Starting phenix.real_space_refine on Thu Nov 20 05:07:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mbr_23744/11_2025/7mbr_23744.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mbr_23744/11_2025/7mbr_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 { model { file = "/net/cci-nas-00/data/ceres_data/7mbr_23744/11_2025/7mbr_23744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mbr_23744/11_2025/7mbr_23744.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mbr_23744/11_2025/7mbr_23744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mbr_23744/11_2025/7mbr_23744.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30708 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7574 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 137} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 952} Chain breaks: 4 Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 585 Unresolved non-hydrogen dihedrals: 368 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ASP:plan': 30, 'ARG:plan': 8, 'GLU:plan': 29, 'GLN:plan1': 13, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 333 Chain: "A" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 103 Unusual residues: {'NAG': 1, 'YUV': 1, 'YUY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 103 Unusual residues: {'NAG': 1, 'YUV': 1, 'YUY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 103 Unusual residues: {'NAG': 1, 'YUV': 1, 'YUY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 103 Unusual residues: {'NAG': 1, 'YUV': 1, 'YUY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, D Time building chain proxies: 9.45, per 1000 atoms: 0.31 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: 2.94 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: 1.00 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: 6.78 Time building geometry restraints manager: 3.83 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: 0.09 Found NCS groups: ncs_group { reference = (chain 'A' and resid 16 through 1092) selection = (chain 'B' and resid 16 through 1092) selection = (chain 'C' and resid 16 through 1092) selection = (chain 'D' and resid 16 through 1092) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 31.680 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.530 ------------------------------------------------------------------------------- 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 : 1.247 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: 0.8367 time to fit residues: 213.3954 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 : 1.189 ------------------------------------------------------------------------------- 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 = 0.054506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.040686 restraints weight = 164382.709| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.78 r_work: 0.2870 rms_B_bonded: 4.48 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 : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.8959 (mmm) cc_final: 0.8483 (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: 0.9599 (OUTLIER) cc_final: 0.9107 (mtm) REVERT: A 1057 GLU cc_start: 0.8988 (tp30) cc_final: 0.8648 (tp30) REVERT: B 114 ASP cc_start: 0.9051 (m-30) cc_final: 0.8850 (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: 0.8995 (tp30) cc_final: 0.8658 (tp30) REVERT: C 114 ASP cc_start: 0.9075 (m-30) cc_final: 0.8868 (m-30) REVERT: C 190 MET cc_start: 0.9034 (mmm) cc_final: 0.8501 (mmm) REVERT: C 721 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8716 (tmm) REVERT: C 726 MET cc_start: 0.9283 (OUTLIER) cc_final: 0.9013 (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: 0.8648 (tp30) REVERT: D 64 MET cc_start: 0.8754 (mmm) cc_final: 0.8525 (mmm) REVERT: D 114 ASP cc_start: 0.9055 (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: 0.8743 (tmm) REVERT: D 726 MET cc_start: 0.9289 (OUTLIER) cc_final: 0.9015 (mmm) REVERT: D 812 MET cc_start: 0.9402 (mmp) cc_final: 0.9102 (mmm) REVERT: D 917 MET cc_start: 0.9598 (OUTLIER) cc_final: 0.9102 (mtm) REVERT: D 1057 GLU cc_start: 0.8983 (tp30) cc_final: 0.8646 (tp30) outliers start: 39 outliers final: 10 residues processed: 161 average time/residue: 0.6950 time to fit residues: 132.1508 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 : 1.143 ------------------------------------------------------------------------------- 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: 0.2980 chunk 19 optimal weight: 0.0170 chunk 207 optimal weight: 8.9990 chunk 356 optimal weight: 0.8980 chunk 373 optimal weight: 8.9990 chunk 220 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 chunk 251 optimal weight: 2.9990 chunk 211 optimal weight: 8.9990 overall best weight: 2.2422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 GLN C 514 GLN D 514 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.054517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.040768 restraints weight = 163578.838| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.78 r_work: 0.2880 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1922 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= 0.134 Angle : 0.487 7.163 43080 Z= 0.251 Chirality : 0.036 0.154 5136 Planarity : 0.004 0.057 5260 Dihedral : 4.882 48.384 5252 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.18 % Allowed : 8.65 % Favored : 90.17 % 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: 2.53 (0.10), residues: 2584 sheet: -0.62 (0.32), residues: 248 loop : -0.27 (0.19), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1080 TYR 0.010 0.001 TYR A 559 PHE 0.008 0.001 PHE B 828 TRP 0.018 0.001 TRP D 760 HIS 0.003 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00284 (31512) covalent geometry : angle 0.48663 (43068) hydrogen bonds : bond 0.03856 ( 2036) hydrogen bonds : angle 3.96787 ( 5988) link_NAG-ASN : bond 0.00039 ( 4) link_NAG-ASN : angle 1.09061 ( 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 178 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.8844 (mppt) REVERT: A 114 ASP cc_start: 0.8960 (m-30) cc_final: 0.8678 (p0) REVERT: A 194 MET cc_start: 0.9499 (mmm) cc_final: 0.9283 (mmm) REVERT: A 721 MET cc_start: 0.9007 (ppp) cc_final: 0.8780 (tmm) REVERT: A 917 MET cc_start: 0.9614 (OUTLIER) cc_final: 0.8993 (mtt) REVERT: A 1057 GLU cc_start: 0.9073 (tp30) cc_final: 0.8657 (tp30) REVERT: B 78 ASP cc_start: 0.9381 (t0) cc_final: 0.8767 (p0) REVERT: B 190 MET cc_start: 0.9074 (mmm) cc_final: 0.8872 (tpt) REVERT: B 194 MET cc_start: 0.9506 (mmm) cc_final: 0.9285 (mmm) REVERT: B 726 MET cc_start: 0.9332 (tpp) cc_final: 0.9113 (tpp) REVERT: B 917 MET cc_start: 0.9613 (OUTLIER) cc_final: 0.8992 (mtt) REVERT: B 1057 GLU cc_start: 0.9073 (tp30) cc_final: 0.8656 (tp30) REVERT: C 73 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.9018 (mmtt) REVERT: C 114 ASP cc_start: 0.9091 (m-30) cc_final: 0.8883 (m-30) REVERT: C 194 MET cc_start: 0.9509 (mmm) cc_final: 0.9297 (mmm) REVERT: C 721 MET cc_start: 0.9011 (ppp) cc_final: 0.8772 (tmm) REVERT: C 917 MET cc_start: 0.9624 (OUTLIER) cc_final: 0.8965 (mtm) REVERT: C 1057 GLU cc_start: 0.9056 (tp30) cc_final: 0.8640 (tp30) REVERT: D 73 LYS cc_start: 0.9278 (OUTLIER) cc_final: 0.8823 (mppt) REVERT: D 194 MET cc_start: 0.9509 (mmm) cc_final: 0.9287 (mmm) REVERT: D 230 MET cc_start: 0.9579 (OUTLIER) cc_final: 0.9351 (tmm) REVERT: D 721 MET cc_start: 0.9012 (ppp) cc_final: 0.8784 (tmm) REVERT: D 917 MET cc_start: 0.9620 (OUTLIER) cc_final: 0.8953 (mtm) REVERT: D 1057 GLU cc_start: 0.9065 (tp30) cc_final: 0.8649 (tp30) outliers start: 35 outliers final: 9 residues processed: 166 average time/residue: 0.7022 time to fit residues: 137.5779 Evaluate side-chains 150 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 1.185 ------------------------------------------------------------------------------- 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 251 optimal weight: 9.9990 chunk 164 optimal weight: 5.9990 chunk 333 optimal weight: 10.0000 chunk 134 optimal weight: 6.9990 chunk 172 optimal weight: 0.9980 chunk 307 optimal weight: 9.9990 chunk 2 optimal weight: 0.1980 chunk 361 optimal weight: 2.9990 chunk 285 optimal weight: 0.9980 chunk 218 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN D 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.054126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.040418 restraints weight = 162670.530| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.82 r_work: 0.2869 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 31516 Z= 0.131 Angle : 0.495 9.259 43080 Z= 0.253 Chirality : 0.036 0.148 5136 Planarity : 0.004 0.060 5260 Dihedral : 4.692 47.463 5252 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.24 % Allowed : 10.13 % 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: 2.46 (0.14), residues: 3944 helix: 2.63 (0.10), residues: 2580 sheet: -0.50 (0.32), residues: 248 loop : -0.26 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 191 TYR 0.010 0.001 TYR D 559 PHE 0.009 0.001 PHE B 567 TRP 0.013 0.001 TRP B 760 HIS 0.003 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00282 (31512) covalent geometry : angle 0.49455 (43068) hydrogen bonds : bond 0.03746 ( 2036) hydrogen bonds : angle 3.91461 ( 5988) link_NAG-ASN : bond 0.00055 ( 4) link_NAG-ASN : angle 1.03770 ( 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 177 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 140 time to evaluate : 1.249 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 64 MET cc_start: 0.8866 (mmm) cc_final: 0.8421 (mmm) REVERT: A 73 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.9030 (mmtt) REVERT: A 190 MET cc_start: 0.9589 (tpt) cc_final: 0.9132 (mmp) REVERT: A 564 MET cc_start: 0.9298 (OUTLIER) cc_final: 0.9009 (mmm) REVERT: A 721 MET cc_start: 0.9023 (ppp) cc_final: 0.8785 (tmm) REVERT: A 726 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.9017 (mmm) REVERT: A 779 MET cc_start: 0.8344 (tmm) cc_final: 0.8068 (tmm) REVERT: A 917 MET cc_start: 0.9607 (OUTLIER) cc_final: 0.8903 (mtm) REVERT: A 1057 GLU cc_start: 0.9133 (tp30) cc_final: 0.8700 (tp30) REVERT: B 73 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.8872 (mppt) REVERT: B 564 MET cc_start: 0.9304 (OUTLIER) cc_final: 0.9007 (mmm) REVERT: B 726 MET cc_start: 0.9397 (tpp) cc_final: 0.9142 (tpp) REVERT: B 917 MET cc_start: 0.9584 (OUTLIER) cc_final: 0.8871 (mtm) REVERT: B 1057 GLU cc_start: 0.9129 (tp30) cc_final: 0.8695 (tp30) REVERT: C 78 ASP cc_start: 0.9370 (t0) cc_final: 0.8749 (p0) REVERT: C 190 MET cc_start: 0.9604 (tpt) cc_final: 0.9148 (mmp) REVERT: C 564 MET cc_start: 0.9279 (OUTLIER) cc_final: 0.8995 (mmm) REVERT: C 721 MET cc_start: 0.8983 (ppp) cc_final: 0.8761 (tmm) REVERT: C 726 MET cc_start: 0.9158 (OUTLIER) cc_final: 0.8938 (mmm) REVERT: C 779 MET cc_start: 0.8289 (tmm) cc_final: 0.8004 (tmm) REVERT: C 917 MET cc_start: 0.9622 (OUTLIER) cc_final: 0.8918 (mtm) REVERT: C 1057 GLU cc_start: 0.9110 (tp30) cc_final: 0.8668 (tp30) REVERT: D 64 MET cc_start: 0.8771 (mmm) cc_final: 0.8386 (mmm) REVERT: D 73 LYS cc_start: 0.9295 (OUTLIER) cc_final: 0.9032 (mmtt) REVERT: D 190 MET cc_start: 0.9583 (tpt) cc_final: 0.9126 (mmp) REVERT: D 230 MET cc_start: 0.9603 (OUTLIER) cc_final: 0.9360 (tmm) REVERT: D 564 MET cc_start: 0.9287 (OUTLIER) cc_final: 0.8996 (mmm) REVERT: D 721 MET cc_start: 0.9019 (ppp) cc_final: 0.8779 (tmm) REVERT: D 726 MET cc_start: 0.9162 (OUTLIER) cc_final: 0.8937 (mmm) REVERT: D 917 MET cc_start: 0.9620 (OUTLIER) cc_final: 0.8921 (mtm) REVERT: D 1057 GLU cc_start: 0.9122 (tp30) cc_final: 0.8689 (tp30) outliers start: 37 outliers final: 6 residues processed: 161 average time/residue: 0.7148 time to fit residues: 135.3844 Evaluate side-chains 158 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 726 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 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 564 MET Chi-restraints excluded: chain C residue 726 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 564 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 279 optimal weight: 6.9990 chunk 341 optimal weight: 40.0000 chunk 299 optimal weight: 10.0000 chunk 218 optimal weight: 8.9990 chunk 225 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 362 optimal weight: 6.9990 chunk 166 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 377 optimal weight: 0.9980 chunk 372 optimal weight: 7.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 792 ASN ** A 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 792 ASN C 422 ASN C 792 ASN ** C 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 792 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.052289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.038431 restraints weight = 166110.687| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 3.80 r_work: 0.2808 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 31516 Z= 0.237 Angle : 0.571 10.389 43080 Z= 0.287 Chirality : 0.037 0.159 5136 Planarity : 0.004 0.059 5260 Dihedral : 4.755 50.061 5252 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.28 % Allowed : 10.73 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.14), residues: 3944 helix: 2.65 (0.10), residues: 2576 sheet: -0.74 (0.32), residues: 260 loop : -0.30 (0.19), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 191 TYR 0.011 0.001 TYR D 559 PHE 0.014 0.001 PHE D 567 TRP 0.015 0.001 TRP D 760 HIS 0.003 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00514 (31512) covalent geometry : angle 0.57016 (43068) hydrogen bonds : bond 0.04033 ( 2036) hydrogen bonds : angle 4.05691 ( 5988) link_NAG-ASN : bond 0.00170 ( 4) link_NAG-ASN : angle 1.38631 ( 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 176 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 1.248 Fit side-chains REVERT: A 73 LYS cc_start: 0.9359 (OUTLIER) cc_final: 0.9110 (mmtt) REVERT: A 190 MET cc_start: 0.9663 (tpt) cc_final: 0.9369 (tpt) REVERT: A 194 MET cc_start: 0.9429 (OUTLIER) cc_final: 0.9186 (mmm) REVERT: A 523 MET cc_start: 0.9478 (mpp) cc_final: 0.9265 (mpp) REVERT: A 721 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8863 (tmm) REVERT: A 917 MET cc_start: 0.9592 (OUTLIER) cc_final: 0.8858 (mtm) REVERT: A 1057 GLU cc_start: 0.9161 (tp30) cc_final: 0.8818 (tm-30) REVERT: B 73 LYS cc_start: 0.9360 (OUTLIER) cc_final: 0.8904 (mppt) REVERT: B 190 MET cc_start: 0.9602 (tpt) cc_final: 0.9224 (mmp) REVERT: B 257 MET cc_start: 0.9349 (mmm) cc_final: 0.8588 (mmm) REVERT: B 523 MET cc_start: 0.9471 (mpp) cc_final: 0.9256 (mpp) REVERT: B 726 MET cc_start: 0.9495 (tpp) cc_final: 0.9284 (tpp) REVERT: B 917 MET cc_start: 0.9594 (OUTLIER) cc_final: 0.8861 (mtm) REVERT: B 1057 GLU cc_start: 0.9167 (tp30) cc_final: 0.8799 (tm-30) REVERT: C 73 LYS cc_start: 0.9380 (OUTLIER) cc_final: 0.8923 (mppt) REVERT: C 190 MET cc_start: 0.9628 (tpt) cc_final: 0.9386 (tpt) REVERT: C 523 MET cc_start: 0.9471 (mpp) cc_final: 0.9252 (mpp) REVERT: C 721 MET cc_start: 0.9053 (ppp) cc_final: 0.8850 (tmm) REVERT: C 917 MET cc_start: 0.9594 (OUTLIER) cc_final: 0.8864 (mtm) REVERT: C 1057 GLU cc_start: 0.9146 (tp30) cc_final: 0.8775 (tm-30) REVERT: D 64 MET cc_start: 0.8872 (mmm) cc_final: 0.8440 (mmm) REVERT: D 73 LYS cc_start: 0.9369 (OUTLIER) cc_final: 0.9120 (mmtt) REVERT: D 190 MET cc_start: 0.9626 (tpt) cc_final: 0.9381 (tpt) REVERT: D 230 MET cc_start: 0.9651 (OUTLIER) cc_final: 0.9359 (tmm) REVERT: D 257 MET cc_start: 0.9387 (mmm) cc_final: 0.8700 (mmm) REVERT: D 523 MET cc_start: 0.9449 (mpp) cc_final: 0.9239 (mpp) REVERT: D 721 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8864 (tmm) REVERT: D 917 MET cc_start: 0.9604 (OUTLIER) cc_final: 0.8905 (mtm) REVERT: D 1057 GLU cc_start: 0.9143 (tp30) cc_final: 0.8804 (tm-30) outliers start: 38 outliers final: 6 residues processed: 157 average time/residue: 0.7344 time to fit residues: 135.6904 Evaluate side-chains 148 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 194 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 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 721 MET 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: 10.0000 chunk 66 optimal weight: 0.9980 chunk 285 optimal weight: 0.8980 chunk 117 optimal weight: 20.0000 chunk 320 optimal weight: 20.0000 chunk 194 optimal weight: 9.9990 chunk 314 optimal weight: 30.0000 chunk 191 optimal weight: 20.0000 chunk 8 optimal weight: 8.9990 chunk 133 optimal weight: 10.0000 chunk 26 optimal weight: 0.0370 overall best weight: 4.1862 ------------------------------------------------------------------------------- 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 = 0.3421 r_free = 0.3421 target = 0.052291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.038412 restraints weight = 165643.798| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.81 r_work: 0.2809 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 31516 Z= 0.198 Angle : 0.570 11.654 43080 Z= 0.283 Chirality : 0.037 0.144 5136 Planarity : 0.004 0.057 5260 Dihedral : 4.707 48.735 5252 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.14 % Allowed : 12.08 % Favored : 86.78 % 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: 2.61 (0.10), residues: 2584 sheet: -0.74 (0.32), residues: 260 loop : -0.32 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 113 TYR 0.011 0.001 TYR B 559 PHE 0.011 0.001 PHE C 567 TRP 0.013 0.001 TRP A 760 HIS 0.002 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00431 (31512) covalent geometry : angle 0.56969 (43068) hydrogen bonds : bond 0.03968 ( 2036) hydrogen bonds : angle 4.01536 ( 5988) link_NAG-ASN : bond 0.00107 ( 4) link_NAG-ASN : angle 1.34891 ( 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 172 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 1.226 Fit side-chains REVERT: A 64 MET cc_start: 0.8968 (mmm) cc_final: 0.8693 (mmm) REVERT: A 73 LYS cc_start: 0.9361 (OUTLIER) cc_final: 0.9112 (mmtt) REVERT: A 190 MET cc_start: 0.9664 (tpt) cc_final: 0.9365 (tpt) REVERT: A 194 MET cc_start: 0.9419 (OUTLIER) cc_final: 0.9177 (mmm) REVERT: A 257 MET cc_start: 0.9401 (mmm) cc_final: 0.8700 (mmm) REVERT: A 523 MET cc_start: 0.9475 (tpp) cc_final: 0.9263 (mpp) REVERT: A 721 MET cc_start: 0.9089 (ppp) cc_final: 0.8848 (tmm) REVERT: A 917 MET cc_start: 0.9599 (OUTLIER) cc_final: 0.8916 (mtm) REVERT: A 1057 GLU cc_start: 0.9181 (tp30) cc_final: 0.8802 (tm-30) REVERT: B 73 LYS cc_start: 0.9381 (OUTLIER) cc_final: 0.8920 (mppt) REVERT: B 190 MET cc_start: 0.9621 (tpt) cc_final: 0.9210 (mmp) REVERT: B 257 MET cc_start: 0.9382 (mmm) cc_final: 0.8681 (mmm) REVERT: B 523 MET cc_start: 0.9473 (tpp) cc_final: 0.9262 (mpp) REVERT: B 726 MET cc_start: 0.9435 (tpp) cc_final: 0.9228 (tpp) REVERT: B 917 MET cc_start: 0.9603 (OUTLIER) cc_final: 0.8927 (mtm) REVERT: B 1057 GLU cc_start: 0.9160 (tp30) cc_final: 0.8792 (tm-30) REVERT: C 73 LYS cc_start: 0.9383 (OUTLIER) cc_final: 0.8922 (mppt) REVERT: C 190 MET cc_start: 0.9634 (tpt) cc_final: 0.9391 (tpt) REVERT: C 257 MET cc_start: 0.9408 (mmm) cc_final: 0.8710 (mmm) REVERT: C 523 MET cc_start: 0.9459 (tpp) cc_final: 0.9237 (mpp) REVERT: C 721 MET cc_start: 0.9081 (ppp) cc_final: 0.8849 (tmm) REVERT: C 917 MET cc_start: 0.9588 (OUTLIER) cc_final: 0.8949 (mtm) REVERT: C 1057 GLU cc_start: 0.9164 (tp30) cc_final: 0.8783 (tm-30) REVERT: D 190 MET cc_start: 0.9640 (tpt) cc_final: 0.9418 (tpt) REVERT: D 230 MET cc_start: 0.9683 (OUTLIER) cc_final: 0.9392 (tmm) REVERT: D 257 MET cc_start: 0.9420 (mmm) cc_final: 0.8763 (mmm) REVERT: D 721 MET cc_start: 0.9097 (ppp) cc_final: 0.8854 (tmm) REVERT: D 917 MET cc_start: 0.9594 (OUTLIER) cc_final: 0.8950 (mtm) REVERT: D 1057 GLU cc_start: 0.9147 (tp30) cc_final: 0.8781 (tm-30) outliers start: 34 outliers final: 11 residues processed: 159 average time/residue: 0.7227 time to fit residues: 135.0927 Evaluate side-chains 156 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 194 MET 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 633 LEU Chi-restraints excluded: chain B residue 785 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 506 LEU Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 917 MET 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: 0.9990 chunk 258 optimal weight: 9.9990 chunk 180 optimal weight: 0.2980 chunk 315 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 chunk 373 optimal weight: 10.0000 chunk 306 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 206 optimal weight: 10.0000 chunk 154 optimal weight: 9.9990 chunk 126 optimal weight: 20.0000 overall best weight: 5.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 GLN A 511 GLN ** A 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 511 GLN ** C 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 511 GLN ** D 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.051162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.037335 restraints weight = 168054.171| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 3.73 r_work: 0.2773 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 31516 Z= 0.269 Angle : 0.648 12.373 43080 Z= 0.318 Chirality : 0.038 0.143 5136 Planarity : 0.004 0.055 5260 Dihedral : 4.865 50.412 5252 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.21 % Allowed : 13.19 % Favored : 85.60 % 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: 2.47 (0.10), residues: 2608 sheet: -0.94 (0.32), residues: 256 loop : -0.47 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 821 TYR 0.012 0.001 TYR C 559 PHE 0.015 0.001 PHE C 567 TRP 0.015 0.001 TRP A 760 HIS 0.004 0.001 HIS C 115 Details of bonding type rmsd covalent geometry : bond 0.00583 (31512) covalent geometry : angle 0.64798 (43068) hydrogen bonds : bond 0.04274 ( 2036) hydrogen bonds : angle 4.19990 ( 5988) link_NAG-ASN : bond 0.00280 ( 4) link_NAG-ASN : angle 1.64094 ( 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 175 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 1.271 Fit side-chains revert: symmetry clash REVERT: A 64 MET cc_start: 0.9013 (mmm) cc_final: 0.8767 (mmm) REVERT: A 190 MET cc_start: 0.9675 (tpt) cc_final: 0.9440 (tpt) REVERT: A 257 MET cc_start: 0.9400 (mmm) cc_final: 0.8733 (mmm) REVERT: A 523 MET cc_start: 0.9505 (tpp) cc_final: 0.9250 (mpp) REVERT: A 564 MET cc_start: 0.9335 (mmm) cc_final: 0.9072 (mmt) REVERT: A 721 MET cc_start: 0.9129 (OUTLIER) cc_final: 0.8919 (tmm) REVERT: A 917 MET cc_start: 0.9607 (OUTLIER) cc_final: 0.8937 (mtm) REVERT: A 1057 GLU cc_start: 0.9218 (tp30) cc_final: 0.8906 (tm-30) REVERT: B 73 LYS cc_start: 0.9369 (OUTLIER) cc_final: 0.8896 (mppt) REVERT: B 257 MET cc_start: 0.9391 (mmm) cc_final: 0.8733 (mmm) REVERT: B 523 MET cc_start: 0.9494 (tpp) cc_final: 0.9240 (mpp) REVERT: B 564 MET cc_start: 0.9346 (mmm) cc_final: 0.9085 (mmt) REVERT: B 726 MET cc_start: 0.9477 (tpp) cc_final: 0.9260 (tpp) REVERT: B 839 PHE cc_start: 0.9369 (OUTLIER) cc_final: 0.8798 (t80) REVERT: B 917 MET cc_start: 0.9603 (OUTLIER) cc_final: 0.8928 (mtm) REVERT: B 1057 GLU cc_start: 0.9214 (tp30) cc_final: 0.8903 (tm-30) REVERT: C 73 LYS cc_start: 0.9370 (OUTLIER) cc_final: 0.8893 (mppt) REVERT: C 190 MET cc_start: 0.9641 (tpt) cc_final: 0.9429 (tpt) REVERT: C 257 MET cc_start: 0.9413 (mmm) cc_final: 0.8755 (mmm) REVERT: C 523 MET cc_start: 0.9507 (tpp) cc_final: 0.9248 (mpp) REVERT: C 564 MET cc_start: 0.9346 (mmm) cc_final: 0.9086 (mmt) REVERT: C 917 MET cc_start: 0.9604 (OUTLIER) cc_final: 0.8932 (mtm) REVERT: C 1057 GLU cc_start: 0.9205 (tp30) cc_final: 0.8893 (tm-30) REVERT: D 190 MET cc_start: 0.9636 (tpt) cc_final: 0.9434 (tpt) REVERT: D 230 MET cc_start: 0.9696 (OUTLIER) cc_final: 0.9477 (tmm) REVERT: D 257 MET cc_start: 0.9402 (mmm) cc_final: 0.8782 (mmm) REVERT: D 564 MET cc_start: 0.9345 (mmm) cc_final: 0.9085 (mmt) REVERT: D 721 MET cc_start: 0.9129 (OUTLIER) cc_final: 0.8919 (tmm) REVERT: D 917 MET cc_start: 0.9603 (OUTLIER) cc_final: 0.8949 (mtm) REVERT: D 1057 GLU cc_start: 0.9209 (tp30) cc_final: 0.8902 (tm-30) outliers start: 36 outliers final: 11 residues processed: 160 average time/residue: 0.7012 time to fit residues: 132.1217 Evaluate side-chains 151 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 917 MET Chi-restraints excluded: chain B residue 73 LYS 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 73 LYS Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 506 LEU 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 721 MET 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: 10.0000 chunk 192 optimal weight: 10.0000 chunk 200 optimal weight: 0.0020 chunk 371 optimal weight: 2.9990 chunk 379 optimal weight: 1.9990 chunk 225 optimal weight: 9.9990 chunk 136 optimal weight: 10.0000 chunk 361 optimal weight: 0.8980 chunk 127 optimal weight: 30.0000 chunk 5 optimal weight: 20.0000 chunk 245 optimal weight: 0.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.052767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.039139 restraints weight = 163732.482| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 3.77 r_work: 0.2838 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 31516 Z= 0.115 Angle : 0.567 13.919 43080 Z= 0.276 Chirality : 0.036 0.144 5136 Planarity : 0.004 0.057 5260 Dihedral : 4.625 45.185 5252 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.08 % Allowed : 13.66 % Favored : 85.26 % 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: 2.60 (0.10), residues: 2596 sheet: -0.81 (0.32), residues: 260 loop : -0.41 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 191 TYR 0.009 0.001 TYR D 559 PHE 0.010 0.001 PHE C 828 TRP 0.012 0.001 TRP C 709 HIS 0.004 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00244 (31512) covalent geometry : angle 0.56711 (43068) hydrogen bonds : bond 0.03764 ( 2036) hydrogen bonds : angle 3.92683 ( 5988) link_NAG-ASN : bond 0.00092 ( 4) link_NAG-ASN : angle 1.19847 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 1.139 Fit side-chains REVERT: A 64 MET cc_start: 0.9006 (mmm) cc_final: 0.8751 (mmm) REVERT: A 190 MET cc_start: 0.9618 (tpt) cc_final: 0.9359 (tpt) REVERT: A 194 MET cc_start: 0.9585 (OUTLIER) cc_final: 0.9376 (mmm) REVERT: A 257 MET cc_start: 0.9441 (mmm) cc_final: 0.8794 (mmm) REVERT: A 564 MET cc_start: 0.9283 (mmm) cc_final: 0.9074 (mmt) REVERT: A 721 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8842 (tmm) REVERT: A 839 PHE cc_start: 0.9387 (OUTLIER) cc_final: 0.8798 (t80) REVERT: A 917 MET cc_start: 0.9585 (OUTLIER) cc_final: 0.9039 (mtm) REVERT: A 1057 GLU cc_start: 0.9185 (tp30) cc_final: 0.8792 (tp30) REVERT: B 257 MET cc_start: 0.9416 (mmm) cc_final: 0.8777 (mmm) REVERT: B 564 MET cc_start: 0.9300 (mmm) cc_final: 0.9095 (mmt) REVERT: B 726 MET cc_start: 0.9402 (tpp) cc_final: 0.9165 (tpp) REVERT: B 839 PHE cc_start: 0.9369 (OUTLIER) cc_final: 0.8800 (t80) REVERT: B 917 MET cc_start: 0.9583 (OUTLIER) cc_final: 0.9034 (mtm) REVERT: B 1057 GLU cc_start: 0.9181 (tp30) cc_final: 0.8768 (tp30) REVERT: C 190 MET cc_start: 0.9635 (tpt) cc_final: 0.9375 (tpt) REVERT: C 257 MET cc_start: 0.9432 (mmm) cc_final: 0.8787 (mmm) REVERT: C 564 MET cc_start: 0.9289 (mmm) cc_final: 0.9083 (mmt) REVERT: C 839 PHE cc_start: 0.9368 (OUTLIER) cc_final: 0.8860 (t80) REVERT: C 917 MET cc_start: 0.9580 (OUTLIER) cc_final: 0.9152 (mtm) REVERT: C 1057 GLU cc_start: 0.9168 (tp30) cc_final: 0.8772 (tp30) REVERT: D 190 MET cc_start: 0.9632 (tpt) cc_final: 0.9385 (tpt) REVERT: D 230 MET cc_start: 0.9668 (OUTLIER) cc_final: 0.9350 (tmm) REVERT: D 241 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8958 (tm) REVERT: D 257 MET cc_start: 0.9417 (mmm) cc_final: 0.8814 (mmm) REVERT: D 370 MET cc_start: 0.9680 (tpt) cc_final: 0.9214 (tpp) REVERT: D 564 MET cc_start: 0.9284 (mmm) cc_final: 0.9080 (mmt) REVERT: D 721 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8847 (tmm) REVERT: D 917 MET cc_start: 0.9582 (OUTLIER) cc_final: 0.9153 (mtm) REVERT: D 1057 GLU cc_start: 0.9174 (tp30) cc_final: 0.8763 (tp30) outliers start: 32 outliers final: 6 residues processed: 161 average time/residue: 0.7651 time to fit residues: 143.3118 Evaluate side-chains 150 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 MET 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 839 PHE Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 917 MET 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 241 LEU Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 721 MET 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: 7.9990 chunk 0 optimal weight: 40.0000 chunk 160 optimal weight: 7.9990 chunk 329 optimal weight: 7.9990 chunk 91 optimal weight: 0.0980 chunk 36 optimal weight: 7.9990 chunk 102 optimal weight: 0.0010 chunk 285 optimal weight: 2.9990 chunk 177 optimal weight: 9.9990 chunk 123 optimal weight: 30.0000 chunk 198 optimal weight: 40.0000 overall best weight: 3.8192 ------------------------------------------------------------------------------- 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 = 0.3417 r_free = 0.3417 target = 0.051928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.038326 restraints weight = 165401.867| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.75 r_work: 0.2807 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 31516 Z= 0.191 Angle : 0.620 13.354 43080 Z= 0.299 Chirality : 0.037 0.148 5136 Planarity : 0.004 0.056 5260 Dihedral : 4.653 46.382 5252 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.87 % Allowed : 13.93 % Favored : 85.20 % 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: 2592 sheet: -0.76 (0.32), residues: 252 loop : -0.42 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 383 TYR 0.010 0.001 TYR D 559 PHE 0.012 0.001 PHE D 567 TRP 0.011 0.001 TRP B 760 HIS 0.004 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00418 (31512) covalent geometry : angle 0.61951 (43068) hydrogen bonds : bond 0.03900 ( 2036) hydrogen bonds : angle 4.01452 ( 5988) link_NAG-ASN : bond 0.00139 ( 4) link_NAG-ASN : angle 1.32646 ( 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 159 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 1.192 Fit side-chains revert: symmetry clash REVERT: A 64 MET cc_start: 0.9037 (mmm) cc_final: 0.8774 (mmm) REVERT: A 190 MET cc_start: 0.9634 (tpt) cc_final: 0.9416 (tpt) REVERT: A 194 MET cc_start: 0.9580 (OUTLIER) cc_final: 0.9375 (mmm) REVERT: A 241 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8971 (tm) REVERT: A 257 MET cc_start: 0.9430 (mmm) cc_final: 0.8793 (mmm) REVERT: A 564 MET cc_start: 0.9294 (mmm) cc_final: 0.9007 (mmt) REVERT: A 721 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8904 (tmm) REVERT: A 839 PHE cc_start: 0.9362 (OUTLIER) cc_final: 0.8816 (t80) REVERT: A 917 MET cc_start: 0.9597 (OUTLIER) cc_final: 0.9045 (mtm) REVERT: A 1057 GLU cc_start: 0.9205 (tp30) cc_final: 0.8858 (tm-30) REVERT: B 64 MET cc_start: 0.8745 (mmm) cc_final: 0.8073 (mmm) REVERT: B 241 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8973 (tm) REVERT: B 257 MET cc_start: 0.9418 (mmm) cc_final: 0.8802 (mmm) REVERT: B 564 MET cc_start: 0.9310 (mmm) cc_final: 0.9029 (mmt) REVERT: B 726 MET cc_start: 0.9443 (tpp) cc_final: 0.9231 (tpp) REVERT: B 839 PHE cc_start: 0.9361 (OUTLIER) cc_final: 0.8820 (t80) REVERT: B 917 MET cc_start: 0.9593 (OUTLIER) cc_final: 0.9040 (mtm) REVERT: B 1057 GLU cc_start: 0.9209 (tp30) cc_final: 0.8870 (tm-30) REVERT: C 190 MET cc_start: 0.9631 (tpt) cc_final: 0.9417 (tpt) REVERT: C 241 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8962 (tm) REVERT: C 257 MET cc_start: 0.9423 (mmm) cc_final: 0.8795 (mmm) REVERT: C 564 MET cc_start: 0.9303 (mmm) cc_final: 0.9019 (mmt) REVERT: C 839 PHE cc_start: 0.9370 (OUTLIER) cc_final: 0.8876 (t80) REVERT: C 917 MET cc_start: 0.9584 (OUTLIER) cc_final: 0.9021 (mtm) REVERT: C 1057 GLU cc_start: 0.9195 (tp30) cc_final: 0.8848 (tm-30) REVERT: D 64 MET cc_start: 0.8752 (mmm) cc_final: 0.8123 (mmm) REVERT: D 190 MET cc_start: 0.9619 (tpt) cc_final: 0.9413 (tpt) REVERT: D 230 MET cc_start: 0.9687 (OUTLIER) cc_final: 0.9374 (tmm) REVERT: D 257 MET cc_start: 0.9421 (mmm) cc_final: 0.8857 (mmm) REVERT: D 564 MET cc_start: 0.9291 (mmm) cc_final: 0.9007 (mmt) REVERT: D 721 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8899 (tmm) REVERT: D 917 MET cc_start: 0.9585 (OUTLIER) cc_final: 0.9024 (mtm) REVERT: D 1057 GLU cc_start: 0.9208 (tp30) cc_final: 0.8874 (tm-30) outliers start: 26 outliers final: 10 residues processed: 151 average time/residue: 0.7143 time to fit residues: 126.8192 Evaluate side-chains 156 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 450 THR 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 241 LEU Chi-restraints excluded: chain B residue 450 THR 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 241 LEU Chi-restraints excluded: chain C residue 450 THR 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 721 MET 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: 10.0000 chunk 59 optimal weight: 0.8980 chunk 127 optimal weight: 30.0000 chunk 146 optimal weight: 0.9980 chunk 263 optimal weight: 3.9990 chunk 338 optimal weight: 20.0000 chunk 85 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 325 optimal weight: 20.0000 chunk 361 optimal weight: 2.9990 chunk 239 optimal weight: 20.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 = 0.3430 r_free = 0.3430 target = 0.052486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.038780 restraints weight = 164316.080| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 3.77 r_work: 0.2825 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 31516 Z= 0.143 Angle : 0.609 14.070 43080 Z= 0.291 Chirality : 0.036 0.143 5136 Planarity : 0.004 0.056 5260 Dihedral : 4.567 45.429 5252 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.87 % Allowed : 14.17 % Favored : 84.96 % 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: 2596 sheet: -0.67 (0.32), residues: 252 loop : -0.41 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 113 TYR 0.009 0.001 TYR C 559 PHE 0.009 0.001 PHE C 828 TRP 0.011 0.001 TRP C 709 HIS 0.004 0.000 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00314 (31512) covalent geometry : angle 0.60925 (43068) hydrogen bonds : bond 0.03759 ( 2036) hydrogen bonds : angle 3.96213 ( 5988) link_NAG-ASN : bond 0.00002 ( 4) link_NAG-ASN : angle 1.19758 ( 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 164 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.9037 (mmm) cc_final: 0.8805 (mmm) REVERT: A 190 MET cc_start: 0.9639 (tpt) cc_final: 0.9431 (tpt) REVERT: A 241 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8948 (tm) REVERT: A 257 MET cc_start: 0.9433 (mmm) cc_final: 0.8816 (mmm) REVERT: A 564 MET cc_start: 0.9308 (mmm) cc_final: 0.9063 (mmt) REVERT: A 839 PHE cc_start: 0.9366 (OUTLIER) cc_final: 0.8816 (t80) REVERT: A 917 MET cc_start: 0.9579 (OUTLIER) cc_final: 0.9054 (mtm) REVERT: A 1057 GLU cc_start: 0.9196 (tp30) cc_final: 0.8784 (tp30) REVERT: B 64 MET cc_start: 0.8768 (mmm) cc_final: 0.8133 (mmm) REVERT: B 241 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8955 (tm) REVERT: B 257 MET cc_start: 0.9416 (mmm) cc_final: 0.8809 (mmm) REVERT: B 564 MET cc_start: 0.9324 (mmm) cc_final: 0.9082 (mmt) REVERT: B 726 MET cc_start: 0.9422 (tpp) cc_final: 0.9199 (tpp) REVERT: B 779 MET cc_start: 0.7905 (ppp) cc_final: 0.7411 (pmm) REVERT: B 839 PHE cc_start: 0.9371 (OUTLIER) cc_final: 0.8831 (t80) REVERT: B 917 MET cc_start: 0.9582 (OUTLIER) cc_final: 0.9059 (mtm) REVERT: B 1057 GLU cc_start: 0.9201 (tp30) cc_final: 0.8787 (tp30) REVERT: C 230 MET cc_start: 0.9422 (ppp) cc_final: 0.9221 (ppp) REVERT: C 241 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8941 (tm) REVERT: C 257 MET cc_start: 0.9431 (mmm) cc_final: 0.8819 (mmm) REVERT: C 564 MET cc_start: 0.9317 (mmm) cc_final: 0.9076 (mmt) REVERT: C 839 PHE cc_start: 0.9376 (OUTLIER) cc_final: 0.8887 (t80) REVERT: C 917 MET cc_start: 0.9570 (OUTLIER) cc_final: 0.9159 (mtm) REVERT: C 1057 GLU cc_start: 0.9183 (tp30) cc_final: 0.8777 (tp30) REVERT: D 64 MET cc_start: 0.8777 (mmm) cc_final: 0.8189 (mmm) REVERT: D 230 MET cc_start: 0.9684 (OUTLIER) cc_final: 0.9359 (tmm) REVERT: D 257 MET cc_start: 0.9440 (mmm) cc_final: 0.8890 (mmm) REVERT: D 370 MET cc_start: 0.9669 (tpt) cc_final: 0.9228 (tpp) REVERT: D 564 MET cc_start: 0.9315 (mmm) cc_final: 0.9071 (mmt) REVERT: D 779 MET cc_start: 0.7933 (ppp) cc_final: 0.7409 (pmm) REVERT: D 839 PHE cc_start: 0.9344 (OUTLIER) cc_final: 0.8948 (t80) REVERT: D 917 MET cc_start: 0.9576 (OUTLIER) cc_final: 0.9168 (mtm) REVERT: D 1057 GLU cc_start: 0.9198 (tp30) cc_final: 0.8817 (tm-30) outliers start: 26 outliers final: 10 residues processed: 156 average time/residue: 0.7257 time to fit residues: 133.2405 Evaluate side-chains 156 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 450 THR 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 241 LEU Chi-restraints excluded: chain B residue 450 THR 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 241 LEU Chi-restraints excluded: chain C residue 450 THR 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 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: 0.6980 chunk 296 optimal weight: 3.9990 chunk 294 optimal weight: 7.9990 chunk 360 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 chunk 348 optimal weight: 1.9990 chunk 320 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 = 0.3423 r_free = 0.3423 target = 0.052162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.038615 restraints weight = 165615.887| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.74 r_work: 0.2818 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 31516 Z= 0.160 Angle : 0.636 14.162 43080 Z= 0.301 Chirality : 0.036 0.143 5136 Planarity : 0.004 0.056 5260 Dihedral : 4.554 46.013 5252 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.91 % Allowed : 14.43 % Favored : 84.66 % 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: 2592 sheet: -0.65 (0.32), residues: 252 loop : -0.40 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 113 TYR 0.010 0.001 TYR C 559 PHE 0.010 0.001 PHE D 567 TRP 0.011 0.001 TRP A 240 HIS 0.003 0.000 HIS C 115 Details of bonding type rmsd covalent geometry : bond 0.00352 (31512) covalent geometry : angle 0.63571 (43068) hydrogen bonds : bond 0.03778 ( 2036) hydrogen bonds : angle 3.98299 ( 5988) link_NAG-ASN : bond 0.00068 ( 4) link_NAG-ASN : angle 1.20113 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9252.06 seconds wall clock time: 158 minutes 38.15 seconds (9518.15 seconds total)