A) 2034 hydrogen bonds defined for protein. 5982 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.84 Time building geometry restraints manager: 3.87 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: 9470 1.34 - 1.46: 4483 1.46 - 1.57: 17267 1.57 - 1.69: 0 1.69 - 1.81: 292 Bond restraints: 31512 Sorted by residual: bond pdb=" C PRO D1003 " pdb=" O PRO D1003 " ideal model delta sigma weight residual 1.243 1.226 0.017 8.50e-03 1.38e+04 4.01e+00 bond pdb=" C PRO C1003 " pdb=" O PRO C1003 " ideal model delta sigma weight residual 1.243 1.226 0.017 8.50e-03 1.38e+04 3.99e+00 bond pdb=" C PRO A1003 " pdb=" O PRO A1003 " ideal model delta sigma weight residual 1.243 1.226 0.017 8.50e-03 1.38e+04 3.99e+00 bond pdb=" C PRO B1003 " pdb=" O PRO B1003 " ideal model delta sigma weight residual 1.243 1.227 0.016 8.50e-03 1.38e+04 3.57e+00 bond pdb=" C3 NAG D3002 " pdb=" O3 NAG D3002 " ideal model delta sigma weight residual 1.403 1.433 -0.030 2.00e-02 2.50e+03 2.22e+00 ... (remaining 31507 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 41864 1.47 - 2.94: 967 2.94 - 4.40: 189 4.40 - 5.87: 34 5.87 - 7.34: 14 Bond angle restraints: 43068 Sorted by residual: angle pdb=" C MET A 917 " pdb=" N PRO A 918 " pdb=" CA PRO A 918 " ideal model delta sigma weight residual 119.85 125.71 -5.86 1.01e+00 9.80e-01 3.36e+01 angle pdb=" C MET D 917 " pdb=" N PRO D 918 " pdb=" CA PRO D 918 " ideal model delta sigma weight residual 119.85 125.69 -5.84 1.01e+00 9.80e-01 3.34e+01 angle pdb=" C MET C 917 " pdb=" N PRO C 918 " pdb=" CA PRO C 918 " ideal model delta sigma weight residual 119.85 125.66 -5.81 1.01e+00 9.80e-01 3.31e+01 angle pdb=" C MET B 917 " pdb=" N PRO B 918 " pdb=" CA PRO B 918 " ideal model delta sigma weight residual 119.85 125.65 -5.80 1.01e+00 9.80e-01 3.29e+01 angle pdb=" C ALA C1002 " pdb=" N PRO C1003 " pdb=" CA PRO C1003 " ideal model delta sigma weight residual 119.66 123.10 -3.44 7.20e-01 1.93e+00 2.29e+01 ... (remaining 43063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.25: 17463 15.25 - 30.50: 1381 30.50 - 45.75: 348 45.75 - 61.00: 68 61.00 - 76.26: 16 Dihedral angle restraints: 19276 sinusoidal: 7600 harmonic: 11676 Sorted by residual: dihedral pdb=" N ASN A 921 " pdb=" CA ASN A 921 " pdb=" CB ASN A 921 " pdb=" CG ASN A 921 " ideal model delta sinusoidal sigma weight residual -180.00 -124.90 -55.10 3 1.50e+01 4.44e-03 9.33e+00 dihedral pdb=" N ASN C 921 " pdb=" CA ASN C 921 " pdb=" CB ASN C 921 " pdb=" CG ASN C 921 " ideal model delta sinusoidal sigma weight residual -180.00 -124.92 -55.08 3 1.50e+01 4.44e-03 9.33e+00 dihedral pdb=" N ASN D 921 " pdb=" CA ASN D 921 " pdb=" CB ASN D 921 " pdb=" CG ASN D 921 " ideal model delta sinusoidal sigma weight residual -180.00 -124.94 -55.06 3 1.50e+01 4.44e-03 9.32e+00 ... (remaining 19273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 4564 0.060 - 0.119: 536 0.119 - 0.179: 16 0.179 - 0.238: 8 0.238 - 0.298: 12 Chirality restraints: 5136 Sorted by residual: chirality pdb=" C41 YUY A1503 " pdb=" C40 YUY A1503 " pdb=" C42 YUY A1503 " pdb=" O7 YUY A1503 " both_signs ideal model delta sigma weight residual False -2.21 -2.51 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" C41 YUY D3001 " pdb=" C40 YUY D3001 " pdb=" C42 YUY D3001 " pdb=" O7 YUY D3001 " both_signs ideal model delta sigma weight residual False -2.21 -2.51 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C41 YUY C1503 " pdb=" C40 YUY C1503 " pdb=" C42 YUY C1503 " pdb=" O7 YUY C1503 " both_signs ideal model delta sigma weight residual False -2.21 -2.51 0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 5133 not shown) Planarity restraints: 5264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 760 " 0.033 2.00e-02 2.50e+03 3.64e-02 3.32e+01 pdb=" CG TRP C 760 " -0.092 2.00e-02 2.50e+03 pdb=" CD1 TRP C 760 " 0.058 2.00e-02 2.50e+03 pdb=" CD2 TRP C 760 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C 760 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP C 760 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 760 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 760 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 760 " 0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP C 760 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 760 " 0.033 2.00e-02 2.50e+03 3.64e-02 3.32e+01 pdb=" CG TRP B 760 " -0.092 2.00e-02 2.50e+03 pdb=" CD1 TRP B 760 " 0.058 2.00e-02 2.50e+03 pdb=" CD2 TRP B 760 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP B 760 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP B 760 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 760 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 760 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 760 " 0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP B 760 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 760 " 0.033 2.00e-02 2.50e+03 3.64e-02 3.31e+01 pdb=" CG TRP A 760 " -0.092 2.00e-02 2.50e+03 pdb=" CD1 TRP A 760 " 0.058 2.00e-02 2.50e+03 pdb=" CD2 TRP A 760 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 760 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP A 760 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 760 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 760 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 760 " 0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP A 760 " 0.005 2.00e-02 2.50e+03 ... (remaining 5261 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 192 2.60 - 3.18: 26777 3.18 - 3.75: 49820 3.75 - 4.33: 65496 4.33 - 4.90: 110699 Nonbonded interactions: 252984 Sorted by model distance: nonbonded pdb=" O MET B 917 " pdb=" O8 YUY B1503 " model vdw 2.028 3.040 nonbonded pdb=" O MET C 917 " pdb=" O8 YUY C1503 " model vdw 2.042 3.040 nonbonded pdb=" O MET D 917 " pdb=" O8 YUY D3001 " model vdw 2.044 3.040 nonbonded pdb=" O MET A 917 " pdb=" O8 YUY A1503 " model vdw 2.059 3.040 nonbonded pdb=" O GLN B 138 " pdb=" OH TYR B 154 " model vdw 2.265 3.040 ... (remaining 252979 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.09 Found NCS groups: ncs_group { reference = (chain 'A' and resid 16 through 1092) selection = (chain 'B' and resid 16 through 1092) selection = (chain 'C' and resid 16 through 1092) selection = (chain 'D' and resid 16 through 1092) } 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: 2.150 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: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 29.850 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 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 0.034 31516 Z= 0.167 Angle : 0.565 7.340 43080 Z= 0.330 Chirality : 0.040 0.298 5136 Planarity : 0.005 0.054 5260 Dihedral : 12.164 76.256 11676 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.74 % Favored : 97.16 % Rotamer: Outliers : 0.30 % Allowed : 1.45 % Favored : 98.25 % 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: 1.88 (0.14), residues: 3944 helix: 2.11 (0.10), residues: 2628 sheet: -0.78 (0.31), residues: 272 loop : -0.39 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D1061 TYR 0.011 0.001 TYR D 989 PHE 0.012 0.001 PHE C 969 TRP 0.092 0.002 TRP C 760 HIS 0.002 0.000 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00309 (31512) covalent geometry : angle 0.56368 (43068) hydrogen bonds : bond 0.11807 ( 2034) hydrogen bonds : angle 5.02176 ( 5982) link_NAG-ASN : bond 0.00156 ( 4) link_NAG-ASN : angle 2.06865 ( 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 169 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 160 time to evaluate : 1.206 Fit side-chains REVERT: A 64 MET cc_start: 0.8288 (mmm) cc_final: 0.7704 (mmt) REVERT: A 136 MET cc_start: 0.8331 (mmp) cc_final: 0.7941 (mmp) REVERT: A 812 MET cc_start: 0.9110 (mmt) cc_final: 0.8782 (mmt) REVERT: A 843 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8038 (mptt) REVERT: B 64 MET cc_start: 0.8300 (mmm) cc_final: 0.7711 (mmt) REVERT: B 136 MET cc_start: 0.8338 (mmp) cc_final: 0.7950 (mmp) REVERT: B 812 MET cc_start: 0.9127 (mmt) cc_final: 0.8805 (mmt) REVERT: B 843 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8034 (mptt) REVERT: C 64 MET cc_start: 0.8301 (mmm) cc_final: 0.7710 (mmt) REVERT: C 136 MET cc_start: 0.8332 (mmp) cc_final: 0.7937 (mmp) REVERT: C 812 MET cc_start: 0.9123 (mmt) cc_final: 0.8796 (mmt) REVERT: C 843 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8045 (mptt) REVERT: D 64 MET cc_start: 0.8360 (mmm) cc_final: 0.7794 (mmt) REVERT: D 136 MET cc_start: 0.8359 (mmp) cc_final: 0.7948 (mmp) REVERT: D 812 MET cc_start: 0.9110 (mmt) cc_final: 0.8771 (mmt) REVERT: D 843 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8035 (mptt) outliers start: 9 outliers final: 0 residues processed: 168 average time/residue: 0.8081 time to fit residues: 158.1357 Evaluate side-chains 132 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 128 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 843 LYS Chi-restraints excluded: chain B residue 843 LYS Chi-restraints excluded: chain C residue 843 LYS Chi-restraints excluded: chain D residue 843 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 0.8980 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 794 ASN ** A 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 HIS B 794 ASN ** B 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 HIS C 794 ASN ** C 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 HIS D 794 ASN ** D 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.074212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.049616 restraints weight = 85397.502| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.56 r_work: 0.2677 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 31516 Z= 0.288 Angle : 0.576 6.913 43080 Z= 0.300 Chirality : 0.040 0.166 5136 Planarity : 0.005 0.059 5260 Dihedral : 5.348 50.279 5268 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.21 % Allowed : 4.58 % Favored : 94.21 % 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: 1.91 (0.14), residues: 3944 helix: 2.15 (0.10), residues: 2628 sheet: -0.57 (0.33), residues: 240 loop : -0.51 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 202 TYR 0.012 0.002 TYR D 989 PHE 0.025 0.002 PHE A 734 TRP 0.029 0.002 TRP D 760 HIS 0.003 0.001 HIS D 58 Details of bonding type rmsd covalent geometry : bond 0.00672 (31512) covalent geometry : angle 0.57597 (43068) hydrogen bonds : bond 0.05353 ( 2034) hydrogen bonds : angle 4.33805 ( 5982) link_NAG-ASN : bond 0.00013 ( 4) link_NAG-ASN : angle 1.45054 ( 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 168 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 1.228 Fit side-chains REVERT: A 64 MET cc_start: 0.8674 (mmm) cc_final: 0.8042 (mmt) REVERT: A 136 MET cc_start: 0.8456 (mmp) cc_final: 0.8112 (mmp) REVERT: A 257 MET cc_start: 0.8886 (mmm) cc_final: 0.8629 (mmm) REVERT: A 370 MET cc_start: 0.9190 (OUTLIER) cc_final: 0.8429 (tpp) REVERT: A 843 LYS cc_start: 0.9447 (OUTLIER) cc_final: 0.8313 (mptt) REVERT: B 64 MET cc_start: 0.8674 (mmm) cc_final: 0.8047 (mmt) REVERT: B 136 MET cc_start: 0.8438 (mmp) cc_final: 0.8088 (mmp) REVERT: B 257 MET cc_start: 0.8888 (mmm) cc_final: 0.8602 (mmm) REVERT: B 370 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8439 (tpp) REVERT: B 843 LYS cc_start: 0.9436 (OUTLIER) cc_final: 0.8322 (mptt) REVERT: C 64 MET cc_start: 0.8676 (mmm) cc_final: 0.8042 (mmt) REVERT: C 136 MET cc_start: 0.8457 (mmp) cc_final: 0.8105 (mmp) REVERT: C 257 MET cc_start: 0.8886 (mmm) cc_final: 0.8621 (mmm) REVERT: C 370 MET cc_start: 0.9184 (OUTLIER) cc_final: 0.8425 (tpp) REVERT: C 843 LYS cc_start: 0.9442 (OUTLIER) cc_final: 0.8312 (mptt) REVERT: D 64 MET cc_start: 0.8649 (mmm) cc_final: 0.8030 (mmt) REVERT: D 136 MET cc_start: 0.8444 (mmp) cc_final: 0.8100 (mmp) REVERT: D 257 MET cc_start: 0.8877 (mmm) cc_final: 0.8616 (mmm) REVERT: D 370 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.8445 (tpp) REVERT: D 814 MET cc_start: 0.9102 (tpt) cc_final: 0.8900 (tpt) REVERT: D 843 LYS cc_start: 0.9438 (OUTLIER) cc_final: 0.8326 (mptt) outliers start: 36 outliers final: 8 residues processed: 160 average time/residue: 0.7506 time to fit residues: 140.6054 Evaluate side-chains 148 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 370 MET Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 843 LYS Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 843 LYS Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 843 LYS Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 370 MET Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 843 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 130 optimal weight: 10.0000 chunk 229 optimal weight: 10.0000 chunk 190 optimal weight: 0.0870 chunk 19 optimal weight: 9.9990 chunk 207 optimal weight: 4.9990 chunk 356 optimal weight: 5.9990 chunk 373 optimal weight: 1.9990 chunk 220 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 chunk 211 optimal weight: 30.0000 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.075441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.051151 restraints weight = 85012.997| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.55 r_work: 0.2717 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 31516 Z= 0.165 Angle : 0.489 6.532 43080 Z= 0.257 Chirality : 0.037 0.159 5136 Planarity : 0.004 0.059 5260 Dihedral : 4.960 46.343 5268 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.84 % Allowed : 7.17 % Favored : 91.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.14), residues: 3944 helix: 2.35 (0.10), residues: 2608 sheet: -0.65 (0.32), residues: 248 loop : -0.53 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1080 TYR 0.013 0.001 TYR B 559 PHE 0.013 0.001 PHE C 734 TRP 0.017 0.001 TRP B 760 HIS 0.002 0.001 HIS D 115 Details of bonding type rmsd covalent geometry : bond 0.00375 (31512) covalent geometry : angle 0.48844 (43068) hydrogen bonds : bond 0.04606 ( 2034) hydrogen bonds : angle 4.10736 ( 5982) link_NAG-ASN : bond 0.00061 ( 4) link_NAG-ASN : angle 1.05137 ( 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 157 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 1.204 Fit side-chains REVERT: A 64 MET cc_start: 0.8600 (mmm) cc_final: 0.7993 (mmt) REVERT: A 136 MET cc_start: 0.8427 (mmp) cc_final: 0.8070 (mmp) REVERT: A 843 LYS cc_start: 0.9397 (OUTLIER) cc_final: 0.8295 (mptt) REVERT: B 64 MET cc_start: 0.8603 (mmm) cc_final: 0.7994 (mmt) REVERT: B 136 MET cc_start: 0.8433 (mmp) cc_final: 0.8074 (mmp) REVERT: B 257 MET cc_start: 0.8948 (mmm) cc_final: 0.8741 (mmm) REVERT: B 370 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8374 (tpp) REVERT: B 843 LYS cc_start: 0.9389 (OUTLIER) cc_final: 0.8289 (mptt) REVERT: C 64 MET cc_start: 0.8594 (mmm) cc_final: 0.7986 (mmt) REVERT: C 136 MET cc_start: 0.8438 (mmp) cc_final: 0.8076 (mmp) REVERT: C 257 MET cc_start: 0.8956 (mmm) cc_final: 0.8749 (mmm) REVERT: C 843 LYS cc_start: 0.9396 (OUTLIER) cc_final: 0.8291 (mptt) REVERT: D 64 MET cc_start: 0.8604 (mmm) cc_final: 0.7997 (mmt) REVERT: D 136 MET cc_start: 0.8465 (mmp) cc_final: 0.8115 (mmp) REVERT: D 257 MET cc_start: 0.8949 (mmm) cc_final: 0.8748 (mmm) REVERT: D 370 MET cc_start: 0.9167 (OUTLIER) cc_final: 0.8397 (tpp) REVERT: D 812 MET cc_start: 0.9362 (OUTLIER) cc_final: 0.9098 (mmm) REVERT: D 814 MET cc_start: 0.9058 (tpt) cc_final: 0.8815 (tpt) REVERT: D 843 LYS cc_start: 0.9397 (OUTLIER) cc_final: 0.8291 (mptt) outliers start: 25 outliers final: 8 residues processed: 144 average time/residue: 0.7773 time to fit residues: 131.4876 Evaluate side-chains 147 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 843 LYS Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 843 LYS Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 843 LYS Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 370 MET Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 812 MET Chi-restraints excluded: chain D residue 843 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 251 optimal weight: 6.9990 chunk 164 optimal weight: 0.0970 chunk 333 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 172 optimal weight: 0.6980 chunk 307 optimal weight: 0.8980 chunk 2 optimal weight: 8.9990 chunk 361 optimal weight: 5.9990 chunk 285 optimal weight: 4.9990 chunk 218 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 overall best weight: 1.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.075952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.051693 restraints weight = 84497.863| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.54 r_work: 0.2732 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31516 Z= 0.142 Angle : 0.477 6.803 43080 Z= 0.249 Chirality : 0.036 0.155 5136 Planarity : 0.004 0.060 5260 Dihedral : 4.774 44.576 5268 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.35 % Allowed : 8.04 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.14), residues: 3944 helix: 2.46 (0.10), residues: 2608 sheet: -0.69 (0.32), residues: 248 loop : -0.53 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1080 TYR 0.012 0.001 TYR D 989 PHE 0.012 0.001 PHE D 734 TRP 0.015 0.001 TRP A 984 HIS 0.002 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00320 (31512) covalent geometry : angle 0.47706 (43068) hydrogen bonds : bond 0.04351 ( 2034) hydrogen bonds : angle 4.00454 ( 5982) link_NAG-ASN : bond 0.00088 ( 4) link_NAG-ASN : angle 0.93192 ( 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 172 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 1.349 Fit side-chains REVERT: A 64 MET cc_start: 0.8580 (mmm) cc_final: 0.7964 (mmt) REVERT: A 136 MET cc_start: 0.8465 (mmp) cc_final: 0.8029 (mmt) REVERT: B 64 MET cc_start: 0.8589 (mmm) cc_final: 0.7979 (mmt) REVERT: B 136 MET cc_start: 0.8463 (mmp) cc_final: 0.8019 (mmt) REVERT: C 64 MET cc_start: 0.8582 (mmm) cc_final: 0.7968 (mmt) REVERT: C 136 MET cc_start: 0.8452 (mmp) cc_final: 0.8003 (mmt) REVERT: D 64 MET cc_start: 0.8589 (mmm) cc_final: 0.7945 (mmt) REVERT: D 136 MET cc_start: 0.8478 (mmp) cc_final: 0.8040 (mmt) REVERT: D 370 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8303 (tpp) REVERT: D 812 MET cc_start: 0.9339 (OUTLIER) cc_final: 0.9058 (mmm) REVERT: D 814 MET cc_start: 0.9011 (tpt) cc_final: 0.8785 (tpt) outliers start: 40 outliers final: 9 residues processed: 151 average time/residue: 0.7036 time to fit residues: 126.3502 Evaluate side-chains 143 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 370 MET Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 812 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 279 optimal weight: 3.9990 chunk 341 optimal weight: 20.0000 chunk 299 optimal weight: 8.9990 chunk 218 optimal weight: 9.9990 chunk 225 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 362 optimal weight: 0.0980 chunk 166 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 377 optimal weight: 0.4980 chunk 372 optimal weight: 2.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.074928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.050032 restraints weight = 85064.861| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 2.69 r_work: 0.2673 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2542 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 31516 Z= 0.176 Angle : 0.498 7.081 43080 Z= 0.258 Chirality : 0.037 0.158 5136 Planarity : 0.004 0.060 5260 Dihedral : 4.692 44.111 5252 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.94 % Allowed : 8.82 % Favored : 90.24 % 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: 2.22 (0.14), residues: 3944 helix: 2.47 (0.10), residues: 2608 sheet: -0.68 (0.31), residues: 248 loop : -0.51 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 887 TYR 0.012 0.001 TYR D 989 PHE 0.014 0.001 PHE B 734 TRP 0.015 0.001 TRP D 984 HIS 0.002 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00404 (31512) covalent geometry : angle 0.49779 (43068) hydrogen bonds : bond 0.04516 ( 2034) hydrogen bonds : angle 4.01266 ( 5982) link_NAG-ASN : bond 0.00058 ( 4) link_NAG-ASN : angle 1.01160 ( 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 160 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 1.350 Fit side-chains REVERT: A 64 MET cc_start: 0.8542 (mmm) cc_final: 0.7872 (mmt) REVERT: A 136 MET cc_start: 0.8311 (mmp) cc_final: 0.7871 (mmt) REVERT: A 190 MET cc_start: 0.8818 (tpp) cc_final: 0.8544 (tpt) REVERT: A 257 MET cc_start: 0.8756 (mmp) cc_final: 0.8531 (mmm) REVERT: B 64 MET cc_start: 0.8475 (mmm) cc_final: 0.7807 (mmt) REVERT: B 136 MET cc_start: 0.8308 (mmp) cc_final: 0.7866 (mmt) REVERT: C 64 MET cc_start: 0.8503 (mmm) cc_final: 0.7847 (mmt) REVERT: C 136 MET cc_start: 0.8289 (mmp) cc_final: 0.7874 (mmt) REVERT: C 190 MET cc_start: 0.8836 (tpp) cc_final: 0.8562 (tpt) REVERT: C 812 MET cc_start: 0.9236 (mmt) cc_final: 0.8956 (mmm) REVERT: D 64 MET cc_start: 0.8447 (mmm) cc_final: 0.7801 (mmt) REVERT: D 136 MET cc_start: 0.8373 (mmp) cc_final: 0.7940 (mmt) REVERT: D 812 MET cc_start: 0.9247 (OUTLIER) cc_final: 0.8978 (mmm) REVERT: D 814 MET cc_start: 0.8999 (tpt) cc_final: 0.8697 (tpt) outliers start: 28 outliers final: 13 residues processed: 144 average time/residue: 0.7402 time to fit residues: 126.3393 Evaluate side-chains 146 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 779 MET Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 812 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 37 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 285 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 320 optimal weight: 20.0000 chunk 194 optimal weight: 0.9980 chunk 314 optimal weight: 20.0000 chunk 191 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 133 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.076020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.051371 restraints weight = 84483.838| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.68 r_work: 0.2710 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 31516 Z= 0.118 Angle : 0.464 7.048 43080 Z= 0.241 Chirality : 0.036 0.152 5136 Planarity : 0.004 0.060 5260 Dihedral : 4.562 43.020 5252 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.94 % Allowed : 9.22 % Favored : 89.84 % 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: 2.31 (0.14), residues: 3944 helix: 2.55 (0.10), residues: 2608 sheet: -0.59 (0.31), residues: 248 loop : -0.52 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 632 TYR 0.012 0.001 TYR B 989 PHE 0.010 0.001 PHE C 828 TRP 0.016 0.001 TRP D 984 HIS 0.002 0.000 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00259 (31512) covalent geometry : angle 0.46350 (43068) hydrogen bonds : bond 0.04062 ( 2034) hydrogen bonds : angle 3.89369 ( 5982) link_NAG-ASN : bond 0.00108 ( 4) link_NAG-ASN : angle 0.95023 ( 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 164 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 1.203 Fit side-chains REVERT: A 64 MET cc_start: 0.8490 (mmm) cc_final: 0.7853 (mmt) REVERT: A 136 MET cc_start: 0.8284 (mmp) cc_final: 0.7777 (mmt) REVERT: A 190 MET cc_start: 0.8782 (tpp) cc_final: 0.8527 (tpt) REVERT: A 257 MET cc_start: 0.8824 (mmp) cc_final: 0.8569 (mmm) REVERT: A 843 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8011 (mptt) REVERT: B 64 MET cc_start: 0.8456 (mmm) cc_final: 0.7804 (mmt) REVERT: B 136 MET cc_start: 0.8351 (mmp) cc_final: 0.7878 (mmt) REVERT: B 190 MET cc_start: 0.8687 (tpt) cc_final: 0.8440 (tpt) REVERT: B 812 MET cc_start: 0.9189 (OUTLIER) cc_final: 0.8929 (mmm) REVERT: B 843 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.7997 (mptt) REVERT: C 64 MET cc_start: 0.8477 (mmm) cc_final: 0.7835 (mmt) REVERT: C 136 MET cc_start: 0.8287 (mmp) cc_final: 0.7812 (mmt) REVERT: C 190 MET cc_start: 0.8792 (tpp) cc_final: 0.8516 (tpt) REVERT: C 843 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8009 (mptt) REVERT: D 64 MET cc_start: 0.8426 (mmm) cc_final: 0.7785 (mmt) REVERT: D 136 MET cc_start: 0.8344 (mmp) cc_final: 0.7853 (mmt) REVERT: D 812 MET cc_start: 0.9191 (OUTLIER) cc_final: 0.8902 (mmm) REVERT: D 814 MET cc_start: 0.9000 (tpt) cc_final: 0.8655 (tpt) REVERT: D 843 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8004 (mptt) outliers start: 28 outliers final: 5 residues processed: 156 average time/residue: 0.7170 time to fit residues: 132.4497 Evaluate side-chains 140 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 843 LYS Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 779 MET Chi-restraints excluded: chain B residue 812 MET Chi-restraints excluded: chain B residue 843 LYS Chi-restraints excluded: chain C residue 843 LYS Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 812 MET Chi-restraints excluded: chain D residue 843 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 348 optimal weight: 1.9990 chunk 258 optimal weight: 0.7980 chunk 180 optimal weight: 3.9990 chunk 315 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 373 optimal weight: 4.9990 chunk 306 optimal weight: 7.9990 chunk 4 optimal weight: 0.3980 chunk 206 optimal weight: 9.9990 chunk 154 optimal weight: 0.6980 chunk 126 optimal weight: 20.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.075986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.051243 restraints weight = 84611.711| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 2.69 r_work: 0.2707 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 31516 Z= 0.126 Angle : 0.465 7.447 43080 Z= 0.241 Chirality : 0.036 0.151 5136 Planarity : 0.004 0.060 5260 Dihedral : 4.509 42.535 5252 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.31 % Allowed : 9.39 % Favored : 89.30 % 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: 2.63 (0.10), residues: 2584 sheet: -0.58 (0.32), residues: 248 loop : -0.36 (0.19), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C1080 TYR 0.012 0.001 TYR D 989 PHE 0.010 0.001 PHE D 567 TRP 0.015 0.001 TRP D 984 HIS 0.002 0.000 HIS D 115 Details of bonding type rmsd covalent geometry : bond 0.00281 (31512) covalent geometry : angle 0.46505 (43068) hydrogen bonds : bond 0.04064 ( 2034) hydrogen bonds : angle 3.87488 ( 5982) link_NAG-ASN : bond 0.00100 ( 4) link_NAG-ASN : angle 0.94587 ( 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 168 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 1.368 Fit side-chains REVERT: A 64 MET cc_start: 0.8470 (mmm) cc_final: 0.7810 (mmt) REVERT: A 136 MET cc_start: 0.8361 (mmp) cc_final: 0.7894 (mmt) REVERT: A 190 MET cc_start: 0.8779 (tpp) cc_final: 0.8548 (tpt) REVERT: A 257 MET cc_start: 0.8870 (mmp) cc_final: 0.8584 (mmm) REVERT: A 450 THR cc_start: 0.9163 (OUTLIER) cc_final: 0.8921 (t) REVERT: A 721 MET cc_start: 0.9052 (ttp) cc_final: 0.8812 (ttp) REVERT: A 843 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.7991 (mptt) REVERT: B 64 MET cc_start: 0.8461 (mmm) cc_final: 0.7799 (mmt) REVERT: B 136 MET cc_start: 0.8361 (mmp) cc_final: 0.7893 (mmt) REVERT: B 190 MET cc_start: 0.8721 (tpt) cc_final: 0.8464 (tpt) REVERT: B 450 THR cc_start: 0.9167 (OUTLIER) cc_final: 0.8917 (t) REVERT: B 721 MET cc_start: 0.9043 (ttp) cc_final: 0.8798 (ttp) REVERT: B 812 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8926 (mmm) REVERT: B 843 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.7988 (mptt) REVERT: C 64 MET cc_start: 0.8458 (mmm) cc_final: 0.7792 (mmt) REVERT: C 136 MET cc_start: 0.8366 (mmp) cc_final: 0.7895 (mmt) REVERT: C 190 MET cc_start: 0.8791 (tpp) cc_final: 0.8561 (tpt) REVERT: C 450 THR cc_start: 0.9154 (OUTLIER) cc_final: 0.8913 (t) REVERT: C 721 MET cc_start: 0.9050 (ttp) cc_final: 0.8806 (ttp) REVERT: C 843 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.7987 (mptt) REVERT: D 64 MET cc_start: 0.8432 (mmm) cc_final: 0.7790 (mmt) REVERT: D 136 MET cc_start: 0.8362 (mmp) cc_final: 0.7876 (mmt) REVERT: D 190 MET cc_start: 0.8792 (tpp) cc_final: 0.8560 (tpt) REVERT: D 450 THR cc_start: 0.9154 (OUTLIER) cc_final: 0.8918 (t) REVERT: D 721 MET cc_start: 0.9046 (ttp) cc_final: 0.8803 (ttp) REVERT: D 812 MET cc_start: 0.9199 (OUTLIER) cc_final: 0.8884 (mmm) REVERT: D 814 MET cc_start: 0.8989 (tpt) cc_final: 0.8636 (tpt) REVERT: D 843 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.7994 (mptt) outliers start: 39 outliers final: 15 residues processed: 153 average time/residue: 0.7238 time to fit residues: 130.8124 Evaluate side-chains 153 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 843 LYS Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 779 MET Chi-restraints excluded: chain B residue 812 MET Chi-restraints excluded: chain B residue 843 LYS Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 779 MET Chi-restraints excluded: chain C residue 843 LYS Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 779 MET Chi-restraints excluded: chain D residue 812 MET Chi-restraints excluded: chain D residue 843 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 142 optimal weight: 4.9990 chunk 192 optimal weight: 6.9990 chunk 200 optimal weight: 20.0000 chunk 371 optimal weight: 0.8980 chunk 379 optimal weight: 3.9990 chunk 225 optimal weight: 20.0000 chunk 136 optimal weight: 4.9990 chunk 361 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 chunk 5 optimal weight: 8.9990 chunk 245 optimal weight: 7.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.074327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.049355 restraints weight = 85254.662| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 2.67 r_work: 0.2652 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2521 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 31516 Z= 0.218 Angle : 0.527 8.249 43080 Z= 0.272 Chirality : 0.038 0.150 5136 Planarity : 0.004 0.061 5260 Dihedral : 4.683 42.813 5252 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.38 % Allowed : 9.35 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.14), residues: 3944 helix: 2.46 (0.10), residues: 2600 sheet: -0.91 (0.31), residues: 260 loop : -0.56 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1080 TYR 0.012 0.001 TYR D 989 PHE 0.016 0.001 PHE A 734 TRP 0.013 0.001 TRP C 984 HIS 0.002 0.001 HIS A 842 Details of bonding type rmsd covalent geometry : bond 0.00507 (31512) covalent geometry : angle 0.52677 (43068) hydrogen bonds : bond 0.04816 ( 2034) hydrogen bonds : angle 4.06551 ( 5982) link_NAG-ASN : bond 0.00018 ( 4) link_NAG-ASN : angle 1.14793 ( 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 173 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 132 time to evaluate : 1.285 Fit side-chains REVERT: A 64 MET cc_start: 0.8491 (mmm) cc_final: 0.7798 (mmt) REVERT: A 136 MET cc_start: 0.8407 (mmp) cc_final: 0.7942 (mmt) REVERT: A 190 MET cc_start: 0.8804 (tpp) cc_final: 0.8581 (tpt) REVERT: A 257 MET cc_start: 0.8873 (mmp) cc_final: 0.8584 (mmm) REVERT: A 721 MET cc_start: 0.9100 (ttp) cc_final: 0.8868 (ttp) REVERT: A 812 MET cc_start: 0.9209 (mmt) cc_final: 0.8918 (mmm) REVERT: A 843 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8058 (mptt) REVERT: B 64 MET cc_start: 0.8479 (mmm) cc_final: 0.7784 (mmt) REVERT: B 136 MET cc_start: 0.8409 (mmp) cc_final: 0.7958 (mmt) REVERT: B 721 MET cc_start: 0.9100 (ttp) cc_final: 0.8867 (ttp) REVERT: B 812 MET cc_start: 0.9210 (mmt) cc_final: 0.8930 (mmm) REVERT: B 843 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.8063 (mptt) REVERT: C 64 MET cc_start: 0.8480 (mmm) cc_final: 0.7785 (mmt) REVERT: C 136 MET cc_start: 0.8403 (mmp) cc_final: 0.7935 (mmt) REVERT: C 190 MET cc_start: 0.8816 (tpp) cc_final: 0.8590 (tpt) REVERT: C 721 MET cc_start: 0.9101 (ttp) cc_final: 0.8869 (ttp) REVERT: C 812 MET cc_start: 0.9209 (mmt) cc_final: 0.8919 (mmm) REVERT: C 843 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8055 (mptt) REVERT: D 136 MET cc_start: 0.8396 (mmp) cc_final: 0.7925 (mmt) REVERT: D 721 MET cc_start: 0.9099 (ttp) cc_final: 0.8867 (ttp) REVERT: D 814 MET cc_start: 0.9106 (tpt) cc_final: 0.8799 (tpt) REVERT: D 843 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.8064 (mptt) outliers start: 41 outliers final: 14 residues processed: 160 average time/residue: 0.6993 time to fit residues: 132.7621 Evaluate side-chains 150 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 843 LYS Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 779 MET Chi-restraints excluded: chain B residue 843 LYS Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 843 LYS Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 779 MET Chi-restraints excluded: chain D residue 812 MET Chi-restraints excluded: chain D residue 843 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 358 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 160 optimal weight: 10.0000 chunk 329 optimal weight: 10.0000 chunk 91 optimal weight: 0.3980 chunk 36 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 285 optimal weight: 2.9990 chunk 177 optimal weight: 0.8980 chunk 123 optimal weight: 10.0000 chunk 198 optimal weight: 30.0000 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.073810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.048654 restraints weight = 85723.819| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 2.69 r_work: 0.2636 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2505 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 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 : 0.006 0.041 31516 Z= 0.258 Angle : 0.561 8.898 43080 Z= 0.287 Chirality : 0.039 0.152 5136 Planarity : 0.004 0.061 5260 Dihedral : 4.851 43.277 5252 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.84 % Allowed : 9.79 % Favored : 89.37 % 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: 2.06 (0.14), residues: 3944 helix: 2.39 (0.10), residues: 2608 sheet: -1.03 (0.30), residues: 260 loop : -0.61 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 887 TYR 0.012 0.002 TYR D 559 PHE 0.016 0.001 PHE D 734 TRP 0.013 0.001 TRP C 890 HIS 0.003 0.001 HIS B 842 Details of bonding type rmsd covalent geometry : bond 0.00601 (31512) covalent geometry : angle 0.56084 (43068) hydrogen bonds : bond 0.05030 ( 2034) hydrogen bonds : angle 4.15189 ( 5982) link_NAG-ASN : bond 0.00050 ( 4) link_NAG-ASN : angle 1.31092 ( 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 157 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 1.173 Fit side-chains REVERT: A 64 MET cc_start: 0.8487 (mmm) cc_final: 0.7850 (mmt) REVERT: A 136 MET cc_start: 0.8428 (mmp) cc_final: 0.7971 (mmt) REVERT: A 190 MET cc_start: 0.8813 (tpp) cc_final: 0.8561 (tpt) REVERT: A 257 MET cc_start: 0.8880 (mmp) cc_final: 0.8564 (mmm) REVERT: A 721 MET cc_start: 0.9133 (ttp) cc_final: 0.8917 (ttp) REVERT: A 812 MET cc_start: 0.9200 (mmt) cc_final: 0.8928 (mmm) REVERT: A 843 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.8049 (mptt) REVERT: B 64 MET cc_start: 0.8480 (mmm) cc_final: 0.7843 (mmt) REVERT: B 136 MET cc_start: 0.8426 (mmp) cc_final: 0.7960 (mmt) REVERT: B 721 MET cc_start: 0.9130 (ttp) cc_final: 0.8913 (ttp) REVERT: B 843 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8046 (mptt) REVERT: C 64 MET cc_start: 0.8474 (mmm) cc_final: 0.7833 (mmt) REVERT: C 136 MET cc_start: 0.8427 (mmp) cc_final: 0.7966 (mmt) REVERT: C 190 MET cc_start: 0.8828 (tpp) cc_final: 0.8574 (tpt) REVERT: C 721 MET cc_start: 0.9134 (ttp) cc_final: 0.8917 (ttp) REVERT: C 843 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8047 (mptt) REVERT: D 64 MET cc_start: 0.8476 (mmm) cc_final: 0.7840 (mmt) REVERT: D 136 MET cc_start: 0.8423 (mmp) cc_final: 0.7969 (mmt) REVERT: D 721 MET cc_start: 0.9135 (ttp) cc_final: 0.8920 (ttp) REVERT: D 814 MET cc_start: 0.9153 (tpt) cc_final: 0.8888 (tpt) REVERT: D 843 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8047 (mptt) outliers start: 25 outliers final: 11 residues processed: 148 average time/residue: 0.7591 time to fit residues: 132.3012 Evaluate side-chains 147 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 843 LYS Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 843 LYS Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 843 LYS Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 843 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 55 optimal weight: 0.7980 chunk 59 optimal weight: 0.2980 chunk 127 optimal weight: 8.9990 chunk 146 optimal weight: 0.8980 chunk 263 optimal weight: 2.9990 chunk 338 optimal weight: 20.0000 chunk 85 optimal weight: 0.6980 chunk 148 optimal weight: 0.9980 chunk 325 optimal weight: 10.0000 chunk 361 optimal weight: 0.8980 chunk 239 optimal weight: 20.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.076451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.051880 restraints weight = 84440.308| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.69 r_work: 0.2726 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 31516 Z= 0.103 Angle : 0.473 9.567 43080 Z= 0.243 Chirality : 0.036 0.183 5136 Planarity : 0.004 0.063 5260 Dihedral : 4.561 41.357 5252 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.54 % Allowed : 10.06 % Favored : 89.40 % 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: 2.26 (0.14), residues: 3944 helix: 2.52 (0.10), residues: 2612 sheet: -0.61 (0.31), residues: 248 loop : -0.57 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 191 TYR 0.013 0.001 TYR D 989 PHE 0.012 0.001 PHE B 828 TRP 0.016 0.001 TRP A 984 HIS 0.003 0.001 HIS B 996 Details of bonding type rmsd covalent geometry : bond 0.00212 (31512) covalent geometry : angle 0.47316 (43068) hydrogen bonds : bond 0.03910 ( 2034) hydrogen bonds : angle 3.89001 ( 5982) link_NAG-ASN : bond 0.00101 ( 4) link_NAG-ASN : angle 1.08457 ( 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 144 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.900 Fit side-chains REVERT: A 64 MET cc_start: 0.8479 (mmm) cc_final: 0.7831 (mmt) REVERT: A 136 MET cc_start: 0.8368 (mmp) cc_final: 0.7899 (mmt) REVERT: A 257 MET cc_start: 0.8882 (mmp) cc_final: 0.8524 (mmm) REVERT: A 721 MET cc_start: 0.9027 (ttp) cc_final: 0.8822 (ttp) REVERT: A 843 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8000 (mptt) REVERT: B 64 MET cc_start: 0.8476 (mmm) cc_final: 0.7826 (mmt) REVERT: B 136 MET cc_start: 0.8362 (mmp) cc_final: 0.7892 (mmt) REVERT: B 721 MET cc_start: 0.9021 (ttp) cc_final: 0.8815 (ttp) REVERT: B 812 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8862 (mmm) REVERT: B 843 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.7996 (mptt) REVERT: C 64 MET cc_start: 0.8466 (mmm) cc_final: 0.7816 (mmt) REVERT: C 136 MET cc_start: 0.8367 (mmp) cc_final: 0.7896 (mmt) REVERT: C 721 MET cc_start: 0.9026 (ttp) cc_final: 0.8821 (ttp) REVERT: D 64 MET cc_start: 0.8461 (mmm) cc_final: 0.7824 (mmt) REVERT: D 136 MET cc_start: 0.8366 (mmp) cc_final: 0.7900 (mmt) REVERT: D 721 MET cc_start: 0.9026 (ttp) cc_final: 0.8821 (ttp) REVERT: D 814 MET cc_start: 0.9047 (tpt) cc_final: 0.8729 (tpt) REVERT: D 843 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8027 (mptt) outliers start: 16 outliers final: 7 residues processed: 139 average time/residue: 0.7750 time to fit residues: 126.2325 Evaluate side-chains 139 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 843 LYS Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 812 MET Chi-restraints excluded: chain B residue 843 LYS Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 843 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 367 optimal weight: 7.9990 chunk 210 optimal weight: 0.4980 chunk 2 optimal weight: 0.0050 chunk 296 optimal weight: 5.9990 chunk 294 optimal weight: 10.0000 chunk 360 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 348 optimal weight: 4.9990 chunk 320 optimal weight: 20.0000 chunk 59 optimal weight: 9.9990 overall best weight: 2.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.075292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.050468 restraints weight = 84876.971| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 2.67 r_work: 0.2686 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2555 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 31516 Z= 0.165 Angle : 0.500 8.560 43080 Z= 0.255 Chirality : 0.037 0.167 5136 Planarity : 0.004 0.064 5260 Dihedral : 4.598 42.257 5252 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.61 % Allowed : 10.03 % Favored : 89.37 % 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: 2.28 (0.14), residues: 3944 helix: 2.55 (0.10), residues: 2608 sheet: -0.68 (0.31), residues: 248 loop : -0.57 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 887 TYR 0.012 0.001 TYR D 989 PHE 0.013 0.001 PHE A 734 TRP 0.014 0.001 TRP B 984 HIS 0.002 0.000 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00381 (31512) covalent geometry : angle 0.49987 (43068) hydrogen bonds : bond 0.04309 ( 2034) hydrogen bonds : angle 3.93775 ( 5982) link_NAG-ASN : bond 0.00050 ( 4) link_NAG-ASN : angle 1.11384 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11113.27 seconds wall clock time: 189 minutes 38.63 seconds (11378.63 seconds total)