Starting phenix.real_space_refine on Sun Jul 5 21:58:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p3q_71251/07_2026/9p3q_71251_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p3q_71251/07_2026/9p3q_71251.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9p3q_71251/07_2026/9p3q_71251_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p3q_71251/07_2026/9p3q_71251_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9p3q_71251/07_2026/9p3q_71251.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p3q_71251/07_2026/9p3q_71251.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 152 5.16 5 C 19628 2.51 5 N 5120 2.21 5 O 5028 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29932 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7468 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 166} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 952} Chain breaks: 4 Unresolved non-hydrogen bonds: 574 Unresolved non-hydrogen angles: 705 Unresolved non-hydrogen dihedrals: 453 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'ASP:plan': 33, 'ARG:plan': 11, 'GLU:plan': 34, 'GLN:plan1': 14, 'HIS:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 379 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 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: 8.84, per 1000 atoms: 0.30 Number of scatterers: 29932 At special positions: 0 Unit cell: (144.55, 144.55, 154.462, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 152 16.00 O 5028 8.00 N 5120 7.00 C 19628 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 D1501 " - " ASN D 921 " Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.4 seconds 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7600 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 12 sheets defined 70.3% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 40 through 50 removed outlier: 3.889A pdb=" N ILE A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 91 removed outlier: 3.510A pdb=" N THR A 79 " --> pdb=" O TRP A 75 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N THR A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 119 removed outlier: 3.575A 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: 3.825A pdb=" N LEU A 143 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 201 Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 226 through 236 Processing helix chain 'A' and resid 248 through 260 Processing helix chain 'A' and resid 263 through 275 Processing helix chain 'A' and resid 280 through 298 Processing helix chain 'A' and resid 311 through 328 removed outlier: 3.620A pdb=" N VAL A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 333 Processing helix chain 'A' and resid 334 through 345 Processing helix chain 'A' and resid 346 through 353 Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 366 through 376 Processing helix chain 'A' and resid 378 through 388 Processing helix chain 'A' and resid 391 through 396 Processing helix chain 'A' and resid 397 through 407 Processing helix chain 'A' and resid 412 through 429 Processing helix chain 'A' and resid 450 through 462 removed outlier: 3.571A pdb=" N VAL A 454 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP A 460 " --> pdb=" O LYS A 456 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE A 461 " --> pdb=" O VAL A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 510 Processing helix chain 'A' and resid 513 through 523 Processing helix chain 'A' and resid 526 through 545 Processing helix chain 'A' and resid 547 through 555 removed outlier: 3.661A pdb=" N ALA A 551 " --> pdb=" O GLU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 574 removed outlier: 3.506A pdb=" N PHE A 562 " --> pdb=" O LYS A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 584 removed outlier: 4.170A pdb=" N SER A 580 " --> pdb=" O ASP A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 601 Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 609 through 622 Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 640 through 644 Processing helix chain 'A' and resid 699 through 714 Processing helix chain 'A' and resid 715 through 740 removed outlier: 3.509A pdb=" N ILE A 732 " --> pdb=" O PHE A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 774 Processing helix chain 'A' and resid 780 through 791 removed outlier: 3.735A pdb=" N ASP A 791 " --> pdb=" O LEU A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 813 removed outlier: 3.520A pdb=" N ALA A 800 " --> pdb=" O CYS A 796 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 801 " --> pdb=" O ALA A 797 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA A 813 " --> pdb=" O SER A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 839 removed outlier: 3.525A pdb=" N MET A 829 " --> pdb=" O ALA A 825 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL A 830 " --> pdb=" O LEU A 826 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE A 831 " --> pdb=" O ASP A 827 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE A 836 " --> pdb=" O THR A 832 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N HIS A 837 " --> pdb=" O LEU A 833 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE A 838 " --> pdb=" O ARG A 834 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE A 839 " --> pdb=" O LEU A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 842 No H-bonds generated for 'chain 'A' and resid 840 through 842' Processing helix chain 'A' and resid 845 through 882 removed outlier: 3.601A pdb=" N ILE A 849 " --> pdb=" O LEU A 845 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 850 " --> pdb=" O GLY A 846 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE A 864 " --> pdb=" O PHE A 860 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE A 865 " --> pdb=" O PHE A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 903 removed outlier: 5.068A pdb=" N ARG A 898 " --> pdb=" O ARG A 894 " (cutoff:3.500A) Proline residue: A 899 - end of helix removed outlier: 3.787A pdb=" N ILE A 903 " --> pdb=" O PRO A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 917 Processing helix chain 'A' and resid 925 through 932 Processing helix chain 'A' and resid 942 through 959 removed outlier: 3.579A pdb=" N VAL A 946 " --> pdb=" O ALA A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 997 removed outlier: 3.982A pdb=" N ILE A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA A 967 " --> pdb=" O ASN A 963 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN A 979 " --> pdb=" O VAL A 975 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP A 981 " --> pdb=" O GLN A 977 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE A 982 " --> pdb=" O GLU A 978 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER A 997 " --> pdb=" O VAL A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1020 removed outlier: 3.912A 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 50 removed outlier: 3.889A pdb=" N ILE B 44 " --> pdb=" O ASP B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 91 removed outlier: 3.510A pdb=" N THR B 79 " --> pdb=" O TRP B 75 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 119 removed outlier: 3.575A 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: 3.825A pdb=" N LEU B 143 " --> pdb=" O ASN B 139 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER B 145 " --> pdb=" O ASP B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 201 Processing helix chain 'B' and resid 223 through 225 No H-bonds generated for 'chain 'B' and resid 223 through 225' Processing helix chain 'B' and resid 226 through 236 Processing helix chain 'B' and resid 248 through 260 Processing helix chain 'B' and resid 263 through 275 Processing helix chain 'B' and resid 280 through 298 Processing helix chain 'B' and resid 311 through 328 removed outlier: 3.620A pdb=" N VAL B 315 " --> pdb=" O GLU B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 333 Processing helix chain 'B' and resid 334 through 345 Processing helix chain 'B' and resid 346 through 353 Processing helix chain 'B' and resid 363 through 365 No H-bonds generated for 'chain 'B' and resid 363 through 365' Processing helix chain 'B' and resid 366 through 376 Processing helix chain 'B' and resid 378 through 388 Processing helix chain 'B' and resid 391 through 396 Processing helix chain 'B' and resid 397 through 407 Processing helix chain 'B' and resid 412 through 429 Processing helix chain 'B' and resid 450 through 462 removed outlier: 3.570A pdb=" N VAL B 454 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP B 460 " --> pdb=" O LYS B 456 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE B 461 " --> pdb=" O VAL B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 510 Processing helix chain 'B' and resid 513 through 523 Processing helix chain 'B' and resid 526 through 545 Processing helix chain 'B' and resid 547 through 555 removed outlier: 3.660A pdb=" N ALA B 551 " --> pdb=" O GLU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 574 removed outlier: 3.505A pdb=" N PHE B 562 " --> pdb=" O LYS B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 584 removed outlier: 4.170A pdb=" N SER B 580 " --> pdb=" O ASP B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 601 Processing helix chain 'B' and resid 603 through 608 Processing helix chain 'B' and resid 609 through 622 Processing helix chain 'B' and resid 629 through 639 Processing helix chain 'B' and resid 640 through 644 Processing helix chain 'B' and resid 699 through 714 Processing helix chain 'B' and resid 715 through 740 removed outlier: 3.509A pdb=" N ILE B 732 " --> pdb=" O PHE B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 774 Processing helix chain 'B' and resid 780 through 791 removed outlier: 3.735A pdb=" N ASP B 791 " --> pdb=" O LEU B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 813 removed outlier: 3.520A pdb=" N ALA B 800 " --> pdb=" O CYS B 796 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE B 801 " --> pdb=" O ALA B 797 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA B 813 " --> pdb=" O SER B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 839 removed outlier: 3.525A pdb=" N MET B 829 " --> pdb=" O ALA B 825 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL B 830 " --> pdb=" O LEU B 826 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE B 831 " --> pdb=" O ASP B 827 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE B 836 " --> pdb=" O THR B 832 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N HIS B 837 " --> pdb=" O LEU B 833 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE B 838 " --> pdb=" O ARG B 834 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE B 839 " --> pdb=" O LEU B 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 842 No H-bonds generated for 'chain 'B' and resid 840 through 842' Processing helix chain 'B' and resid 845 through 882 removed outlier: 3.601A pdb=" N ILE B 849 " --> pdb=" O LEU B 845 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE B 850 " --> pdb=" O GLY B 846 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE B 864 " --> pdb=" O PHE B 860 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE B 865 " --> pdb=" O PHE B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 903 removed outlier: 5.068A pdb=" N ARG B 898 " --> pdb=" O ARG B 894 " (cutoff:3.500A) Proline residue: B 899 - end of helix removed outlier: 3.786A pdb=" N ILE B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 917 Processing helix chain 'B' and resid 925 through 932 Processing helix chain 'B' and resid 942 through 959 removed outlier: 3.579A pdb=" N VAL B 946 " --> pdb=" O ALA B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 997 removed outlier: 3.983A pdb=" N ILE B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA B 967 " --> pdb=" O ASN B 963 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLU B 978 " --> pdb=" O GLN B 974 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN B 979 " --> pdb=" O VAL B 975 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP B 981 " --> pdb=" O GLN B 977 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE B 982 " --> pdb=" O GLU B 978 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER B 997 " --> pdb=" O VAL B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1005 through 1020 removed outlier: 3.913A 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 50 removed outlier: 3.889A pdb=" N ILE C 44 " --> pdb=" O ASP C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 91 removed outlier: 3.510A pdb=" N THR C 79 " --> pdb=" O TRP C 75 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER C 90 " --> pdb=" O LYS C 86 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N THR C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 119 removed outlier: 3.574A 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: 3.826A pdb=" N LEU C 143 " --> pdb=" O ASN C 139 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER C 145 " --> pdb=" O ASP C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 201 Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'C' and resid 226 through 236 Processing helix chain 'C' and resid 248 through 260 Processing helix chain 'C' and resid 263 through 275 Processing helix chain 'C' and resid 280 through 298 Processing helix chain 'C' and resid 311 through 328 removed outlier: 3.620A pdb=" N VAL C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 333 Processing helix chain 'C' and resid 334 through 345 Processing helix chain 'C' and resid 346 through 353 Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 366 through 376 Processing helix chain 'C' and resid 378 through 388 Processing helix chain 'C' and resid 391 through 396 Processing helix chain 'C' and resid 397 through 407 Processing helix chain 'C' and resid 412 through 429 Processing helix chain 'C' and resid 450 through 462 removed outlier: 3.570A pdb=" N VAL C 454 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP C 460 " --> pdb=" O LYS C 456 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE C 461 " --> pdb=" O VAL C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 510 Processing helix chain 'C' and resid 513 through 523 Processing helix chain 'C' and resid 526 through 545 Processing helix chain 'C' and resid 547 through 555 removed outlier: 3.661A pdb=" N ALA C 551 " --> pdb=" O GLU C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 574 removed outlier: 3.506A pdb=" N PHE C 562 " --> pdb=" O LYS C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 584 removed outlier: 4.170A pdb=" N SER C 580 " --> pdb=" O ASP C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 601 Processing helix chain 'C' and resid 603 through 608 Processing helix chain 'C' and resid 609 through 622 Processing helix chain 'C' and resid 629 through 639 Processing helix chain 'C' and resid 640 through 644 Processing helix chain 'C' and resid 699 through 714 Processing helix chain 'C' and resid 715 through 740 removed outlier: 3.510A pdb=" N ILE C 732 " --> pdb=" O PHE C 728 " (cutoff:3.500A) Processing helix chain 'C' and resid 751 through 774 Processing helix chain 'C' and resid 780 through 791 removed outlier: 3.735A pdb=" N ASP C 791 " --> pdb=" O LEU C 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 791 through 813 removed outlier: 3.519A pdb=" N ALA C 800 " --> pdb=" O CYS C 796 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE C 801 " --> pdb=" O ALA C 797 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA C 813 " --> pdb=" O SER C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 839 removed outlier: 3.525A pdb=" N MET C 829 " --> pdb=" O ALA C 825 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL C 830 " --> pdb=" O LEU C 826 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE C 831 " --> pdb=" O ASP C 827 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE C 836 " --> pdb=" O THR C 832 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N HIS C 837 " --> pdb=" O LEU C 833 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE C 838 " --> pdb=" O ARG C 834 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE C 839 " --> pdb=" O LEU C 835 " (cutoff:3.500A) Processing helix chain 'C' and resid 840 through 842 No H-bonds generated for 'chain 'C' and resid 840 through 842' Processing helix chain 'C' and resid 845 through 882 removed outlier: 3.601A pdb=" N ILE C 849 " --> pdb=" O LEU C 845 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE C 850 " --> pdb=" O GLY C 846 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE C 864 " --> pdb=" O PHE C 860 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE C 865 " --> pdb=" O PHE C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 903 removed outlier: 5.068A pdb=" N ARG C 898 " --> pdb=" O ARG C 894 " (cutoff:3.500A) Proline residue: C 899 - end of helix removed outlier: 3.787A pdb=" N ILE C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 917 Processing helix chain 'C' and resid 925 through 932 Processing helix chain 'C' and resid 942 through 959 removed outlier: 3.579A pdb=" N VAL C 946 " --> pdb=" O ALA C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 997 removed outlier: 3.982A pdb=" N ILE C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA C 967 " --> pdb=" O ASN C 963 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU C 978 " --> pdb=" O GLN C 974 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN C 979 " --> pdb=" O VAL C 975 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP C 981 " --> pdb=" O GLN C 977 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE C 982 " --> pdb=" O GLU C 978 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER C 997 " --> pdb=" O VAL C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1020 removed outlier: 3.912A 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 50 removed outlier: 3.889A pdb=" N ILE D 44 " --> pdb=" O ASP D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 91 removed outlier: 3.509A pdb=" N THR D 79 " --> pdb=" O TRP D 75 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER D 90 " --> pdb=" O LYS D 86 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 119 removed outlier: 3.575A 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: 3.825A pdb=" N LEU D 143 " --> pdb=" O ASN D 139 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER D 145 " --> pdb=" O ASP D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 201 Processing helix chain 'D' and resid 223 through 225 No H-bonds generated for 'chain 'D' and resid 223 through 225' Processing helix chain 'D' and resid 226 through 236 Processing helix chain 'D' and resid 248 through 260 Processing helix chain 'D' and resid 263 through 275 Processing helix chain 'D' and resid 280 through 298 Processing helix chain 'D' and resid 311 through 328 removed outlier: 3.620A pdb=" N VAL D 315 " --> pdb=" O GLU D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 333 Processing helix chain 'D' and resid 334 through 345 Processing helix chain 'D' and resid 346 through 353 Processing helix chain 'D' and resid 363 through 365 No H-bonds generated for 'chain 'D' and resid 363 through 365' Processing helix chain 'D' and resid 366 through 376 Processing helix chain 'D' and resid 378 through 388 Processing helix chain 'D' and resid 391 through 396 Processing helix chain 'D' and resid 397 through 407 Processing helix chain 'D' and resid 412 through 429 Processing helix chain 'D' and resid 450 through 462 removed outlier: 3.571A pdb=" N VAL D 454 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP D 460 " --> pdb=" O LYS D 456 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE D 461 " --> pdb=" O VAL D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 510 Processing helix chain 'D' and resid 513 through 523 Processing helix chain 'D' and resid 526 through 545 Processing helix chain 'D' and resid 547 through 555 removed outlier: 3.660A pdb=" N ALA D 551 " --> pdb=" O GLU D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 574 removed outlier: 3.506A pdb=" N PHE D 562 " --> pdb=" O LYS D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 584 removed outlier: 4.170A pdb=" N SER D 580 " --> pdb=" O ASP D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 601 Processing helix chain 'D' and resid 603 through 608 Processing helix chain 'D' and resid 609 through 622 Processing helix chain 'D' and resid 629 through 639 Processing helix chain 'D' and resid 640 through 644 Processing helix chain 'D' and resid 699 through 714 Processing helix chain 'D' and resid 715 through 740 removed outlier: 3.510A pdb=" N ILE D 732 " --> pdb=" O PHE D 728 " (cutoff:3.500A) Processing helix chain 'D' and resid 751 through 774 Processing helix chain 'D' and resid 780 through 791 removed outlier: 3.736A pdb=" N ASP D 791 " --> pdb=" O LEU D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 791 through 813 removed outlier: 3.520A pdb=" N ALA D 800 " --> pdb=" O CYS D 796 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE D 801 " --> pdb=" O ALA D 797 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA D 813 " --> pdb=" O SER D 809 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 839 removed outlier: 3.526A pdb=" N MET D 829 " --> pdb=" O ALA D 825 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL D 830 " --> pdb=" O LEU D 826 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE D 831 " --> pdb=" O ASP D 827 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE D 836 " --> pdb=" O THR D 832 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N HIS D 837 " --> pdb=" O LEU D 833 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE D 838 " --> pdb=" O ARG D 834 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE D 839 " --> pdb=" O LEU D 835 " (cutoff:3.500A) Processing helix chain 'D' and resid 840 through 842 No H-bonds generated for 'chain 'D' and resid 840 through 842' Processing helix chain 'D' and resid 845 through 882 removed outlier: 3.601A pdb=" N ILE D 849 " --> pdb=" O LEU D 845 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE D 850 " --> pdb=" O GLY D 846 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE D 864 " --> pdb=" O PHE D 860 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N PHE D 865 " --> pdb=" O PHE D 861 " (cutoff:3.500A) Processing helix chain 'D' and resid 887 through 903 removed outlier: 5.068A pdb=" N ARG D 898 " --> pdb=" O ARG D 894 " (cutoff:3.500A) Proline residue: D 899 - end of helix removed outlier: 3.787A pdb=" N ILE D 903 " --> pdb=" O PRO D 899 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 917 Processing helix chain 'D' and resid 925 through 932 Processing helix chain 'D' and resid 942 through 959 removed outlier: 3.579A pdb=" N VAL D 946 " --> pdb=" O ALA D 942 " (cutoff:3.500A) Processing helix chain 'D' and resid 959 through 997 removed outlier: 3.982A pdb=" N ILE D 966 " --> pdb=" O LEU D 962 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA D 967 " --> pdb=" O ASN D 963 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU D 978 " --> pdb=" O GLN D 974 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN D 979 " --> pdb=" O VAL D 975 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP D 981 " --> pdb=" O GLN D 977 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE D 982 " --> pdb=" O GLU D 978 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER D 997 " --> pdb=" O VAL D 993 " (cutoff:3.500A) Processing helix chain 'D' and resid 1005 through 1020 removed outlier: 3.913A 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 18 through 22 removed outlier: 3.521A pdb=" N PHE A 32 " --> pdb=" O GLY A 18 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR A 28 " --> pdb=" O PHE A 22 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N PHE A 174 " --> pdb=" O ARG A 29 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LYS A 31 " --> pdb=" O PHE A 174 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LEU A 176 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL A 33 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLY A 130 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL A 177 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA A 132 " --> pdb=" O VAL A 177 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 127 removed outlier: 6.104A pdb=" N VAL A 60 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU A 218 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ALA A 62 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 220 " --> pdb=" O ALA A 62 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N MET A 64 " --> pdb=" O VAL A 220 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 202 through 204 Processing sheet with id=AA4, first strand: chain 'B' and resid 18 through 22 removed outlier: 3.521A pdb=" N PHE B 32 " --> pdb=" O GLY B 18 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR B 28 " --> pdb=" O PHE B 22 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N PHE B 174 " --> pdb=" O ARG B 29 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LYS B 31 " --> pdb=" O PHE B 174 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LEU B 176 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL B 33 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLY B 130 " --> pdb=" O ILE B 175 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL B 177 " --> pdb=" O GLY B 130 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA B 132 " --> pdb=" O VAL B 177 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 126 through 127 removed outlier: 6.104A pdb=" N VAL B 60 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU B 218 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ALA B 62 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N VAL B 220 " --> pdb=" O ALA B 62 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N MET B 64 " --> pdb=" O VAL B 220 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 202 through 204 Processing sheet with id=AA7, first strand: chain 'C' and resid 18 through 22 removed outlier: 3.521A pdb=" N PHE C 32 " --> pdb=" O GLY C 18 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR C 28 " --> pdb=" O PHE C 22 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N PHE C 174 " --> pdb=" O ARG C 29 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LYS C 31 " --> pdb=" O PHE C 174 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LEU C 176 " --> pdb=" O LYS C 31 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL C 33 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLY C 130 " --> pdb=" O ILE C 175 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL C 177 " --> pdb=" O GLY C 130 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA C 132 " --> pdb=" O VAL C 177 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 126 through 127 removed outlier: 6.104A pdb=" N VAL C 60 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU C 218 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ALA C 62 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL C 220 " --> pdb=" O ALA C 62 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N MET C 64 " --> pdb=" O VAL C 220 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 202 through 204 Processing sheet with id=AB1, first strand: chain 'D' and resid 18 through 22 removed outlier: 3.522A pdb=" N PHE D 32 " --> pdb=" O GLY D 18 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR D 28 " --> pdb=" O PHE D 22 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N PHE D 174 " --> pdb=" O ARG D 29 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LYS D 31 " --> pdb=" O PHE D 174 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N LEU D 176 " --> pdb=" O LYS D 31 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL D 33 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLY D 130 " --> pdb=" O ILE D 175 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL D 177 " --> pdb=" O GLY D 130 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA D 132 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 126 through 127 removed outlier: 6.104A pdb=" N VAL D 60 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU D 218 " --> pdb=" O VAL D 60 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ALA D 62 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL D 220 " --> pdb=" O ALA D 62 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N MET D 64 " --> pdb=" O VAL D 220 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 202 through 204 1940 hydrogen bonds defined for protein. 5748 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: 6.45 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4544 1.30 - 1.43: 8301 1.43 - 1.56: 17595 1.56 - 1.69: 0 1.69 - 1.81: 244 Bond restraints: 30684 Sorted by residual: bond pdb=" C ASP D 387 " pdb=" O ASP D 387 " ideal model delta sigma weight residual 1.236 1.175 0.062 1.25e-02 6.40e+03 2.45e+01 bond pdb=" C ASP A 387 " pdb=" O ASP A 387 " ideal model delta sigma weight residual 1.236 1.175 0.062 1.25e-02 6.40e+03 2.45e+01 bond pdb=" C ASP B 387 " pdb=" O ASP B 387 " ideal model delta sigma weight residual 1.236 1.175 0.062 1.25e-02 6.40e+03 2.42e+01 bond pdb=" C SER B 568 " pdb=" O SER B 568 " ideal model delta sigma weight residual 1.236 1.180 0.057 1.15e-02 7.56e+03 2.42e+01 bond pdb=" C ASP C 387 " pdb=" O ASP C 387 " ideal model delta sigma weight residual 1.236 1.175 0.061 1.25e-02 6.40e+03 2.38e+01 ... (remaining 30679 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 34854 1.55 - 3.10: 5437 3.10 - 4.65: 1444 4.65 - 6.20: 165 6.20 - 7.75: 32 Bond angle restraints: 41932 Sorted by residual: angle pdb=" C HIS D 415 " pdb=" CA HIS D 415 " pdb=" CB HIS D 415 " ideal model delta sigma weight residual 110.88 103.13 7.75 1.57e+00 4.06e-01 2.44e+01 angle pdb=" C HIS A 415 " pdb=" CA HIS A 415 " pdb=" CB HIS A 415 " ideal model delta sigma weight residual 110.88 103.13 7.75 1.57e+00 4.06e-01 2.43e+01 angle pdb=" C HIS C 415 " pdb=" CA HIS C 415 " pdb=" CB HIS C 415 " ideal model delta sigma weight residual 110.88 103.17 7.71 1.57e+00 4.06e-01 2.41e+01 angle pdb=" C HIS B 415 " pdb=" CA HIS B 415 " pdb=" CB HIS B 415 " ideal model delta sigma weight residual 110.88 103.20 7.68 1.57e+00 4.06e-01 2.40e+01 angle pdb=" C SER C1064 " pdb=" N GLY C1065 " pdb=" CA GLY C1065 " ideal model delta sigma weight residual 120.00 125.10 -5.10 1.10e+00 8.26e-01 2.15e+01 ... (remaining 41927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.24: 16601 21.24 - 42.47: 1143 42.47 - 63.71: 196 63.71 - 84.94: 32 84.94 - 106.18: 36 Dihedral angle restraints: 18008 sinusoidal: 6328 harmonic: 11680 Sorted by residual: dihedral pdb=" CA TYR B 748 " pdb=" C TYR B 748 " pdb=" N GLY B 749 " pdb=" CA GLY B 749 " ideal model delta harmonic sigma weight residual 180.00 154.88 25.12 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA TYR C 748 " pdb=" C TYR C 748 " pdb=" N GLY C 749 " pdb=" CA GLY C 749 " ideal model delta harmonic sigma weight residual 180.00 154.88 25.12 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA TYR A 748 " pdb=" C TYR A 748 " pdb=" N GLY A 749 " pdb=" CA GLY A 749 " ideal model delta harmonic sigma weight residual 180.00 154.88 25.12 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 18005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3291 0.054 - 0.109: 992 0.109 - 0.163: 491 0.163 - 0.217: 170 0.217 - 0.272: 36 Chirality restraints: 4980 Sorted by residual: chirality pdb=" C1 NAG A1501 " pdb=" ND2 ASN A 921 " pdb=" C2 NAG A1501 " pdb=" O5 NAG A1501 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C1 NAG B1501 " pdb=" ND2 ASN B 921 " pdb=" C2 NAG B1501 " pdb=" O5 NAG B1501 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C1 NAG C1501 " pdb=" ND2 ASN C 921 " pdb=" C2 NAG C1501 " pdb=" O5 NAG C1501 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 4977 not shown) Planarity restraints: 5204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1501 " 0.098 2.00e-02 2.50e+03 8.08e-02 8.15e+01 pdb=" C7 NAG C1501 " -0.027 2.00e-02 2.50e+03 pdb=" C8 NAG C1501 " 0.074 2.00e-02 2.50e+03 pdb=" N2 NAG C1501 " -0.128 2.00e-02 2.50e+03 pdb=" O7 NAG C1501 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D1501 " -0.098 2.00e-02 2.50e+03 8.07e-02 8.14e+01 pdb=" C7 NAG D1501 " 0.027 2.00e-02 2.50e+03 pdb=" C8 NAG D1501 " -0.074 2.00e-02 2.50e+03 pdb=" N2 NAG D1501 " 0.128 2.00e-02 2.50e+03 pdb=" O7 NAG D1501 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1501 " -0.098 2.00e-02 2.50e+03 8.07e-02 8.13e+01 pdb=" C7 NAG A1501 " 0.027 2.00e-02 2.50e+03 pdb=" C8 NAG A1501 " -0.074 2.00e-02 2.50e+03 pdb=" N2 NAG A1501 " 0.128 2.00e-02 2.50e+03 pdb=" O7 NAG A1501 " 0.017 2.00e-02 2.50e+03 ... (remaining 5201 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 11122 2.88 - 3.39: 31256 3.39 - 3.89: 49672 3.89 - 4.40: 55843 4.40 - 4.90: 93121 Nonbonded interactions: 241014 Sorted by model distance: nonbonded pdb=" OD1 ASP D 336 " pdb=" N GLU D 337 " model vdw 2.381 3.120 nonbonded pdb=" OD1 ASP A 336 " pdb=" N GLU A 337 " model vdw 2.382 3.120 nonbonded pdb=" OD1 ASP C 336 " pdb=" N GLU C 337 " model vdw 2.382 3.120 nonbonded pdb=" OD1 ASP B 336 " pdb=" N GLU B 337 " model vdw 2.382 3.120 nonbonded pdb=" O GLY C 130 " pdb=" N ILE C 175 " model vdw 2.392 3.120 ... (remaining 241009 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.070 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: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 30.600 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6492 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 : 0.008 0.062 30688 Z= 0.612 Angle : 1.227 7.751 41944 Z= 0.942 Chirality : 0.071 0.272 4980 Planarity : 0.007 0.081 5200 Dihedral : 15.694 106.181 10408 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.81 % Allowed : 4.21 % Favored : 92.99 % 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: 1.15 (0.14), residues: 3944 helix: 1.44 (0.10), residues: 2508 sheet: 0.35 (0.28), residues: 248 loop : -0.49 (0.19), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 708 TYR 0.038 0.003 TYR C1070 PHE 0.013 0.002 PHE D 520 TRP 0.016 0.002 TRP D 620 HIS 0.009 0.002 HIS B 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00818 / 0.61 (30684) covalent geometry : angle 1.22705 / 0.94 (41932) hydrogen bonds : bond 0.19298 / 13.40 ( 1940) hydrogen bonds : angle 6.95674 / 5.07 ( 5748) link_NAG-ASN : bond 0.00502 / 0.25 ( 4) link_NAG-ASN : angle 2.16302 / 1.46 ( 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 481 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 401 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 721 MET cc_start: 0.7274 (tpp) cc_final: 0.7073 (tpt) outliers start: 80 outliers final: 8 residues processed: 468 average time/residue: 0.1673 time to fit residues: 130.7313 Evaluate side-chains 232 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 224 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 832 THR Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 832 THR Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 832 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.0000 overall best weight: 2.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 GLN A 170 ASN A 201 GLN A 842 HIS B 170 ASN C 170 ASN D 170 ASN D 201 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.066204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.053320 restraints weight = 172675.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.054833 restraints weight = 93626.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.055867 restraints weight = 62152.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.056468 restraints weight = 47214.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.056958 restraints weight = 39763.399| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 30688 Z= 0.159 Angle : 0.632 10.442 41944 Z= 0.319 Chirality : 0.040 0.216 4980 Planarity : 0.005 0.052 5200 Dihedral : 7.648 69.737 4336 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.79 % Allowed : 11.33 % Favored : 86.89 % 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: 1.95 (0.14), residues: 3944 helix: 2.03 (0.10), residues: 2540 sheet: 0.30 (0.27), residues: 284 loop : -0.08 (0.20), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 225 TYR 0.023 0.002 TYR C 941 PHE 0.020 0.002 PHE A 864 TRP 0.020 0.002 TRP D 944 HIS 0.007 0.001 HIS A 837 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (30684) covalent geometry : angle 0.63153 / 0.32 (41932) hydrogen bonds : bond 0.04913 / 3.38 ( 1940) hydrogen bonds : angle 4.32636 / 3.19 ( 5748) link_NAG-ASN : bond 0.00343 / 0.17 ( 4) link_NAG-ASN : angle 0.59762 / 0.36 ( 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 284 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 233 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 868 VAL cc_start: 0.8598 (t) cc_final: 0.8382 (p) REVERT: B 82 LYS cc_start: 0.8862 (mmtm) cc_final: 0.8488 (mmtt) REVERT: C 82 LYS cc_start: 0.8787 (mmtm) cc_final: 0.8507 (mmtt) outliers start: 51 outliers final: 28 residues processed: 275 average time/residue: 0.1696 time to fit residues: 80.8576 Evaluate side-chains 225 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 197 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 1072 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 1072 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 334 optimal weight: 0.6980 chunk 330 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 331 optimal weight: 0.5980 chunk 42 optimal weight: 7.9990 chunk 249 optimal weight: 0.9990 chunk 309 optimal weight: 20.0000 chunk 212 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 360 optimal weight: 9.9990 chunk 275 optimal weight: 4.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 201 GLN B 842 HIS C 201 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.062162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.049129 restraints weight = 172913.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.050548 restraints weight = 93691.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.051543 restraints weight = 62657.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.052184 restraints weight = 48145.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.052524 restraints weight = 40525.243| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 30688 Z= 0.140 Angle : 0.542 7.215 41944 Z= 0.275 Chirality : 0.037 0.222 4980 Planarity : 0.005 0.057 5200 Dihedral : 4.867 40.816 4329 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.33 % Allowed : 12.73 % Favored : 85.94 % 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: 2.32 (0.14), residues: 3944 helix: 2.29 (0.10), residues: 2564 sheet: 0.75 (0.29), residues: 268 loop : -0.02 (0.20), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 225 TYR 0.011 0.001 TYR D 45 PHE 0.025 0.001 PHE A 861 TRP 0.020 0.001 TRP B 984 HIS 0.004 0.001 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (30684) covalent geometry : angle 0.54122 / 0.27 (41932) hydrogen bonds : bond 0.04293 / 2.97 ( 1940) hydrogen bonds : angle 3.82990 / 2.83 ( 5748) link_NAG-ASN : bond 0.00438 / 0.22 ( 4) link_NAG-ASN : angle 1.54794 / 1.08 ( 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 238 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 200 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 645 THR cc_start: 0.8594 (OUTLIER) cc_final: 0.8359 (p) REVERT: B 82 LYS cc_start: 0.8925 (mmtm) cc_final: 0.8710 (mmtt) REVERT: C 82 LYS cc_start: 0.8851 (mmtm) cc_final: 0.8609 (mmtt) REVERT: C 230 MET cc_start: 0.8559 (tpp) cc_final: 0.8252 (tpp) REVERT: D 230 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8136 (tpp) outliers start: 38 outliers final: 24 residues processed: 233 average time/residue: 0.1634 time to fit residues: 67.3479 Evaluate side-chains 208 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 856 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 140 optimal weight: 0.1980 chunk 53 optimal weight: 9.9990 chunk 187 optimal weight: 20.0000 chunk 203 optimal weight: 0.4980 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 273 optimal weight: 8.9990 chunk 177 optimal weight: 9.9990 chunk 128 optimal weight: 20.0000 chunk 272 optimal weight: 7.9990 chunk 107 optimal weight: 20.0000 overall best weight: 4.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 ASN A 292 GLN B 292 GLN B 514 GLN B 771 GLN C 107 ASN C 292 GLN C 514 GLN C 771 GLN D 107 ASN D 292 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.051770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.038803 restraints weight = 177182.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.040031 restraints weight = 95772.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.040875 restraints weight = 65242.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.041355 restraints weight = 51032.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.041757 restraints weight = 44147.378| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.5971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 30688 Z= 0.220 Angle : 0.700 15.770 41944 Z= 0.350 Chirality : 0.042 0.268 4980 Planarity : 0.006 0.064 5200 Dihedral : 4.722 35.618 4329 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.45 % Allowed : 13.32 % Favored : 84.22 % 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: 2.05 (0.14), residues: 3944 helix: 2.12 (0.10), residues: 2532 sheet: 0.31 (0.28), residues: 268 loop : -0.04 (0.20), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 225 TYR 0.048 0.003 TYR A 519 PHE 0.029 0.002 PHE D 861 TRP 0.030 0.002 TRP A 240 HIS 0.036 0.002 HIS B1010 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.22 (30684) covalent geometry : angle 0.69884 / 0.35 (41932) hydrogen bonds : bond 0.05401 / 3.76 ( 1940) hydrogen bonds : angle 4.21899 / 3.11 ( 5748) link_NAG-ASN : bond 0.00069 / 0.03 ( 4) link_NAG-ASN : angle 1.98475 / 1.33 ( 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 222 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 152 time to evaluate : 1.208 Fit side-chains REVERT: A 81 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8576 (ttp80) REVERT: A 397 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8705 (t) REVERT: A 645 THR cc_start: 0.8673 (OUTLIER) cc_final: 0.8431 (p) REVERT: A 880 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8700 (mm) REVERT: A 917 MET cc_start: 0.8199 (ppp) cc_final: 0.7682 (mtp) REVERT: B 397 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8763 (t) REVERT: C 397 THR cc_start: 0.8975 (OUTLIER) cc_final: 0.8653 (t) REVERT: D 230 MET cc_start: 0.8718 (tpp) cc_final: 0.7973 (tpp) REVERT: D 397 THR cc_start: 0.9006 (OUTLIER) cc_final: 0.8663 (t) outliers start: 70 outliers final: 40 residues processed: 220 average time/residue: 0.1582 time to fit residues: 61.8694 Evaluate side-chains 191 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 144 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 796 CYS Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 764 LEU Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 832 THR Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 497 CYS Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 852 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 348 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 47 optimal weight: 2.9990 chunk 314 optimal weight: 30.0000 chunk 273 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 21 optimal weight: 0.3980 chunk 327 optimal weight: 6.9990 chunk 203 optimal weight: 2.9990 chunk 343 optimal weight: 7.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 514 GLN C 842 HIS D 771 GLN D 842 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.052048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.039125 restraints weight = 176490.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.040410 restraints weight = 94403.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.041270 restraints weight = 63630.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.041783 restraints weight = 49605.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.042169 restraints weight = 42601.241| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.6162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30688 Z= 0.122 Angle : 0.508 10.599 41944 Z= 0.261 Chirality : 0.036 0.154 4980 Planarity : 0.005 0.063 5200 Dihedral : 4.094 30.374 4329 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.19 % Allowed : 14.97 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.58 (0.14), residues: 3944 helix: 2.60 (0.10), residues: 2532 sheet: 0.49 (0.29), residues: 252 loop : -0.02 (0.20), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 191 TYR 0.016 0.001 TYR A 519 PHE 0.017 0.001 PHE A 862 TRP 0.013 0.001 TRP A 620 HIS 0.010 0.001 HIS B1010 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (30684) covalent geometry : angle 0.50688 / 0.26 (41932) hydrogen bonds : bond 0.04381 / 3.04 ( 1940) hydrogen bonds : angle 3.70225 / 2.74 ( 5748) link_NAG-ASN : bond 0.00073 / 0.04 ( 4) link_NAG-ASN : angle 2.04410 / 1.43 ( 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 184 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 1.199 Fit side-chains REVERT: A 230 MET cc_start: 0.9308 (tpp) cc_final: 0.9059 (tpt) REVERT: A 397 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8672 (t) REVERT: A 645 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8456 (p) REVERT: A 917 MET cc_start: 0.8204 (ppp) cc_final: 0.7699 (mtp) REVERT: B 81 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8533 (ttp80) REVERT: B 523 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8229 (mtt) REVERT: C 230 MET cc_start: 0.9126 (tpp) cc_final: 0.8570 (tpp) REVERT: C 523 MET cc_start: 0.8318 (mtt) cc_final: 0.8089 (mtt) REVERT: D 230 MET cc_start: 0.8944 (tpp) cc_final: 0.8096 (tpp) outliers start: 34 outliers final: 23 residues processed: 180 average time/residue: 0.1689 time to fit residues: 53.0373 Evaluate side-chains 171 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain B residue 81 ARG Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 737 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 68 optimal weight: 1.9990 chunk 118 optimal weight: 20.0000 chunk 264 optimal weight: 4.9990 chunk 355 optimal weight: 4.9990 chunk 391 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 386 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 320 optimal weight: 2.9990 chunk 214 optimal weight: 0.7980 chunk 197 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 402 GLN B 514 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.050755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.038000 restraints weight = 176777.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.039224 restraints weight = 94473.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.040073 restraints weight = 64115.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.040597 restraints weight = 49887.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.040805 restraints weight = 42762.932| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.6642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30688 Z= 0.140 Angle : 0.513 9.456 41944 Z= 0.262 Chirality : 0.036 0.221 4980 Planarity : 0.004 0.062 5200 Dihedral : 3.803 25.813 4329 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.44 % Allowed : 15.53 % Favored : 83.03 % 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: 2.70 (0.14), residues: 3944 helix: 2.68 (0.10), residues: 2552 sheet: 0.52 (0.30), residues: 252 loop : 0.02 (0.21), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 495 TYR 0.016 0.001 TYR C 953 PHE 0.014 0.001 PHE D 861 TRP 0.014 0.001 TRP B 984 HIS 0.008 0.001 HIS B1010 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (30684) covalent geometry : angle 0.51222 / 0.26 (41932) hydrogen bonds : bond 0.04170 / 2.89 ( 1940) hydrogen bonds : angle 3.63199 / 2.68 ( 5748) link_NAG-ASN : bond 0.00108 / 0.05 ( 4) link_NAG-ASN : angle 1.32430 / 0.90 ( 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 183 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 142 time to evaluate : 1.193 Fit side-chains REVERT: A 397 THR cc_start: 0.8994 (OUTLIER) cc_final: 0.8757 (t) REVERT: A 645 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8450 (p) REVERT: A 917 MET cc_start: 0.8251 (ppp) cc_final: 0.7811 (mtp) REVERT: B 81 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8596 (ttp80) REVERT: B 397 THR cc_start: 0.9038 (OUTLIER) cc_final: 0.8793 (t) REVERT: C 230 MET cc_start: 0.9172 (tpp) cc_final: 0.8573 (tpp) REVERT: C 397 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8713 (t) REVERT: C 493 MET cc_start: 0.8448 (mmm) cc_final: 0.8236 (mmm) REVERT: C 523 MET cc_start: 0.8167 (mtt) cc_final: 0.7916 (mtt) REVERT: D 230 MET cc_start: 0.9065 (tpp) cc_final: 0.8206 (tpp) REVERT: D 397 THR cc_start: 0.9057 (OUTLIER) cc_final: 0.8800 (t) outliers start: 41 outliers final: 24 residues processed: 179 average time/residue: 0.1663 time to fit residues: 52.2876 Evaluate side-chains 172 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain B residue 81 ARG Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 454 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 214 optimal weight: 0.9980 chunk 265 optimal weight: 10.0000 chunk 152 optimal weight: 9.9990 chunk 369 optimal weight: 20.0000 chunk 324 optimal weight: 10.0000 chunk 129 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 258 optimal weight: 0.0170 chunk 114 optimal weight: 20.0000 chunk 226 optimal weight: 20.0000 chunk 304 optimal weight: 10.0000 overall best weight: 5.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 514 GLN B 107 ASN B 514 GLN C 514 GLN D 514 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.048167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.035600 restraints weight = 179942.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.036777 restraints weight = 95837.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.037579 restraints weight = 65010.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.038043 restraints weight = 50793.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.038186 restraints weight = 43917.393| |-----------------------------------------------------------------------------| r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.7421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30688 Z= 0.201 Angle : 0.580 15.342 41944 Z= 0.295 Chirality : 0.038 0.219 4980 Planarity : 0.005 0.064 5200 Dihedral : 3.936 16.832 4328 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.40 % Allowed : 15.71 % Favored : 82.89 % 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: 2.51 (0.14), residues: 3944 helix: 2.57 (0.10), residues: 2540 sheet: 0.18 (0.29), residues: 256 loop : -0.03 (0.21), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG D 811 TYR 0.013 0.001 TYR B 205 PHE 0.021 0.001 PHE D 861 TRP 0.017 0.001 TRP A 984 HIS 0.010 0.001 HIS B1010 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.20 (30684) covalent geometry : angle 0.57995 / 0.30 (41932) hydrogen bonds : bond 0.04894 / 3.40 ( 1940) hydrogen bonds : angle 3.87506 / 2.86 ( 5748) link_NAG-ASN : bond 0.00031 / 0.02 ( 4) link_NAG-ASN : angle 1.52515 / 1.05 ( 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 181 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 1.200 Fit side-chains REVERT: A 370 MET cc_start: 0.9205 (tpt) cc_final: 0.8556 (tpp) REVERT: A 645 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8438 (p) REVERT: A 917 MET cc_start: 0.8427 (ppp) cc_final: 0.8173 (mtp) REVERT: B 81 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8555 (ttp80) REVERT: B 397 THR cc_start: 0.9140 (OUTLIER) cc_final: 0.8889 (t) REVERT: C 230 MET cc_start: 0.9320 (tpp) cc_final: 0.9096 (tpp) REVERT: C 397 THR cc_start: 0.9143 (OUTLIER) cc_final: 0.8862 (t) REVERT: C 493 MET cc_start: 0.8598 (mmm) cc_final: 0.8331 (mmm) REVERT: C 523 MET cc_start: 0.8339 (mtt) cc_final: 0.8054 (mtt) REVERT: D 397 THR cc_start: 0.9145 (OUTLIER) cc_final: 0.8826 (t) REVERT: D 917 MET cc_start: 0.7674 (mmt) cc_final: 0.7469 (mmt) outliers start: 40 outliers final: 27 residues processed: 175 average time/residue: 0.1769 time to fit residues: 53.2348 Evaluate side-chains 171 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 862 PHE Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain B residue 81 ARG Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 454 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 327 optimal weight: 0.9980 chunk 3 optimal weight: 20.0000 chunk 188 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 293 optimal weight: 3.9990 chunk 390 optimal weight: 6.9990 chunk 204 optimal weight: 6.9990 chunk 268 optimal weight: 20.0000 chunk 319 optimal weight: 1.9990 chunk 285 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.048357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.035852 restraints weight = 180717.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.037043 restraints weight = 95099.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.037865 restraints weight = 64002.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.038338 restraints weight = 49784.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.038737 restraints weight = 42938.763| |-----------------------------------------------------------------------------| r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.7611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30688 Z= 0.154 Angle : 0.528 9.800 41944 Z= 0.268 Chirality : 0.036 0.135 4980 Planarity : 0.005 0.066 5200 Dihedral : 3.743 16.649 4328 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.30 % Allowed : 16.34 % Favored : 82.36 % 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: 2.64 (0.14), residues: 3944 helix: 2.70 (0.10), residues: 2548 sheet: 0.13 (0.29), residues: 256 loop : -0.09 (0.21), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 811 TYR 0.015 0.001 TYR A 519 PHE 0.013 0.001 PHE D 861 TRP 0.013 0.001 TRP C 984 HIS 0.008 0.001 HIS B1010 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (30684) covalent geometry : angle 0.52829 / 0.27 (41932) hydrogen bonds : bond 0.04395 / 3.05 ( 1940) hydrogen bonds : angle 3.67294 / 2.71 ( 5748) link_NAG-ASN : bond 0.00110 / 0.05 ( 4) link_NAG-ASN : angle 1.01163 / 0.68 ( 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 178 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 141 time to evaluate : 1.143 Fit side-chains REVERT: B 81 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8628 (ttp80) REVERT: B 230 MET cc_start: 0.9242 (tpp) cc_final: 0.9001 (tpp) REVERT: B 397 THR cc_start: 0.9133 (OUTLIER) cc_final: 0.8909 (t) REVERT: B 523 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.8077 (mtt) REVERT: C 230 MET cc_start: 0.9268 (tpp) cc_final: 0.9029 (tpp) REVERT: C 397 THR cc_start: 0.9164 (OUTLIER) cc_final: 0.8913 (t) REVERT: C 493 MET cc_start: 0.8585 (mmm) cc_final: 0.8267 (mmm) REVERT: C 523 MET cc_start: 0.8272 (mtt) cc_final: 0.7982 (mtt) REVERT: D 397 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8918 (t) outliers start: 37 outliers final: 26 residues processed: 173 average time/residue: 0.1632 time to fit residues: 50.2564 Evaluate side-chains 169 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain B residue 81 ARG Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 454 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 224 optimal weight: 7.9990 chunk 344 optimal weight: 0.7980 chunk 276 optimal weight: 10.0000 chunk 154 optimal weight: 8.9990 chunk 112 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 368 optimal weight: 1.9990 chunk 256 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 103 optimal weight: 0.1980 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3223 r_free = 0.3223 target = 0.048567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.036163 restraints weight = 179715.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.037357 restraints weight = 94678.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.038184 restraints weight = 63685.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.038664 restraints weight = 49496.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.038819 restraints weight = 42586.928| |-----------------------------------------------------------------------------| r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.7748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30688 Z= 0.124 Angle : 0.506 10.502 41944 Z= 0.256 Chirality : 0.036 0.139 4980 Planarity : 0.005 0.066 5200 Dihedral : 3.638 16.448 4328 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.23 % Allowed : 16.37 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.76 (0.14), residues: 3944 helix: 2.78 (0.10), residues: 2552 sheet: 0.22 (0.29), residues: 252 loop : -0.01 (0.21), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 811 TYR 0.010 0.001 TYR A 989 PHE 0.011 0.001 PHE D 861 TRP 0.013 0.001 TRP B 620 HIS 0.008 0.001 HIS B1010 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (30684) covalent geometry : angle 0.50582 / 0.26 (41932) hydrogen bonds : bond 0.04106 / 2.84 ( 1940) hydrogen bonds : angle 3.54116 / 2.62 ( 5748) link_NAG-ASN : bond 0.00148 / 0.07 ( 4) link_NAG-ASN : angle 1.05852 / 0.72 ( 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 176 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 1.265 Fit side-chains REVERT: A 230 MET cc_start: 0.9399 (tpp) cc_final: 0.9112 (tpt) REVERT: B 81 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8610 (ttp80) REVERT: B 397 THR cc_start: 0.9108 (OUTLIER) cc_final: 0.8889 (t) REVERT: C 230 MET cc_start: 0.9296 (tpp) cc_final: 0.9051 (tpp) REVERT: C 397 THR cc_start: 0.9132 (OUTLIER) cc_final: 0.8874 (t) REVERT: C 493 MET cc_start: 0.8629 (mmm) cc_final: 0.8291 (mmm) REVERT: C 523 MET cc_start: 0.8209 (mtt) cc_final: 0.7936 (mtt) REVERT: D 397 THR cc_start: 0.9160 (OUTLIER) cc_final: 0.8916 (t) outliers start: 35 outliers final: 22 residues processed: 171 average time/residue: 0.1635 time to fit residues: 49.9516 Evaluate side-chains 165 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain B residue 81 ARG Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 454 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 104 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 335 optimal weight: 1.9990 chunk 246 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 358 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 514 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.048573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.036264 restraints weight = 180311.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.037456 restraints weight = 94722.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.038276 restraints weight = 63740.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.038758 restraints weight = 49605.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.039122 restraints weight = 42533.705| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.7887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30688 Z= 0.123 Angle : 0.513 9.341 41944 Z= 0.256 Chirality : 0.036 0.135 4980 Planarity : 0.004 0.065 5200 Dihedral : 3.568 16.164 4328 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.98 % Allowed : 16.55 % Favored : 82.47 % 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: 2.77 (0.14), residues: 3944 helix: 2.79 (0.10), residues: 2552 sheet: 0.25 (0.29), residues: 252 loop : -0.02 (0.21), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 811 TYR 0.013 0.001 TYR A 519 PHE 0.009 0.001 PHE D 861 TRP 0.013 0.001 TRP D 620 HIS 0.010 0.001 HIS A1010 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (30684) covalent geometry : angle 0.51241 / 0.26 (41932) hydrogen bonds : bond 0.03988 / 2.75 ( 1940) hydrogen bonds : angle 3.49623 / 2.59 ( 5748) link_NAG-ASN : bond 0.00174 / 0.09 ( 4) link_NAG-ASN : angle 0.95755 / 0.65 ( 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 170 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 1.145 Fit side-chains REVERT: A 370 MET cc_start: 0.9258 (tpt) cc_final: 0.8592 (tpp) REVERT: B 81 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8577 (ttp80) REVERT: C 230 MET cc_start: 0.9312 (tpp) cc_final: 0.9069 (tpp) REVERT: C 371 MET cc_start: 0.9432 (tpp) cc_final: 0.9174 (mmm) REVERT: C 397 THR cc_start: 0.9116 (OUTLIER) cc_final: 0.8868 (t) REVERT: C 493 MET cc_start: 0.8625 (mmm) cc_final: 0.8044 (mmm) REVERT: C 523 MET cc_start: 0.8260 (mtt) cc_final: 0.8009 (mtt) REVERT: D 230 MET cc_start: 0.9240 (tpp) cc_final: 0.8796 (tpp) REVERT: D 397 THR cc_start: 0.9179 (OUTLIER) cc_final: 0.8949 (t) REVERT: D 523 MET cc_start: 0.8214 (mtt) cc_final: 0.7955 (mtt) outliers start: 28 outliers final: 24 residues processed: 169 average time/residue: 0.1537 time to fit residues: 46.3823 Evaluate side-chains 168 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain B residue 81 ARG Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 454 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 258 optimal weight: 2.9990 chunk 351 optimal weight: 0.7980 chunk 387 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 350 optimal weight: 0.9990 chunk 250 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 302 optimal weight: 9.9990 chunk 254 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.049107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.036824 restraints weight = 180317.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.038016 restraints weight = 94625.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.038859 restraints weight = 63780.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.039359 restraints weight = 49596.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.039527 restraints weight = 42427.891| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.7964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 30688 Z= 0.100 Angle : 0.494 9.859 41944 Z= 0.247 Chirality : 0.035 0.146 4980 Planarity : 0.004 0.063 5200 Dihedral : 3.494 15.894 4328 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.98 % Allowed : 16.58 % Favored : 82.43 % 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: 2.85 (0.14), residues: 3944 helix: 2.83 (0.10), residues: 2556 sheet: 0.32 (0.29), residues: 252 loop : 0.04 (0.21), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 811 TYR 0.018 0.001 TYR A 519 PHE 0.011 0.001 PHE A 862 TRP 0.014 0.001 TRP D 620 HIS 0.013 0.001 HIS D1010 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (30684) covalent geometry : angle 0.49360 / 0.25 (41932) hydrogen bonds : bond 0.03681 / 2.54 ( 1940) hydrogen bonds : angle 3.37009 / 2.50 ( 5748) link_NAG-ASN : bond 0.00242 / 0.12 ( 4) link_NAG-ASN : angle 0.94388 / 0.63 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4651.99 seconds wall clock time: 81 minutes 26.02 seconds (4886.02 seconds total)