Starting phenix.real_space_refine on Tue Apr 7 19:34:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mbr_23744/04_2026/7mbr_23744.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mbr_23744/04_2026/7mbr_23744.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7mbr_23744/04_2026/7mbr_23744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mbr_23744/04_2026/7mbr_23744.map" model { file = "/net/cci-nas-00/data/ceres_data/7mbr_23744/04_2026/7mbr_23744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mbr_23744/04_2026/7mbr_23744.cif" } 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= 0.001 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30708 Number of models: 1 Model: "" Number of chains: 8 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: "B" 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: "C" 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: "D" 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 Time building chain proxies: 7.62, per 1000 atoms: 0.25 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: 2.19 Conformation dependent library (CDL) restraints added in 1.3 seconds 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7600 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 8 sheets defined 70.5% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 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: 3.651A 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: 3.796A 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: 3.774A pdb=" N HIS A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 3.731A 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 524 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: 4.173A 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: 3.966A 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: 4.837A pdb=" N LYS A 857 " --> pdb=" O GLU A 853 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASP A 858 " --> pdb=" O ARG A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 902 removed outlier: 5.059A 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: 3.761A pdb=" N ASN A 990 " --> pdb=" O PHE A 986 " (cutoff:3.500A) removed outlier: 3.926A 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: 3.652A 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: 3.796A pdb=" N LEU B 143 " --> pdb=" O ASN B 139 " (cutoff:3.500A) removed outlier: 3.996A 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: 3.544A 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: 3.773A 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: 4.761A pdb=" N GLU B 368 " --> pdb=" O GLN B 364 " (cutoff:3.500A) removed outlier: 4.831A 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: 3.535A pdb=" N THR B 416 " --> pdb=" O ASN B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 462 removed outlier: 3.620A 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: 3.848A 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: 3.967A pdb=" N ASP B 791 " --> pdb=" O LEU B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 813 removed outlier: 3.595A 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: 4.011A 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: 5.058A 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: 3.668A 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: 5.075A pdb=" N ASN B 979 " --> pdb=" O VAL B 975 " (cutoff:3.500A) removed outlier: 3.542A 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: 3.924A pdb=" N SER B 997 " --> pdb=" O VAL B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1005 through 1020 removed outlier: 4.119A 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: 3.796A pdb=" N LEU C 143 " --> pdb=" O ASN C 139 " (cutoff:3.500A) removed outlier: 3.996A 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: 3.729A 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: 3.535A pdb=" N THR C 416 " --> pdb=" O ASN C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 462 removed outlier: 3.618A 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: 3.534A pdb=" N ALA C 530 " --> pdb=" O GLU C 526 " (cutoff:3.500A) removed outlier: 4.174A 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: 3.967A 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: 4.011A 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: 4.546A 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: 3.712A pdb=" N VAL C 946 " --> pdb=" O ALA C 942 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU C 961 " --> pdb=" O THR C 957 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LEU C 962 " --> pdb=" O ASN C 958 " (cutoff:3.500A) removed outlier: 5.174A 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: 3.542A 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: 4.118A 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: 3.795A 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: 3.545A 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: 3.730A 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: 4.832A 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: 3.534A pdb=" N ALA D 530 " --> pdb=" O GLU D 526 " (cutoff:3.500A) removed outlier: 4.173A 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: 3.849A 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: 4.838A pdb=" N LYS D 857 " --> pdb=" O GLU D 853 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASP D 858 " --> pdb=" O ARG D 854 " (cutoff:3.500A) Processing helix chain 'D' and resid 887 through 902 removed outlier: 5.059A 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: 5.086A 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: 5.074A 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: 4.120A 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: 3.629A 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: 7.882A pdb=" N ILE A 175 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLY A 130 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL A 177 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA A 132 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL A 60 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU A 218 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA A 62 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.618A 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: 3.628A 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: 6.459A 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: 5.954A 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: 3.617A 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: 7.211A 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: 5.954A pdb=" N VAL C 60 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 7.159A 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: 5.957A 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: 3.627A 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: 7.882A pdb=" N ILE D 175 " --> pdb=" O ALA D 128 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLY D 130 " --> pdb=" O ILE D 175 " (cutoff:3.500A) removed outlier: 6.741A 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: 5.953A 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: 6.122A 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: 6.336A 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) 2036 hydrogen bonds defined for protein. 5988 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.05 Time building geometry restraints manager: 3.05 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: 9468 1.34 - 1.46: 4503 1.46 - 1.57: 17249 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 1.227 0.016 8.50e-03 1.38e+04 3.74e+00 bond pdb=" C PRO A1003 " pdb=" O PRO A1003 " ideal model delta sigma weight residual 1.243 1.227 0.016 8.50e-03 1.38e+04 3.73e+00 bond pdb=" C PRO B1003 " pdb=" O PRO B1003 " ideal model delta sigma weight residual 1.243 1.228 0.015 8.50e-03 1.38e+04 3.31e+00 bond pdb=" C PRO C1003 " pdb=" O PRO C1003 " ideal model delta sigma weight residual 1.243 1.228 0.015 8.50e-03 1.38e+04 3.30e+00 bond pdb=" C3 NAG A1501 " pdb=" O3 NAG A1501 " ideal model delta sigma weight residual 1.403 1.432 -0.029 2.00e-02 2.50e+03 2.15e+00 ... (remaining 31507 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 41855 1.46 - 2.93: 974 2.93 - 4.39: 191 4.39 - 5.85: 34 5.85 - 7.31: 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 3.37e+01 angle pdb=" C MET C 917 " pdb=" N PRO C 918 " pdb=" CA PRO C 918 " ideal model delta sigma weight residual 119.85 125.70 -5.85 1.01e+00 9.80e-01 3.35e+01 angle pdb=" C MET B 917 " pdb=" N PRO B 918 " pdb=" CA PRO B 918 " ideal model delta sigma weight residual 119.85 125.63 -5.78 1.01e+00 9.80e-01 3.28e+01 angle pdb=" C MET D 917 " pdb=" N PRO D 918 " pdb=" CA PRO D 918 " ideal model delta sigma weight residual 119.85 125.63 -5.78 1.01e+00 9.80e-01 3.27e+01 angle pdb=" C ALA C1002 " pdb=" N PRO C1003 " pdb=" CA PRO C1003 " ideal model delta sigma weight residual 119.66 123.14 -3.48 7.20e-01 1.93e+00 2.33e+01 ... (remaining 43063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.26: 17464 15.26 - 30.51: 1380 30.51 - 45.77: 348 45.77 - 61.02: 68 61.02 - 76.28: 16 Dihedral angle restraints: 19276 sinusoidal: 7600 harmonic: 11676 Sorted by residual: 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 -124.86 -55.14 3 1.50e+01 4.44e-03 9.33e+00 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 -124.91 -55.09 3 1.50e+01 4.44e-03 9.33e+00 dihedral pdb=" N ASN B 921 " pdb=" CA ASN B 921 " pdb=" CB ASN B 921 " pdb=" CG ASN B 921 " ideal model delta sinusoidal sigma weight residual -180.00 -124.93 -55.07 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: 4570 0.060 - 0.120: 530 0.120 - 0.180: 16 0.180 - 0.240: 8 0.240 - 0.300: 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 2.24e+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 2.22e+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 0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 5133 not shown) Planarity restraints: 5264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 760 " 0.032 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 D 760 " 0.033 2.00e-02 2.50e+03 3.64e-02 3.31e+01 pdb=" CG TRP D 760 " -0.092 2.00e-02 2.50e+03 pdb=" CD1 TRP D 760 " 0.058 2.00e-02 2.50e+03 pdb=" CD2 TRP D 760 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP D 760 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP D 760 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 760 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 760 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 760 " 0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP D 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 3.63e-02 3.29e+01 pdb=" CG TRP A 760 " -0.091 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 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 760 " 0.001 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: 26768 3.18 - 3.75: 49812 3.75 - 4.33: 65503 4.33 - 4.90: 110688 Nonbonded interactions: 252963 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 2.045 3.040 nonbonded pdb=" O MET A 917 " pdb=" O8 YUY A1503 " model vdw 2.059 3.040 nonbonded pdb=" O GLN C 138 " pdb=" OH TYR C 154 " model vdw 2.265 3.040 ... (remaining 252958 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.08 Found NCS groups: ncs_group { reference = (chain 'A' and resid 16 through 1092) 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: 2.090 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: 0.030 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.690 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 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= 0.168 Angle : 0.565 7.314 43080 Z= 0.330 Chirality : 0.040 0.300 5136 Planarity : 0.005 0.054 5260 Dihedral : 12.164 76.276 11676 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.76 % Favored : 97.13 % Rotamer: Outliers : 0.34 % Allowed : 1.45 % Favored : 98.22 % 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 B1061 TYR 0.011 0.001 TYR A 989 PHE 0.011 0.001 PHE A 969 TRP 0.092 0.002 TRP C 760 HIS 0.003 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00310 (31512) covalent geometry : angle 0.56368 (43068) hydrogen bonds : bond 0.11870 ( 2036) hydrogen bonds : angle 5.03353 ( 5988) link_NAG-ASN : bond 0.00182 ( 4) link_NAG-ASN : angle 2.06651 ( 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 224 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 214 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ASP cc_start: 0.8396 (m-30) cc_final: 0.8165 (m-30) REVERT: B 114 ASP cc_start: 0.8396 (m-30) cc_final: 0.8159 (m-30) REVERT: C 114 ASP cc_start: 0.8389 (m-30) cc_final: 0.8143 (m-30) REVERT: D 114 ASP cc_start: 0.8355 (m-30) cc_final: 0.8119 (m-30) outliers start: 10 outliers final: 4 residues processed: 222 average time/residue: 0.8161 time to fit residues: 208.8549 Evaluate side-chains 142 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 138 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 785 MET Chi-restraints excluded: chain B residue 785 MET Chi-restraints excluded: chain C residue 785 MET Chi-restraints excluded: chain D residue 785 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 0.0980 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 9.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 HIS A 794 ASN A 882 HIS A1010 HIS B 452 HIS B 794 ASN B 882 HIS B1010 HIS C 452 HIS C 794 ASN C 882 HIS C1010 HIS D 452 HIS D 794 ASN D 882 HIS D1010 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.054512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.040656 restraints weight = 164429.727| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.78 r_work: 0.2870 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 31516 Z= 0.209 Angle : 0.569 7.173 43080 Z= 0.293 Chirality : 0.038 0.155 5136 Planarity : 0.005 0.057 5260 Dihedral : 5.535 52.096 5264 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.31 % Allowed : 6.80 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.14), residues: 3944 helix: 2.32 (0.10), residues: 2580 sheet: -0.67 (0.33), residues: 248 loop : -0.24 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 125 TYR 0.011 0.001 TYR C 989 PHE 0.017 0.001 PHE A 447 TRP 0.040 0.002 TRP C 760 HIS 0.004 0.001 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00455 (31512) covalent geometry : angle 0.56794 (43068) hydrogen bonds : bond 0.04221 ( 2036) hydrogen bonds : angle 4.18504 ( 5988) link_NAG-ASN : bond 0.00055 ( 4) link_NAG-ASN : angle 1.74550 ( 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 186 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 147 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.8959 (mmm) cc_final: 0.8484 (mmm) REVERT: A 721 MET cc_start: 0.9030 (ppp) cc_final: 0.8754 (tmm) REVERT: A 726 MET cc_start: 0.9282 (OUTLIER) cc_final: 0.9017 (mmm) REVERT: A 812 MET cc_start: 0.9387 (mmp) cc_final: 0.9092 (mmm) REVERT: A 917 MET cc_start: 0.9600 (OUTLIER) cc_final: 0.9107 (mtm) REVERT: A 1057 GLU cc_start: 0.8989 (tp30) cc_final: 0.8650 (tp30) REVERT: B 114 ASP cc_start: 0.9051 (m-30) cc_final: 0.8851 (m-30) REVERT: B 190 MET cc_start: 0.8993 (mmm) cc_final: 0.8445 (mmm) REVERT: B 812 MET cc_start: 0.9377 (mmp) cc_final: 0.9085 (mmm) REVERT: B 917 MET cc_start: 0.9597 (OUTLIER) cc_final: 0.9107 (mtm) REVERT: B 1057 GLU cc_start: 0.8996 (tp30) cc_final: 0.8660 (tp30) REVERT: C 114 ASP cc_start: 0.9075 (m-30) cc_final: 0.8869 (m-30) REVERT: C 190 MET cc_start: 0.9034 (mmm) cc_final: 0.8501 (mmm) REVERT: C 721 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8717 (tmm) REVERT: C 726 MET cc_start: 0.9284 (OUTLIER) cc_final: 0.9014 (mmm) REVERT: C 812 MET cc_start: 0.9412 (mmp) cc_final: 0.9116 (mmm) REVERT: C 917 MET cc_start: 0.9607 (OUTLIER) cc_final: 0.9115 (mtm) REVERT: C 1057 GLU cc_start: 0.8982 (tp30) cc_final: 0.8649 (tp30) REVERT: D 64 MET cc_start: 0.8755 (mmm) cc_final: 0.8525 (mmm) REVERT: D 114 ASP cc_start: 0.9056 (m-30) cc_final: 0.8853 (m-30) REVERT: D 190 MET cc_start: 0.8991 (mmm) cc_final: 0.8494 (mmm) REVERT: D 230 MET cc_start: 0.9587 (OUTLIER) cc_final: 0.9356 (tmm) REVERT: D 721 MET cc_start: 0.9020 (ppp) cc_final: 0.8744 (tmm) REVERT: D 726 MET cc_start: 0.9290 (OUTLIER) cc_final: 0.9016 (mmm) REVERT: D 812 MET cc_start: 0.9402 (mmp) cc_final: 0.9103 (mmm) REVERT: D 917 MET cc_start: 0.9597 (OUTLIER) cc_final: 0.9102 (mtm) REVERT: D 1057 GLU cc_start: 0.8984 (tp30) cc_final: 0.8648 (tp30) outliers start: 39 outliers final: 10 residues processed: 161 average time/residue: 0.6896 time to fit residues: 130.9678 Evaluate side-chains 161 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 917 MET Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 917 MET Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 726 MET Chi-restraints excluded: chain C residue 836 ILE Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 917 MET Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 726 MET Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain D residue 917 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 130 optimal weight: 20.0000 chunk 229 optimal weight: 20.0000 chunk 190 optimal weight: 0.0770 chunk 19 optimal weight: 0.0370 chunk 207 optimal weight: 8.9990 chunk 356 optimal weight: 4.9990 chunk 373 optimal weight: 8.9990 chunk 220 optimal weight: 20.0000 chunk 136 optimal weight: 6.9990 chunk 251 optimal weight: 2.9990 chunk 211 optimal weight: 20.0000 overall best weight: 3.0222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN B 422 ASN D 422 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.054009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.040048 restraints weight = 164143.723| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.86 r_work: 0.2860 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 31516 Z= 0.154 Angle : 0.499 7.024 43080 Z= 0.258 Chirality : 0.036 0.154 5136 Planarity : 0.004 0.057 5260 Dihedral : 4.905 48.960 5252 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.28 % Allowed : 9.02 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.14), residues: 3944 helix: 2.55 (0.10), residues: 2580 sheet: -0.65 (0.32), residues: 248 loop : -0.30 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1080 TYR 0.010 0.001 TYR A 559 PHE 0.008 0.001 PHE D 567 TRP 0.020 0.001 TRP A 760 HIS 0.003 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00332 (31512) covalent geometry : angle 0.49912 (43068) hydrogen bonds : bond 0.03940 ( 2036) hydrogen bonds : angle 3.99720 ( 5988) link_NAG-ASN : bond 0.00005 ( 4) link_NAG-ASN : angle 1.17630 ( 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 180 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 142 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.8828 (mppt) REVERT: A 114 ASP cc_start: 0.9004 (m-30) cc_final: 0.8775 (p0) REVERT: A 194 MET cc_start: 0.9520 (mmm) cc_final: 0.9296 (mmm) REVERT: A 257 MET cc_start: 0.9273 (mmm) cc_final: 0.8661 (mpm) REVERT: A 721 MET cc_start: 0.9020 (ppp) cc_final: 0.8801 (tmm) REVERT: A 917 MET cc_start: 0.9619 (OUTLIER) cc_final: 0.8938 (mtm) REVERT: A 1057 GLU cc_start: 0.9098 (tp30) cc_final: 0.8690 (tp30) REVERT: B 73 LYS cc_start: 0.9302 (OUTLIER) cc_final: 0.8870 (mppt) REVERT: B 78 ASP cc_start: 0.9377 (t0) cc_final: 0.8770 (p0) REVERT: B 194 MET cc_start: 0.9521 (mmm) cc_final: 0.9299 (mmm) REVERT: B 726 MET cc_start: 0.9373 (tpp) cc_final: 0.9164 (tpp) REVERT: B 917 MET cc_start: 0.9609 (OUTLIER) cc_final: 0.8923 (mtm) REVERT: B 1057 GLU cc_start: 0.9095 (tp30) cc_final: 0.8688 (tp30) REVERT: C 73 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.9025 (mmtt) REVERT: C 721 MET cc_start: 0.9045 (ppp) cc_final: 0.8802 (tmm) REVERT: C 917 MET cc_start: 0.9628 (OUTLIER) cc_final: 0.8975 (mtm) REVERT: C 1057 GLU cc_start: 0.9086 (tp30) cc_final: 0.8680 (tp30) REVERT: D 64 MET cc_start: 0.8894 (mmm) cc_final: 0.8691 (mmm) REVERT: D 73 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.8819 (mppt) REVERT: D 194 MET cc_start: 0.9529 (mmm) cc_final: 0.9286 (mmm) REVERT: D 230 MET cc_start: 0.9588 (OUTLIER) cc_final: 0.9360 (tmm) REVERT: D 721 MET cc_start: 0.9026 (ppp) cc_final: 0.8807 (tmm) REVERT: D 917 MET cc_start: 0.9625 (OUTLIER) cc_final: 0.8972 (mtm) REVERT: D 1057 GLU cc_start: 0.9092 (tp30) cc_final: 0.8684 (tp30) outliers start: 38 outliers final: 10 residues processed: 166 average time/residue: 0.6834 time to fit residues: 134.1465 Evaluate side-chains 151 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 785 MET Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 917 MET Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 917 MET Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 785 MET Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 917 MET Chi-restraints excluded: chain D residue 73 LYS Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain D residue 917 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 251 optimal weight: 9.9990 chunk 164 optimal weight: 0.4980 chunk 333 optimal weight: 0.3980 chunk 134 optimal weight: 0.4980 chunk 172 optimal weight: 0.9980 chunk 307 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 361 optimal weight: 3.9990 chunk 285 optimal weight: 4.9990 chunk 218 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN B 422 ASN C 514 GLN D 422 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.054926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.041255 restraints weight = 161932.513| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.86 r_work: 0.2896 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 31516 Z= 0.100 Angle : 0.481 8.912 43080 Z= 0.245 Chirality : 0.035 0.148 5136 Planarity : 0.004 0.060 5260 Dihedral : 4.644 46.151 5252 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.14 % Allowed : 10.23 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.14), residues: 3944 helix: 2.60 (0.10), residues: 2580 sheet: -0.44 (0.33), residues: 248 loop : -0.28 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1080 TYR 0.009 0.001 TYR D 559 PHE 0.009 0.001 PHE B 828 TRP 0.011 0.001 TRP B 760 HIS 0.004 0.000 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00201 (31512) covalent geometry : angle 0.48109 (43068) hydrogen bonds : bond 0.03625 ( 2036) hydrogen bonds : angle 3.85989 ( 5988) link_NAG-ASN : bond 0.00168 ( 4) link_NAG-ASN : angle 0.85214 ( 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 180 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.9568 (tpt) cc_final: 0.9153 (mmp) REVERT: A 564 MET cc_start: 0.9269 (OUTLIER) cc_final: 0.8975 (mmm) REVERT: A 721 MET cc_start: 0.8990 (ppp) cc_final: 0.8744 (tmm) REVERT: A 917 MET cc_start: 0.9620 (OUTLIER) cc_final: 0.8971 (mtt) REVERT: A 1057 GLU cc_start: 0.9116 (tp30) cc_final: 0.8667 (tp30) REVERT: B 78 ASP cc_start: 0.9377 (t0) cc_final: 0.8765 (p0) REVERT: B 190 MET cc_start: 0.9570 (tpt) cc_final: 0.9145 (mmp) REVERT: B 564 MET cc_start: 0.9260 (OUTLIER) cc_final: 0.8962 (mmm) REVERT: B 726 MET cc_start: 0.9380 (tpp) cc_final: 0.9116 (tpp) REVERT: B 917 MET cc_start: 0.9605 (OUTLIER) cc_final: 0.8952 (mtt) REVERT: B 1057 GLU cc_start: 0.9110 (tp30) cc_final: 0.8659 (tp30) REVERT: C 78 ASP cc_start: 0.9371 (t0) cc_final: 0.8748 (p0) REVERT: C 190 MET cc_start: 0.9579 (tpt) cc_final: 0.9154 (mmp) REVERT: C 564 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.8958 (mmm) REVERT: C 721 MET cc_start: 0.8961 (ppp) cc_final: 0.8736 (tmm) REVERT: C 917 MET cc_start: 0.9608 (OUTLIER) cc_final: 0.8973 (mtt) REVERT: C 1057 GLU cc_start: 0.9126 (tp30) cc_final: 0.8664 (tp30) REVERT: D 64 MET cc_start: 0.8878 (mmm) cc_final: 0.8676 (mmm) REVERT: D 73 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.9026 (mmtt) REVERT: D 190 MET cc_start: 0.9561 (tpt) cc_final: 0.9140 (mmp) REVERT: D 230 MET cc_start: 0.9584 (OUTLIER) cc_final: 0.9352 (tmm) REVERT: D 564 MET cc_start: 0.9245 (OUTLIER) cc_final: 0.8953 (mmm) REVERT: D 721 MET cc_start: 0.8985 (ppp) cc_final: 0.8735 (tmm) REVERT: D 917 MET cc_start: 0.9610 (OUTLIER) cc_final: 0.8978 (mtt) REVERT: D 1057 GLU cc_start: 0.9104 (tp30) cc_final: 0.8653 (tp30) outliers start: 34 outliers final: 9 residues processed: 165 average time/residue: 0.7140 time to fit residues: 138.0947 Evaluate side-chains 156 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 785 MET Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 917 MET Chi-restraints excluded: chain B residue 564 MET Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 917 MET Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 564 MET Chi-restraints excluded: chain C residue 785 MET Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 917 MET Chi-restraints excluded: chain D residue 73 LYS Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 564 MET Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain D residue 917 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 279 optimal weight: 0.4980 chunk 341 optimal weight: 40.0000 chunk 299 optimal weight: 0.0370 chunk 218 optimal weight: 8.9990 chunk 225 optimal weight: 30.0000 chunk 28 optimal weight: 20.0000 chunk 362 optimal weight: 7.9990 chunk 166 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 377 optimal weight: 0.8980 chunk 372 optimal weight: 0.0670 overall best weight: 1.0998 ------------------------------------------------------------------------------- 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 = 0.3488 r_free = 0.3488 target = 0.054945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.041132 restraints weight = 162441.749| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 3.87 r_work: 0.2895 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 31516 Z= 0.104 Angle : 0.495 11.332 43080 Z= 0.248 Chirality : 0.035 0.145 5136 Planarity : 0.004 0.060 5260 Dihedral : 4.505 45.342 5252 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.98 % Allowed : 10.63 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.14), residues: 3944 helix: 2.70 (0.10), residues: 2568 sheet: -0.30 (0.34), residues: 248 loop : -0.33 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1069 TYR 0.010 0.001 TYR B 559 PHE 0.008 0.001 PHE B 828 TRP 0.012 0.001 TRP C 793 HIS 0.003 0.000 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00219 (31512) covalent geometry : angle 0.49469 (43068) hydrogen bonds : bond 0.03507 ( 2036) hydrogen bonds : angle 3.79394 ( 5988) link_NAG-ASN : bond 0.00120 ( 4) link_NAG-ASN : angle 0.83358 ( 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 172 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 1.144 Fit side-chains revert: symmetry clash REVERT: A 73 LYS cc_start: 0.9299 (OUTLIER) cc_final: 0.9044 (mmtt) REVERT: A 190 MET cc_start: 0.9632 (tpt) cc_final: 0.9100 (mmp) REVERT: A 564 MET cc_start: 0.9281 (mmm) cc_final: 0.9038 (mmm) REVERT: A 721 MET cc_start: 0.8983 (ppp) cc_final: 0.8748 (tmm) REVERT: A 917 MET cc_start: 0.9620 (OUTLIER) cc_final: 0.8970 (mtm) REVERT: A 1057 GLU cc_start: 0.9176 (tp30) cc_final: 0.8710 (tp30) REVERT: B 78 ASP cc_start: 0.9374 (t0) cc_final: 0.8757 (p0) REVERT: B 190 MET cc_start: 0.9604 (tpt) cc_final: 0.9155 (mmp) REVERT: B 564 MET cc_start: 0.9267 (mmm) cc_final: 0.9023 (mmm) REVERT: B 726 MET cc_start: 0.9361 (tpp) cc_final: 0.9116 (tpp) REVERT: B 917 MET cc_start: 0.9619 (OUTLIER) cc_final: 0.8958 (mtm) REVERT: B 1057 GLU cc_start: 0.9163 (tp30) cc_final: 0.8703 (tp30) REVERT: C 190 MET cc_start: 0.9605 (tpt) cc_final: 0.9172 (mmp) REVERT: C 564 MET cc_start: 0.9254 (mmm) cc_final: 0.8973 (mmm) REVERT: C 721 MET cc_start: 0.8970 (ppp) cc_final: 0.8749 (tmm) REVERT: C 917 MET cc_start: 0.9602 (OUTLIER) cc_final: 0.8917 (mtm) REVERT: C 1057 GLU cc_start: 0.9154 (tp30) cc_final: 0.8683 (tp30) REVERT: D 64 MET cc_start: 0.8904 (mmm) cc_final: 0.8648 (mmm) REVERT: D 190 MET cc_start: 0.9601 (tpt) cc_final: 0.9153 (mmp) REVERT: D 230 MET cc_start: 0.9593 (ttm) cc_final: 0.9364 (tmm) REVERT: D 257 MET cc_start: 0.9394 (mmm) cc_final: 0.8768 (mmm) REVERT: D 564 MET cc_start: 0.9288 (mmm) cc_final: 0.9040 (mmm) REVERT: D 721 MET cc_start: 0.8996 (ppp) cc_final: 0.8761 (tmm) REVERT: D 917 MET cc_start: 0.9599 (OUTLIER) cc_final: 0.8901 (mtm) REVERT: D 1057 GLU cc_start: 0.9151 (tp30) cc_final: 0.8687 (tp30) outliers start: 29 outliers final: 7 residues processed: 157 average time/residue: 0.7063 time to fit residues: 130.9947 Evaluate side-chains 145 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 785 MET Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 917 MET Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 917 MET Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 917 MET Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain D residue 917 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 37 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 285 optimal weight: 3.9990 chunk 117 optimal weight: 9.9990 chunk 320 optimal weight: 30.0000 chunk 194 optimal weight: 8.9990 chunk 314 optimal weight: 20.0000 chunk 191 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 133 optimal weight: 20.0000 chunk 26 optimal weight: 30.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN A 511 GLN A 792 ASN ** A 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 GLN B 422 ASN B 511 GLN B 792 ASN ** B 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C 511 GLN C 792 ASN ** C 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 ASN D 511 GLN D 792 ASN ** D 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.051329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.037237 restraints weight = 167537.043| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 3.78 r_work: 0.2770 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 31516 Z= 0.333 Angle : 0.692 11.305 43080 Z= 0.345 Chirality : 0.040 0.143 5136 Planarity : 0.005 0.059 5260 Dihedral : 4.972 52.306 5252 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.28 % Allowed : 11.84 % Favored : 86.88 % 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: 2.41 (0.10), residues: 2584 sheet: -0.81 (0.32), residues: 256 loop : -0.27 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 113 TYR 0.016 0.002 TYR A 470 PHE 0.019 0.002 PHE B 567 TRP 0.018 0.002 TRP D 713 HIS 0.003 0.001 HIS C 842 Details of bonding type rmsd covalent geometry : bond 0.00722 (31512) covalent geometry : angle 0.69116 (43068) hydrogen bonds : bond 0.04556 ( 2036) hydrogen bonds : angle 4.30079 ( 5988) link_NAG-ASN : bond 0.00400 ( 4) link_NAG-ASN : angle 1.87824 ( 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 174 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 1.226 Fit side-chains revert: symmetry clash REVERT: A 73 LYS cc_start: 0.9362 (OUTLIER) cc_final: 0.8896 (mppt) REVERT: A 190 MET cc_start: 0.9603 (tpt) cc_final: 0.9335 (tpt) REVERT: A 257 MET cc_start: 0.9407 (mmm) cc_final: 0.8711 (mmm) REVERT: A 523 MET cc_start: 0.9446 (OUTLIER) cc_final: 0.9202 (mpp) REVERT: A 721 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8930 (tmm) REVERT: A 917 MET cc_start: 0.9615 (OUTLIER) cc_final: 0.8895 (mtm) REVERT: A 1057 GLU cc_start: 0.9186 (tp30) cc_final: 0.8869 (tm-30) REVERT: B 73 LYS cc_start: 0.9374 (OUTLIER) cc_final: 0.8912 (mppt) REVERT: B 190 MET cc_start: 0.9603 (tpt) cc_final: 0.9344 (tpt) REVERT: B 370 MET cc_start: 0.9579 (tpp) cc_final: 0.8834 (tpp) REVERT: B 523 MET cc_start: 0.9448 (mpp) cc_final: 0.9185 (mpp) REVERT: B 726 MET cc_start: 0.9498 (tpp) cc_final: 0.9281 (tpp) REVERT: B 917 MET cc_start: 0.9620 (OUTLIER) cc_final: 0.8888 (mtm) REVERT: B 1057 GLU cc_start: 0.9200 (tp30) cc_final: 0.8882 (tm-30) REVERT: C 73 LYS cc_start: 0.9381 (OUTLIER) cc_final: 0.8918 (mppt) REVERT: C 190 MET cc_start: 0.9605 (tpt) cc_final: 0.9352 (tpt) REVERT: C 257 MET cc_start: 0.9401 (mmm) cc_final: 0.8705 (mmm) REVERT: C 523 MET cc_start: 0.9440 (OUTLIER) cc_final: 0.9194 (mpp) REVERT: C 917 MET cc_start: 0.9604 (OUTLIER) cc_final: 0.8897 (mtm) REVERT: C 1057 GLU cc_start: 0.9186 (tp30) cc_final: 0.8872 (tm-30) REVERT: D 64 MET cc_start: 0.9075 (mmm) cc_final: 0.8872 (mmm) REVERT: D 73 LYS cc_start: 0.9378 (OUTLIER) cc_final: 0.8926 (mppt) REVERT: D 190 MET cc_start: 0.9597 (tpt) cc_final: 0.9333 (tpt) REVERT: D 230 MET cc_start: 0.9678 (OUTLIER) cc_final: 0.9468 (tmm) REVERT: D 257 MET cc_start: 0.9411 (mmm) cc_final: 0.8746 (mmm) REVERT: D 523 MET cc_start: 0.9409 (mpp) cc_final: 0.9180 (mpp) REVERT: D 917 MET cc_start: 0.9608 (OUTLIER) cc_final: 0.8907 (mtm) REVERT: D 1057 GLU cc_start: 0.9184 (tp30) cc_final: 0.8869 (tm-30) outliers start: 38 outliers final: 7 residues processed: 153 average time/residue: 0.7331 time to fit residues: 131.4105 Evaluate side-chains 153 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 917 MET Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 917 MET Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 917 MET Chi-restraints excluded: chain D residue 73 LYS Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain D residue 917 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 348 optimal weight: 0.6980 chunk 258 optimal weight: 7.9990 chunk 180 optimal weight: 2.9990 chunk 315 optimal weight: 20.0000 chunk 68 optimal weight: 9.9990 chunk 373 optimal weight: 3.9990 chunk 306 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 206 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 402 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.052737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.039036 restraints weight = 163342.059| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.77 r_work: 0.2828 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 31516 Z= 0.129 Angle : 0.556 12.719 43080 Z= 0.273 Chirality : 0.036 0.144 5136 Planarity : 0.004 0.059 5260 Dihedral : 4.672 47.630 5252 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.08 % Allowed : 12.35 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.14), residues: 3944 helix: 2.59 (0.10), residues: 2584 sheet: -0.76 (0.32), residues: 260 loop : -0.34 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 113 TYR 0.011 0.001 TYR B 559 PHE 0.009 0.001 PHE D 828 TRP 0.011 0.001 TRP A 984 HIS 0.005 0.001 HIS C 115 Details of bonding type rmsd covalent geometry : bond 0.00280 (31512) covalent geometry : angle 0.55524 (43068) hydrogen bonds : bond 0.03928 ( 2036) hydrogen bonds : angle 3.97429 ( 5988) link_NAG-ASN : bond 0.00022 ( 4) link_NAG-ASN : angle 1.24987 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 0.982 Fit side-chains REVERT: A 64 MET cc_start: 0.8857 (mmm) cc_final: 0.8309 (mmm) REVERT: A 73 LYS cc_start: 0.9367 (OUTLIER) cc_final: 0.9131 (mmtt) REVERT: A 190 MET cc_start: 0.9608 (tpt) cc_final: 0.9399 (tpt) REVERT: A 257 MET cc_start: 0.9419 (mmm) cc_final: 0.8728 (mmm) REVERT: A 721 MET cc_start: 0.9066 (ppp) cc_final: 0.8856 (tmm) REVERT: A 917 MET cc_start: 0.9603 (OUTLIER) cc_final: 0.9010 (mtm) REVERT: A 1057 GLU cc_start: 0.9166 (tp30) cc_final: 0.8827 (tm-30) REVERT: B 73 LYS cc_start: 0.9383 (OUTLIER) cc_final: 0.8928 (mppt) REVERT: B 190 MET cc_start: 0.9623 (tpt) cc_final: 0.9364 (tpt) REVERT: B 257 MET cc_start: 0.9403 (mmm) cc_final: 0.8734 (mmm) REVERT: B 370 MET cc_start: 0.9570 (tpp) cc_final: 0.8706 (tpp) REVERT: B 523 MET cc_start: 0.9399 (OUTLIER) cc_final: 0.9155 (mpp) REVERT: B 726 MET cc_start: 0.9425 (tpp) cc_final: 0.9200 (tpp) REVERT: B 917 MET cc_start: 0.9602 (OUTLIER) cc_final: 0.8986 (mtm) REVERT: B 1057 GLU cc_start: 0.9181 (tp30) cc_final: 0.8798 (tm-30) REVERT: C 64 MET cc_start: 0.8882 (mmm) cc_final: 0.8332 (mmm) REVERT: C 73 LYS cc_start: 0.9389 (OUTLIER) cc_final: 0.8931 (mppt) REVERT: C 190 MET cc_start: 0.9625 (tpt) cc_final: 0.9368 (tpt) REVERT: C 257 MET cc_start: 0.9414 (mmm) cc_final: 0.8732 (mmm) REVERT: C 917 MET cc_start: 0.9597 (OUTLIER) cc_final: 0.8995 (mtm) REVERT: C 1057 GLU cc_start: 0.9153 (tp30) cc_final: 0.8767 (tm-30) REVERT: D 64 MET cc_start: 0.8996 (mmm) cc_final: 0.8785 (mmm) REVERT: D 190 MET cc_start: 0.9622 (tpt) cc_final: 0.9361 (tpt) REVERT: D 230 MET cc_start: 0.9676 (OUTLIER) cc_final: 0.9372 (tmm) REVERT: D 257 MET cc_start: 0.9409 (mmm) cc_final: 0.8762 (mmm) REVERT: D 917 MET cc_start: 0.9595 (OUTLIER) cc_final: 0.9026 (mtm) REVERT: D 1057 GLU cc_start: 0.9171 (tp30) cc_final: 0.8822 (tm-30) outliers start: 32 outliers final: 10 residues processed: 157 average time/residue: 0.7079 time to fit residues: 130.7173 Evaluate side-chains 152 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 917 MET Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 917 MET Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 785 MET Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 917 MET Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain D residue 917 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 142 optimal weight: 8.9990 chunk 192 optimal weight: 10.0000 chunk 200 optimal weight: 0.4980 chunk 371 optimal weight: 0.9990 chunk 379 optimal weight: 1.9990 chunk 225 optimal weight: 4.9990 chunk 136 optimal weight: 8.9990 chunk 361 optimal weight: 2.9990 chunk 127 optimal weight: 40.0000 chunk 5 optimal weight: 3.9990 chunk 245 optimal weight: 7.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- 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 = 0.3441 r_free = 0.3441 target = 0.052974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.039187 restraints weight = 163969.067| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 3.80 r_work: 0.2837 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.3297 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= 0.131 Angle : 0.555 12.124 43080 Z= 0.272 Chirality : 0.036 0.142 5136 Planarity : 0.004 0.061 5260 Dihedral : 4.573 45.582 5252 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.04 % Allowed : 13.26 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.14), residues: 3944 helix: 2.61 (0.10), residues: 2592 sheet: -0.69 (0.32), residues: 260 loop : -0.39 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 113 TYR 0.010 0.001 TYR A 559 PHE 0.010 0.001 PHE B 567 TRP 0.013 0.001 TRP D 760 HIS 0.007 0.000 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00285 (31512) covalent geometry : angle 0.55474 (43068) hydrogen bonds : bond 0.03724 ( 2036) hydrogen bonds : angle 3.90205 ( 5988) link_NAG-ASN : bond 0.00015 ( 4) link_NAG-ASN : angle 1.13471 ( 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 170 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 1.153 Fit side-chains REVERT: A 190 MET cc_start: 0.9612 (tpt) cc_final: 0.9340 (tpt) REVERT: A 257 MET cc_start: 0.9437 (mmm) cc_final: 0.8752 (mmm) REVERT: A 721 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8822 (tmm) REVERT: A 839 PHE cc_start: 0.9364 (OUTLIER) cc_final: 0.8863 (t80) REVERT: A 917 MET cc_start: 0.9574 (OUTLIER) cc_final: 0.8935 (mtm) REVERT: A 1057 GLU cc_start: 0.9194 (tp30) cc_final: 0.8829 (tm-30) REVERT: B 190 MET cc_start: 0.9626 (tpt) cc_final: 0.9382 (tpt) REVERT: B 257 MET cc_start: 0.9421 (mmm) cc_final: 0.8755 (mmm) REVERT: B 370 MET cc_start: 0.9539 (tpp) cc_final: 0.8670 (tpp) REVERT: B 726 MET cc_start: 0.9423 (tpp) cc_final: 0.9207 (tpp) REVERT: B 839 PHE cc_start: 0.9365 (OUTLIER) cc_final: 0.8847 (t80) REVERT: B 917 MET cc_start: 0.9577 (OUTLIER) cc_final: 0.8937 (mtm) REVERT: B 1057 GLU cc_start: 0.9199 (tp30) cc_final: 0.8836 (tm-30) REVERT: C 190 MET cc_start: 0.9624 (tpt) cc_final: 0.9363 (tpt) REVERT: C 257 MET cc_start: 0.9426 (mmm) cc_final: 0.8765 (mmm) REVERT: C 839 PHE cc_start: 0.9368 (OUTLIER) cc_final: 0.8851 (t80) REVERT: C 917 MET cc_start: 0.9576 (OUTLIER) cc_final: 0.8937 (mtm) REVERT: C 1057 GLU cc_start: 0.9177 (tp30) cc_final: 0.8811 (tm-30) REVERT: D 64 MET cc_start: 0.9005 (mmm) cc_final: 0.8768 (mmm) REVERT: D 190 MET cc_start: 0.9626 (tpt) cc_final: 0.9372 (tpt) REVERT: D 230 MET cc_start: 0.9679 (ttm) cc_final: 0.9374 (tmm) REVERT: D 257 MET cc_start: 0.9421 (mmm) cc_final: 0.8788 (mmm) REVERT: D 839 PHE cc_start: 0.9360 (OUTLIER) cc_final: 0.8863 (t80) REVERT: D 917 MET cc_start: 0.9575 (OUTLIER) cc_final: 0.8944 (mtm) REVERT: D 1057 GLU cc_start: 0.9190 (tp30) cc_final: 0.8827 (tm-30) outliers start: 31 outliers final: 11 residues processed: 161 average time/residue: 0.6873 time to fit residues: 131.2005 Evaluate side-chains 153 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 917 MET Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 839 PHE Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 917 MET Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 839 PHE Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 917 MET Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 839 PHE Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain D residue 917 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 358 optimal weight: 3.9990 chunk 0 optimal weight: 40.0000 chunk 160 optimal weight: 4.9990 chunk 329 optimal weight: 10.0000 chunk 91 optimal weight: 0.0050 chunk 36 optimal weight: 0.3980 chunk 102 optimal weight: 7.9990 chunk 285 optimal weight: 0.9980 chunk 177 optimal weight: 9.9990 chunk 123 optimal weight: 30.0000 chunk 198 optimal weight: 40.0000 overall best weight: 2.0798 ------------------------------------------------------------------------------- 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 = 0.3444 r_free = 0.3444 target = 0.052962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.039405 restraints weight = 163967.801| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.78 r_work: 0.2844 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31516 Z= 0.131 Angle : 0.574 13.935 43080 Z= 0.278 Chirality : 0.036 0.143 5136 Planarity : 0.004 0.059 5260 Dihedral : 4.539 44.840 5252 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.87 % Allowed : 13.32 % Favored : 85.80 % 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: 2.39 (0.14), residues: 3944 helix: 2.63 (0.10), residues: 2584 sheet: -0.64 (0.32), residues: 260 loop : -0.43 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 113 TYR 0.009 0.001 TYR C 559 PHE 0.010 0.001 PHE D 567 TRP 0.010 0.001 TRP C 709 HIS 0.005 0.001 HIS C 115 Details of bonding type rmsd covalent geometry : bond 0.00287 (31512) covalent geometry : angle 0.57406 (43068) hydrogen bonds : bond 0.03676 ( 2036) hydrogen bonds : angle 3.91908 ( 5988) link_NAG-ASN : bond 0.00025 ( 4) link_NAG-ASN : angle 1.08921 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: A 190 MET cc_start: 0.9603 (tpt) cc_final: 0.9361 (tpt) REVERT: A 257 MET cc_start: 0.9435 (mmm) cc_final: 0.8774 (mmm) REVERT: A 721 MET cc_start: 0.9073 (ppp) cc_final: 0.8824 (tmm) REVERT: A 839 PHE cc_start: 0.9380 (OUTLIER) cc_final: 0.8906 (t80) REVERT: A 917 MET cc_start: 0.9574 (OUTLIER) cc_final: 0.8944 (mtm) REVERT: A 1057 GLU cc_start: 0.9202 (tp30) cc_final: 0.8833 (tm-30) REVERT: B 64 MET cc_start: 0.8684 (mmm) cc_final: 0.8059 (mmm) REVERT: B 190 MET cc_start: 0.9632 (tpt) cc_final: 0.9408 (tpt) REVERT: B 257 MET cc_start: 0.9432 (mmm) cc_final: 0.8779 (mmm) REVERT: B 370 MET cc_start: 0.9522 (tpp) cc_final: 0.8644 (tpp) REVERT: B 726 MET cc_start: 0.9411 (tpp) cc_final: 0.9169 (tpp) REVERT: B 839 PHE cc_start: 0.9372 (OUTLIER) cc_final: 0.8906 (t80) REVERT: B 917 MET cc_start: 0.9577 (OUTLIER) cc_final: 0.8938 (mtm) REVERT: B 1057 GLU cc_start: 0.9193 (tp30) cc_final: 0.8821 (tm-30) REVERT: C 190 MET cc_start: 0.9624 (tpt) cc_final: 0.9399 (tpt) REVERT: C 257 MET cc_start: 0.9426 (mmm) cc_final: 0.8770 (mmm) REVERT: C 839 PHE cc_start: 0.9376 (OUTLIER) cc_final: 0.8898 (t80) REVERT: C 917 MET cc_start: 0.9577 (OUTLIER) cc_final: 0.8944 (mtm) REVERT: C 1057 GLU cc_start: 0.9183 (tp30) cc_final: 0.8811 (tm-30) REVERT: D 64 MET cc_start: 0.9009 (mmm) cc_final: 0.8765 (mmm) REVERT: D 190 MET cc_start: 0.9626 (tpt) cc_final: 0.9384 (tpt) REVERT: D 230 MET cc_start: 0.9668 (OUTLIER) cc_final: 0.9361 (tmm) REVERT: D 257 MET cc_start: 0.9425 (mmm) cc_final: 0.8798 (mmm) REVERT: D 839 PHE cc_start: 0.9363 (OUTLIER) cc_final: 0.8902 (t80) REVERT: D 917 MET cc_start: 0.9578 (OUTLIER) cc_final: 0.8953 (mtm) REVERT: D 1057 GLU cc_start: 0.9188 (tp30) cc_final: 0.8818 (tm-30) outliers start: 26 outliers final: 12 residues processed: 158 average time/residue: 0.7054 time to fit residues: 131.5678 Evaluate side-chains 154 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 917 MET Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 839 PHE Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 917 MET Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 839 PHE Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 917 MET Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 839 PHE Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain D residue 917 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 55 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 127 optimal weight: 0.3980 chunk 146 optimal weight: 0.0000 chunk 263 optimal weight: 2.9990 chunk 338 optimal weight: 20.0000 chunk 85 optimal weight: 4.9990 chunk 148 optimal weight: 0.9990 chunk 325 optimal weight: 20.0000 chunk 361 optimal weight: 5.9990 chunk 239 optimal weight: 20.0000 overall best weight: 1.8790 ------------------------------------------------------------------------------- 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 = 0.3448 r_free = 0.3448 target = 0.053151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.039554 restraints weight = 163617.644| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.80 r_work: 0.2851 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31516 Z= 0.126 Angle : 0.592 13.030 43080 Z= 0.282 Chirality : 0.036 0.162 5136 Planarity : 0.004 0.058 5260 Dihedral : 4.467 44.221 5252 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.74 % Allowed : 13.49 % Favored : 85.77 % 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: 2.40 (0.14), residues: 3944 helix: 2.62 (0.10), residues: 2584 sheet: -0.56 (0.32), residues: 252 loop : -0.40 (0.19), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 113 TYR 0.009 0.001 TYR B 559 PHE 0.008 0.001 PHE D 828 TRP 0.011 0.001 TRP C 240 HIS 0.004 0.000 HIS C 115 Details of bonding type rmsd covalent geometry : bond 0.00277 (31512) covalent geometry : angle 0.59226 (43068) hydrogen bonds : bond 0.03607 ( 2036) hydrogen bonds : angle 3.91482 ( 5988) link_NAG-ASN : bond 0.00031 ( 4) link_NAG-ASN : angle 1.03948 ( 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 159 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 1.115 Fit side-chains revert: symmetry clash REVERT: A 190 MET cc_start: 0.9600 (tpt) cc_final: 0.9371 (tpt) REVERT: A 257 MET cc_start: 0.9443 (mmm) cc_final: 0.8797 (mmm) REVERT: A 721 MET cc_start: 0.9062 (ppp) cc_final: 0.8829 (tmm) REVERT: A 839 PHE cc_start: 0.9380 (OUTLIER) cc_final: 0.8943 (t80) REVERT: A 917 MET cc_start: 0.9579 (OUTLIER) cc_final: 0.8941 (mtm) REVERT: A 1057 GLU cc_start: 0.9204 (tp30) cc_final: 0.8775 (tp30) REVERT: B 64 MET cc_start: 0.8705 (mmm) cc_final: 0.8148 (mmm) REVERT: B 190 MET cc_start: 0.9628 (tpt) cc_final: 0.9415 (tpt) REVERT: B 257 MET cc_start: 0.9423 (mmm) cc_final: 0.8778 (mmm) REVERT: B 370 MET cc_start: 0.9497 (tpp) cc_final: 0.8738 (tpp) REVERT: B 726 MET cc_start: 0.9395 (tpp) cc_final: 0.9157 (tpp) REVERT: B 839 PHE cc_start: 0.9379 (OUTLIER) cc_final: 0.8944 (t80) REVERT: B 917 MET cc_start: 0.9587 (OUTLIER) cc_final: 0.8953 (mtm) REVERT: B 1057 GLU cc_start: 0.9196 (tp30) cc_final: 0.8763 (tp30) REVERT: C 190 MET cc_start: 0.9622 (tpt) cc_final: 0.9413 (tpt) REVERT: C 257 MET cc_start: 0.9428 (mmm) cc_final: 0.8778 (mmm) REVERT: C 839 PHE cc_start: 0.9382 (OUTLIER) cc_final: 0.8937 (t80) REVERT: C 917 MET cc_start: 0.9583 (OUTLIER) cc_final: 0.8957 (mtm) REVERT: C 1057 GLU cc_start: 0.9192 (tp30) cc_final: 0.8759 (tp30) REVERT: D 64 MET cc_start: 0.9009 (mmm) cc_final: 0.8761 (mmm) REVERT: D 190 MET cc_start: 0.9627 (tpt) cc_final: 0.9396 (tpt) REVERT: D 230 MET cc_start: 0.9669 (OUTLIER) cc_final: 0.9352 (tmm) REVERT: D 257 MET cc_start: 0.9444 (mmm) cc_final: 0.8849 (mmm) REVERT: D 839 PHE cc_start: 0.9384 (OUTLIER) cc_final: 0.8935 (t80) REVERT: D 917 MET cc_start: 0.9593 (OUTLIER) cc_final: 0.8979 (mtm) REVERT: D 1057 GLU cc_start: 0.9191 (tp30) cc_final: 0.8758 (tp30) outliers start: 22 outliers final: 12 residues processed: 153 average time/residue: 0.7219 time to fit residues: 129.9843 Evaluate side-chains 157 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 917 MET Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 839 PHE Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 917 MET Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 839 PHE Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 917 MET Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 839 PHE Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain D residue 917 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 367 optimal weight: 9.9990 chunk 210 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 296 optimal weight: 5.9990 chunk 294 optimal weight: 10.0000 chunk 360 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 chunk 348 optimal weight: 5.9990 chunk 320 optimal weight: 30.0000 chunk 59 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 = 0.3386 r_free = 0.3386 target = 0.050863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.037115 restraints weight = 169216.886| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 3.72 r_work: 0.2771 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 31516 Z= 0.317 Angle : 0.726 13.232 43080 Z= 0.352 Chirality : 0.040 0.177 5136 Planarity : 0.005 0.055 5260 Dihedral : 4.806 50.793 5252 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.91 % Allowed : 13.59 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.14), residues: 3944 helix: 2.51 (0.10), residues: 2584 sheet: -0.60 (0.34), residues: 220 loop : -0.38 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 113 TYR 0.025 0.002 TYR D 519 PHE 0.016 0.001 PHE A 567 TRP 0.017 0.002 TRP B 760 HIS 0.003 0.001 HIS C 115 Details of bonding type rmsd covalent geometry : bond 0.00687 (31512) covalent geometry : angle 0.72562 (43068) hydrogen bonds : bond 0.04257 ( 2036) hydrogen bonds : angle 4.30043 ( 5988) link_NAG-ASN : bond 0.00382 ( 4) link_NAG-ASN : angle 1.65194 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8977.29 seconds wall clock time: 153 minutes 57.41 seconds (9237.41 seconds total)