Starting phenix.real_space_refine on Sat Feb 7 04:47:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p3q_71251/02_2026/9p3q_71251_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p3q_71251/02_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_71251/02_2026/9p3q_71251_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p3q_71251/02_2026/9p3q_71251_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9p3q_71251/02_2026/9p3q_71251.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p3q_71251/02_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-2.0-5952/lib/python3.9/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, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 8.58, per 1000 atoms: 0.29 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: 3.00 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: 0.83 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: 6.31 Time building geometry restraints manager: 3.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 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: 0.09 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: 3.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 30.100 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 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 covalent geometry : bond 0.00818 (30684) covalent geometry : angle 1.22705 (41932) hydrogen bonds : bond 0.19298 ( 1940) hydrogen bonds : angle 6.95674 ( 5748) link_NAG-ASN : bond 0.00502 ( 4) link_NAG-ASN : angle 2.16302 ( 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 : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 721 MET cc_start: 0.7274 (tpp) cc_final: 0.7072 (tpt) outliers start: 80 outliers final: 8 residues processed: 468 average time/residue: 0.1797 time to fit residues: 140.0905 Evaluate side-chains 230 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 222 time to evaluate : 1.123 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3654 r_free = 0.3654 target = 0.066121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.053238 restraints weight = 172521.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.054742 restraints weight = 93433.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.055763 restraints weight = 62091.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.056414 restraints weight = 47277.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.056819 restraints weight = 39547.008| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2447 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= 0.154 Angle : 0.634 10.642 41944 Z= 0.319 Chirality : 0.040 0.231 4980 Planarity : 0.005 0.053 5200 Dihedral : 7.542 68.003 4336 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.96 % Allowed : 11.19 % Favored : 86.85 % 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: 1.93 (0.13), residues: 3944 helix: 2.01 (0.10), residues: 2540 sheet: 0.29 (0.27), residues: 284 loop : -0.08 (0.20), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 225 TYR 0.023 0.002 TYR C 941 PHE 0.018 0.002 PHE A 864 TRP 0.014 0.001 TRP A 944 HIS 0.006 0.001 HIS A 837 Details of bonding type rmsd covalent geometry : bond 0.00320 (30684) covalent geometry : angle 0.63434 (41932) hydrogen bonds : bond 0.04860 ( 1940) hydrogen bonds : angle 4.28712 ( 5748) link_NAG-ASN : bond 0.00359 ( 4) link_NAG-ASN : angle 0.69380 ( 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 290 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 234 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 TYR cc_start: 0.6335 (t80) cc_final: 0.5593 (t80) REVERT: A 216 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8266 (tp) REVERT: A 868 VAL cc_start: 0.8597 (t) cc_final: 0.8383 (p) REVERT: A 968 MET cc_start: 0.8641 (mtp) cc_final: 0.8326 (mtt) REVERT: B 82 LYS cc_start: 0.8863 (mmtm) cc_final: 0.8492 (mmtt) REVERT: C 82 LYS cc_start: 0.8792 (mmtm) cc_final: 0.8525 (mmtt) REVERT: D 205 TYR cc_start: 0.7241 (p90) cc_final: 0.6954 (p90) outliers start: 56 outliers final: 29 residues processed: 281 average time/residue: 0.1578 time to fit residues: 76.8628 Evaluate side-chains 225 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 216 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 945 LEU 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: 9.9990 chunk 330 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 331 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 chunk 249 optimal weight: 1.9990 chunk 309 optimal weight: 30.0000 chunk 212 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 360 optimal weight: 10.0000 chunk 275 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 292 GLN B 201 GLN B 514 GLN B 771 GLN B 842 HIS C 107 ASN C 201 GLN C 292 GLN C 402 GLN C 771 GLN C 842 HIS D 107 ASN D 771 GLN D 842 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.054558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.041343 restraints weight = 175379.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.042619 restraints weight = 95368.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.043503 restraints weight = 65019.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.044080 restraints weight = 50667.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.044410 restraints weight = 43154.618| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.5050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 30688 Z= 0.234 Angle : 0.711 9.994 41944 Z= 0.361 Chirality : 0.043 0.341 4980 Planarity : 0.006 0.074 5200 Dihedral : 4.813 39.405 4329 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.89 % Allowed : 12.90 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.14), residues: 3944 helix: 2.01 (0.10), residues: 2520 sheet: 0.53 (0.29), residues: 272 loop : -0.23 (0.20), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG C 225 TYR 0.025 0.002 TYR A 519 PHE 0.033 0.002 PHE A 861 TRP 0.028 0.002 TRP B 944 HIS 0.011 0.002 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00520 (30684) covalent geometry : angle 0.71040 (41932) hydrogen bonds : bond 0.05793 ( 1940) hydrogen bonds : angle 4.23865 ( 5748) link_NAG-ASN : bond 0.00121 ( 4) link_NAG-ASN : angle 1.92569 ( 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 218 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 164 time to evaluate : 1.208 Fit side-chains revert: symmetry clash REVERT: A 230 MET cc_start: 0.8900 (tpp) cc_final: 0.8594 (tpp) REVERT: C 64 MET cc_start: 0.7816 (mmm) cc_final: 0.7533 (mmp) REVERT: C 82 LYS cc_start: 0.8948 (mmtm) cc_final: 0.8715 (mmtt) REVERT: C 230 MET cc_start: 0.8917 (tpp) cc_final: 0.8265 (tpp) REVERT: C 917 MET cc_start: 0.7660 (ppp) cc_final: 0.7432 (mtp) REVERT: D 230 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8192 (tpp) outliers start: 54 outliers final: 31 residues processed: 214 average time/residue: 0.1574 time to fit residues: 59.9537 Evaluate side-chains 180 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 454 VAL 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 166 SER Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 303 VAL 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 454 VAL Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 737 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: 30.0000 chunk 53 optimal weight: 10.0000 chunk 187 optimal weight: 9.9990 chunk 203 optimal weight: 0.0170 chunk 5 optimal weight: 0.0070 chunk 33 optimal weight: 4.9990 chunk 273 optimal weight: 10.0000 chunk 177 optimal weight: 8.9990 chunk 128 optimal weight: 6.9990 chunk 272 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 overall best weight: 2.6042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.054380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.041237 restraints weight = 173581.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.042539 restraints weight = 94444.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.043425 restraints weight = 64103.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.043923 restraints weight = 49928.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.044304 restraints weight = 43177.851| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.5411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30688 Z= 0.125 Angle : 0.509 7.422 41944 Z= 0.263 Chirality : 0.036 0.141 4980 Planarity : 0.005 0.060 5200 Dihedral : 4.354 34.130 4329 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.44 % Allowed : 13.39 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.49 (0.14), residues: 3944 helix: 2.51 (0.10), residues: 2532 sheet: 0.70 (0.30), residues: 252 loop : -0.07 (0.20), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 191 TYR 0.012 0.001 TYR C 205 PHE 0.011 0.001 PHE D 861 TRP 0.029 0.001 TRP C 644 HIS 0.011 0.001 HIS B1010 Details of bonding type rmsd covalent geometry : bond 0.00272 (30684) covalent geometry : angle 0.50824 (41932) hydrogen bonds : bond 0.04273 ( 1940) hydrogen bonds : angle 3.73356 ( 5748) link_NAG-ASN : bond 0.00192 ( 4) link_NAG-ASN : angle 1.99369 ( 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 192 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: A 917 MET cc_start: 0.7863 (ppp) cc_final: 0.7136 (mtp) REVERT: B 371 MET cc_start: 0.9292 (tpp) cc_final: 0.9051 (mmm) REVERT: B 397 THR cc_start: 0.8853 (OUTLIER) cc_final: 0.8634 (t) REVERT: C 64 MET cc_start: 0.8088 (mmm) cc_final: 0.7807 (mmp) REVERT: C 397 THR cc_start: 0.8712 (OUTLIER) cc_final: 0.8472 (t) REVERT: D 230 MET cc_start: 0.8736 (tpp) cc_final: 0.7914 (tpp) REVERT: D 564 MET cc_start: 0.9019 (mtm) cc_final: 0.8804 (mtp) outliers start: 41 outliers final: 27 residues processed: 190 average time/residue: 0.1351 time to fit residues: 46.0891 Evaluate side-chains 175 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 454 VAL 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 A residue 1029 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 397 THR Chi-restraints excluded: chain B residue 454 VAL 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 303 VAL Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 166 SER 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 852 VAL Chi-restraints excluded: chain D residue 917 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 348 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 314 optimal weight: 10.0000 chunk 273 optimal weight: 10.0000 chunk 164 optimal weight: 6.9990 chunk 21 optimal weight: 20.0000 chunk 327 optimal weight: 5.9990 chunk 203 optimal weight: 10.0000 chunk 343 optimal weight: 9.9990 overall best weight: 4.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS C 514 GLN D 292 GLN D 514 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.049996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.037150 restraints weight = 178254.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.038358 restraints weight = 95721.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.039191 restraints weight = 65135.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.039678 restraints weight = 50820.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.040059 restraints weight = 43823.193| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.6599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 30688 Z= 0.194 Angle : 0.594 7.830 41944 Z= 0.301 Chirality : 0.038 0.162 4980 Planarity : 0.005 0.063 5200 Dihedral : 4.058 29.412 4329 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.24 % Allowed : 14.06 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.14), residues: 3944 helix: 2.50 (0.10), residues: 2532 sheet: 0.52 (0.30), residues: 256 loop : -0.13 (0.20), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 191 TYR 0.019 0.002 TYR A 231 PHE 0.016 0.001 PHE C 637 TRP 0.035 0.002 TRP A 240 HIS 0.009 0.001 HIS C 115 Details of bonding type rmsd covalent geometry : bond 0.00429 (30684) covalent geometry : angle 0.59310 (41932) hydrogen bonds : bond 0.04992 ( 1940) hydrogen bonds : angle 3.92710 ( 5748) link_NAG-ASN : bond 0.00054 ( 4) link_NAG-ASN : angle 1.77025 ( 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 210 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 146 time to evaluate : 1.086 Fit side-chains REVERT: A 81 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8535 (ttp80) REVERT: A 917 MET cc_start: 0.8192 (ppp) cc_final: 0.7740 (mtp) REVERT: B 81 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8586 (ttp80) REVERT: B 230 MET cc_start: 0.9007 (tpp) cc_final: 0.8744 (tpp) REVERT: C 230 MET cc_start: 0.9373 (tpp) cc_final: 0.8766 (tpp) REVERT: C 397 THR cc_start: 0.9068 (OUTLIER) cc_final: 0.8769 (t) REVERT: D 81 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8565 (ttp80) REVERT: D 230 MET cc_start: 0.9075 (tpp) cc_final: 0.8276 (tpp) REVERT: D 397 THR cc_start: 0.9087 (OUTLIER) cc_final: 0.8771 (t) REVERT: D 465 THR cc_start: 0.9260 (OUTLIER) cc_final: 0.8993 (p) REVERT: D 564 MET cc_start: 0.9084 (mtm) cc_final: 0.8867 (mtm) outliers start: 64 outliers final: 42 residues processed: 210 average time/residue: 0.1668 time to fit residues: 59.8282 Evaluate side-chains 190 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 142 time to evaluate : 1.222 ------------------------------------------------------------------------------- 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 81 ARG Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 454 VAL 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 835 LEU Chi-restraints excluded: chain A residue 852 VAL 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 166 SER Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 764 LEU 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 164 VAL Chi-restraints excluded: chain C residue 166 SER 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 C residue 737 VAL Chi-restraints excluded: chain C residue 764 LEU Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 465 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 68 optimal weight: 20.0000 chunk 118 optimal weight: 0.4980 chunk 264 optimal weight: 6.9990 chunk 355 optimal weight: 10.0000 chunk 391 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 386 optimal weight: 6.9990 chunk 60 optimal weight: 0.0050 chunk 320 optimal weight: 3.9990 chunk 214 optimal weight: 50.0000 chunk 197 optimal weight: 3.9990 overall best weight: 1.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 514 GLN C 89 GLN C 514 GLN D 514 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.050954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.038189 restraints weight = 175720.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.039429 restraints weight = 93690.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.040262 restraints weight = 63420.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.040856 restraints weight = 49536.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.041177 restraints weight = 41973.457| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.6749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 30688 Z= 0.107 Angle : 0.491 8.228 41944 Z= 0.251 Chirality : 0.036 0.172 4980 Planarity : 0.004 0.062 5200 Dihedral : 3.862 24.864 4329 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.44 % Allowed : 15.04 % Favored : 83.52 % 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: 2.74 (0.14), residues: 3944 helix: 2.73 (0.10), residues: 2548 sheet: 0.54 (0.30), residues: 252 loop : -0.01 (0.21), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 811 TYR 0.011 0.001 TYR C 519 PHE 0.013 0.001 PHE D 861 TRP 0.012 0.001 TRP A 620 HIS 0.006 0.001 HIS B1010 Details of bonding type rmsd covalent geometry : bond 0.00226 (30684) covalent geometry : angle 0.49054 (41932) hydrogen bonds : bond 0.04057 ( 1940) hydrogen bonds : angle 3.55911 ( 5748) link_NAG-ASN : bond 0.00173 ( 4) link_NAG-ASN : angle 1.58493 ( 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 189 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 148 time to evaluate : 0.862 Fit side-chains REVERT: A 81 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8601 (ttp80) REVERT: A 917 MET cc_start: 0.8208 (ppp) cc_final: 0.7770 (mtp) REVERT: B 370 MET cc_start: 0.8932 (tpp) cc_final: 0.8415 (tpp) REVERT: B 371 MET cc_start: 0.9194 (tpp) cc_final: 0.8991 (mmm) REVERT: B 397 THR cc_start: 0.9021 (OUTLIER) cc_final: 0.8799 (t) REVERT: C 493 MET cc_start: 0.8431 (mmm) cc_final: 0.8153 (mmm) REVERT: C 930 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.9010 (mm) REVERT: D 230 MET cc_start: 0.9027 (tpp) cc_final: 0.8235 (tpp) REVERT: D 397 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8756 (t) outliers start: 41 outliers final: 25 residues processed: 187 average time/residue: 0.1532 time to fit residues: 49.6673 Evaluate side-chains 173 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 81 ARG 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 731 LEU Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 1029 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 359 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 166 SER 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 C residue 930 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 243 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 214 optimal weight: 30.0000 chunk 265 optimal weight: 10.0000 chunk 152 optimal weight: 10.0000 chunk 369 optimal weight: 20.0000 chunk 324 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 258 optimal weight: 10.0000 chunk 114 optimal weight: 20.0000 chunk 226 optimal weight: 20.0000 chunk 304 optimal weight: 6.9990 overall best weight: 8.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 ASN B 514 GLN C 514 GLN D 514 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.047535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.034966 restraints weight = 181042.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.036073 restraints weight = 97387.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.036876 restraints weight = 66464.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.037387 restraints weight = 52185.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.037564 restraints weight = 44827.202| |-----------------------------------------------------------------------------| r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.7422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 30688 Z= 0.293 Angle : 0.662 11.811 41944 Z= 0.335 Chirality : 0.040 0.181 4980 Planarity : 0.005 0.065 5200 Dihedral : 4.044 18.353 4328 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.07 % Allowed : 15.22 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.14), residues: 3944 helix: 2.43 (0.10), residues: 2528 sheet: 0.25 (0.29), residues: 256 loop : -0.24 (0.20), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 225 TYR 0.015 0.002 TYR A 205 PHE 0.019 0.002 PHE D 861 TRP 0.019 0.002 TRP A 984 HIS 0.010 0.001 HIS D 115 Details of bonding type rmsd covalent geometry : bond 0.00655 (30684) covalent geometry : angle 0.66212 (41932) hydrogen bonds : bond 0.05330 ( 1940) hydrogen bonds : angle 4.11681 ( 5748) link_NAG-ASN : bond 0.00165 ( 4) link_NAG-ASN : angle 1.46740 ( 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 200 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 141 time to evaluate : 1.233 Fit side-chains REVERT: A 81 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.8609 (ttp80) REVERT: A 493 MET cc_start: 0.8265 (mmm) cc_final: 0.7993 (mmm) REVERT: A 917 MET cc_start: 0.8423 (ppp) cc_final: 0.8138 (mtp) REVERT: B 81 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8621 (ttp80) REVERT: B 230 MET cc_start: 0.9161 (tpp) cc_final: 0.8945 (tpp) REVERT: B 397 THR cc_start: 0.9175 (OUTLIER) cc_final: 0.8915 (t) REVERT: B 523 MET cc_start: 0.8406 (mtt) cc_final: 0.8202 (mtt) REVERT: C 397 THR cc_start: 0.9198 (OUTLIER) cc_final: 0.8917 (t) REVERT: D 397 THR cc_start: 0.9199 (OUTLIER) cc_final: 0.8903 (t) REVERT: D 523 MET cc_start: 0.8316 (mtt) cc_final: 0.8030 (mtt) REVERT: D 564 MET cc_start: 0.9113 (mtm) cc_final: 0.8892 (mtm) outliers start: 59 outliers final: 40 residues processed: 197 average time/residue: 0.1432 time to fit residues: 49.9374 Evaluate side-chains 185 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 140 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 249 VAL 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 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 81 ARG 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 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 764 LEU Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 166 SER 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 C residue 731 LEU Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 270 LEU 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 Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 852 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 327 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 188 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 293 optimal weight: 0.9980 chunk 390 optimal weight: 2.9990 chunk 204 optimal weight: 0.8980 chunk 268 optimal weight: 10.0000 chunk 319 optimal weight: 2.9990 chunk 285 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.048932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.036369 restraints weight = 179229.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.037582 restraints weight = 94376.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.038417 restraints weight = 63575.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.038801 restraints weight = 49416.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.039244 restraints weight = 43214.378| |-----------------------------------------------------------------------------| r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.7521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 30688 Z= 0.116 Angle : 0.526 15.057 41944 Z= 0.264 Chirality : 0.036 0.150 4980 Planarity : 0.005 0.063 5200 Dihedral : 3.816 17.066 4328 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.37 % Allowed : 15.78 % Favored : 82.85 % 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: 2.61 (0.14), residues: 3944 helix: 2.69 (0.10), residues: 2548 sheet: 0.15 (0.29), residues: 256 loop : -0.14 (0.21), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 811 TYR 0.018 0.001 TYR C 519 PHE 0.012 0.001 PHE B 861 TRP 0.013 0.001 TRP A 620 HIS 0.005 0.001 HIS B1010 Details of bonding type rmsd covalent geometry : bond 0.00248 (30684) covalent geometry : angle 0.52562 (41932) hydrogen bonds : bond 0.04339 ( 1940) hydrogen bonds : angle 3.63144 ( 5748) link_NAG-ASN : bond 0.00204 ( 4) link_NAG-ASN : angle 1.17864 ( 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 181 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 142 time to evaluate : 1.284 Fit side-chains REVERT: A 81 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8550 (ttp80) REVERT: A 370 MET cc_start: 0.9201 (tpp) cc_final: 0.8873 (tpp) REVERT: A 493 MET cc_start: 0.8198 (mmm) cc_final: 0.7793 (mmm) REVERT: A 917 MET cc_start: 0.8462 (ppp) cc_final: 0.8203 (mtp) REVERT: B 81 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8596 (ttp80) REVERT: B 370 MET cc_start: 0.9107 (tpp) cc_final: 0.8667 (tpp) REVERT: B 397 THR cc_start: 0.9121 (OUTLIER) cc_final: 0.8910 (t) REVERT: C 230 MET cc_start: 0.9372 (tpp) cc_final: 0.9113 (tpp) REVERT: C 397 THR cc_start: 0.9119 (OUTLIER) cc_final: 0.8911 (t) REVERT: D 397 THR cc_start: 0.9139 (OUTLIER) cc_final: 0.8879 (t) REVERT: D 523 MET cc_start: 0.8228 (mtt) cc_final: 0.7986 (mtt) outliers start: 39 outliers final: 26 residues processed: 178 average time/residue: 0.1510 time to fit residues: 47.5873 Evaluate side-chains 171 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 243 LEU 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 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 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 C residue 731 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 270 LEU 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: 0.0670 chunk 344 optimal weight: 0.0470 chunk 276 optimal weight: 9.9990 chunk 154 optimal weight: 10.0000 chunk 112 optimal weight: 20.0000 chunk 91 optimal weight: 9.9990 chunk 368 optimal weight: 2.9990 chunk 256 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 55 optimal weight: 8.9990 chunk 103 optimal weight: 0.3980 overall best weight: 2.5020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.3230 r_free = 0.3230 target = 0.048889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.036417 restraints weight = 179517.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.037609 restraints weight = 94922.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.038440 restraints weight = 64100.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.038822 restraints weight = 49884.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.039226 restraints weight = 43547.792| |-----------------------------------------------------------------------------| r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.7706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30688 Z= 0.121 Angle : 0.513 10.457 41944 Z= 0.257 Chirality : 0.036 0.137 4980 Planarity : 0.004 0.064 5200 Dihedral : 3.613 16.733 4328 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.19 % Allowed : 16.20 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.72 (0.14), residues: 3944 helix: 2.77 (0.10), residues: 2552 sheet: 0.20 (0.29), residues: 256 loop : -0.09 (0.21), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 811 TYR 0.013 0.001 TYR C 519 PHE 0.011 0.001 PHE D 861 TRP 0.014 0.001 TRP A 240 HIS 0.005 0.001 HIS B1010 Details of bonding type rmsd covalent geometry : bond 0.00268 (30684) covalent geometry : angle 0.51233 (41932) hydrogen bonds : bond 0.04001 ( 1940) hydrogen bonds : angle 3.51843 ( 5748) link_NAG-ASN : bond 0.00125 ( 4) link_NAG-ASN : angle 1.11538 ( 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 178 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 1.351 Fit side-chains REVERT: A 81 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8649 (ttp80) REVERT: A 370 MET cc_start: 0.9262 (tpp) cc_final: 0.8850 (tpp) REVERT: A 493 MET cc_start: 0.8239 (mmm) cc_final: 0.7855 (mmm) REVERT: B 81 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8601 (ttp80) REVERT: B 230 MET cc_start: 0.9391 (ttm) cc_final: 0.8986 (tpp) REVERT: B 370 MET cc_start: 0.9082 (tpp) cc_final: 0.8815 (tpp) REVERT: C 230 MET cc_start: 0.9372 (tpp) cc_final: 0.9101 (tpp) REVERT: D 397 THR cc_start: 0.9124 (OUTLIER) cc_final: 0.8866 (t) REVERT: D 523 MET cc_start: 0.8213 (mtt) cc_final: 0.7978 (mtt) outliers start: 34 outliers final: 25 residues processed: 176 average time/residue: 0.1605 time to fit residues: 50.2679 Evaluate side-chains 169 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 243 LEU 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 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 190 MET 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 C residue 91 THR Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 270 LEU 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: 0.0980 chunk 80 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 100 optimal weight: 40.0000 chunk 335 optimal weight: 6.9990 chunk 246 optimal weight: 5.9990 chunk 23 optimal weight: 20.0000 chunk 135 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 358 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 overall best weight: 5.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.3187 r_free = 0.3187 target = 0.047401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.034974 restraints weight = 181668.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.036142 restraints weight = 96515.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.036933 restraints weight = 65438.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.037395 restraints weight = 51239.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.037623 restraints weight = 44197.587| |-----------------------------------------------------------------------------| r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.7994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 30688 Z= 0.200 Angle : 0.590 11.106 41944 Z= 0.294 Chirality : 0.038 0.202 4980 Planarity : 0.005 0.062 5200 Dihedral : 3.798 16.767 4328 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.09 % Allowed : 16.48 % 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: 2.52 (0.14), residues: 3944 helix: 2.65 (0.10), residues: 2544 sheet: 0.13 (0.28), residues: 256 loop : -0.23 (0.21), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 811 TYR 0.015 0.001 TYR A 205 PHE 0.014 0.001 PHE D 861 TRP 0.016 0.001 TRP A 984 HIS 0.013 0.001 HIS D1010 Details of bonding type rmsd covalent geometry : bond 0.00447 (30684) covalent geometry : angle 0.59010 (41932) hydrogen bonds : bond 0.04699 ( 1940) hydrogen bonds : angle 3.79017 ( 5748) link_NAG-ASN : bond 0.00053 ( 4) link_NAG-ASN : angle 1.04285 ( 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 169 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 1.430 Fit side-chains REVERT: A 81 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8566 (ttp80) REVERT: A 493 MET cc_start: 0.8227 (mmm) cc_final: 0.7859 (mmm) REVERT: A 917 MET cc_start: 0.7491 (mtp) cc_final: 0.7270 (mmt) REVERT: B 81 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8589 (ttp80) REVERT: B 230 MET cc_start: 0.9384 (ttm) cc_final: 0.9005 (tpp) REVERT: B 370 MET cc_start: 0.9200 (tpp) cc_final: 0.8759 (tpp) REVERT: B 523 MET cc_start: 0.8260 (mtt) cc_final: 0.7966 (mtt) REVERT: D 397 THR cc_start: 0.9159 (OUTLIER) cc_final: 0.8913 (t) REVERT: D 523 MET cc_start: 0.8348 (mtt) cc_final: 0.8066 (mtt) outliers start: 31 outliers final: 27 residues processed: 168 average time/residue: 0.1640 time to fit residues: 48.8054 Evaluate side-chains 168 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 243 LEU 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 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 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 454 VAL Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 270 LEU 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: 0.5980 chunk 351 optimal weight: 0.8980 chunk 387 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 350 optimal weight: 2.9990 chunk 250 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 302 optimal weight: 10.0000 chunk 254 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 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 = 0.3232 r_free = 0.3232 target = 0.048854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.036566 restraints weight = 179206.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.037796 restraints weight = 93408.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.038624 restraints weight = 62578.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.039101 restraints weight = 48732.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.039472 restraints weight = 41781.807| |-----------------------------------------------------------------------------| r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.8033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 30688 Z= 0.101 Angle : 0.513 11.391 41944 Z= 0.255 Chirality : 0.035 0.136 4980 Planarity : 0.004 0.064 5200 Dihedral : 3.601 16.234 4328 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % 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: 2.74 (0.14), residues: 3944 helix: 2.79 (0.10), residues: 2552 sheet: 0.29 (0.29), residues: 252 loop : -0.12 (0.21), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 811 TYR 0.020 0.001 TYR C 519 PHE 0.009 0.001 PHE C 862 TRP 0.014 0.001 TRP D 620 HIS 0.012 0.001 HIS D1010 Details of bonding type rmsd covalent geometry : bond 0.00210 (30684) covalent geometry : angle 0.51306 (41932) hydrogen bonds : bond 0.03870 ( 1940) hydrogen bonds : angle 3.41716 ( 5748) link_NAG-ASN : bond 0.00270 ( 4) link_NAG-ASN : angle 0.88828 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4389.05 seconds wall clock time: 76 minutes 59.57 seconds (4619.57 seconds total)