Starting phenix.real_space_refine on Sun Jul 5 00:45:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8slp_40579/07_2026/8slp_40579.cif Found real_map, /net/cci-nas-00/data/ceres_data/8slp_40579/07_2026/8slp_40579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8slp_40579/07_2026/8slp_40579.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8slp_40579/07_2026/8slp_40579.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8slp_40579/07_2026/8slp_40579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8slp_40579/07_2026/8slp_40579.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.024 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 8 9.91 5 S 80 5.16 5 C 15664 2.51 5 N 4348 2.21 5 O 4256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24356 Number of models: 1 Model: "" Number of chains: 2 Chain: "D" Number of atoms: 6087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 910, 6087 Classifications: {'peptide': 910} Incomplete info: {'truncation_to_alanine': 370} Link IDs: {'PTRANS': 36, 'TRANS': 873} Chain breaks: 13 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 1351 Unresolved non-hydrogen angles: 1719 Unresolved non-hydrogen dihedrals: 1101 Unresolved non-hydrogen chiralities: 129 Planarities with less than four sites: {'GLU:plan': 37, 'ASN:plan1': 11, 'PHE:plan': 21, 'ARG:plan': 25, 'HIS:plan': 11, 'TRP:plan': 3, 'ASP:plan': 31, 'GLN:plan1': 23, 'TYR:plan': 9} Unresolved non-hydrogen planarities: 762 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Restraints were copied for chains: A, B, C Time building chain proxies: 6.38, per 1000 atoms: 0.26 Number of scatterers: 24356 At special positions: 0 Unit cell: (148.96, 148.96, 152.32, 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 8 19.99 S 80 16.00 O 4256 8.00 N 4348 7.00 C 15664 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 Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 1.3 seconds 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6976 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 16 sheets defined 71.5% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'D' and resid 48 through 61 Processing helix chain 'D' and resid 81 through 98 Processing helix chain 'D' and resid 111 through 126 removed outlier: 4.364A pdb=" N HIS D 115 " --> pdb=" O GLY D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 153 Processing helix chain 'D' and resid 202 through 212 Processing helix chain 'D' and resid 239 through 249 Processing helix chain 'D' and resid 262 through 269 Processing helix chain 'D' and resid 279 through 288 Processing helix chain 'D' and resid 295 through 311 Processing helix chain 'D' and resid 312 through 314 No H-bonds generated for 'chain 'D' and resid 312 through 314' Processing helix chain 'D' and resid 328 through 345 removed outlier: 3.504A pdb=" N SER D 343 " --> pdb=" O LYS D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 362 Processing helix chain 'D' and resid 364 through 370 Processing helix chain 'D' and resid 383 through 393 Processing helix chain 'D' and resid 395 through 405 removed outlier: 3.580A pdb=" N VAL D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 413 Processing helix chain 'D' and resid 414 through 424 Processing helix chain 'D' and resid 429 through 443 removed outlier: 3.608A pdb=" N GLU D 433 " --> pdb=" O SER D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 477 Processing helix chain 'D' and resid 515 through 527 removed outlier: 3.570A pdb=" N GLN D 527 " --> pdb=" O TRP D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 542 through 557 removed outlier: 3.505A pdb=" N ALA D 546 " --> pdb=" O GLU D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 572 removed outlier: 3.746A pdb=" N THR D 569 " --> pdb=" O GLU D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 589 removed outlier: 4.339A pdb=" N ASN D 589 " --> pdb=" O GLU D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 600 removed outlier: 3.804A pdb=" N ALA D 596 " --> pdb=" O ASP D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 610 through 617 Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 625 through 637 Processing helix chain 'D' and resid 638 through 641 Processing helix chain 'D' and resid 645 through 655 Processing helix chain 'D' and resid 717 through 728 Processing helix chain 'D' and resid 729 through 754 removed outlier: 3.610A pdb=" N VAL D 733 " --> pdb=" O ALA D 729 " (cutoff:3.500A) Processing helix chain 'D' and resid 760 through 787 removed outlier: 3.711A pdb=" N SER D 764 " --> pdb=" O PRO D 760 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N SER D 766 " --> pdb=" O GLY D 762 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU D 767 " --> pdb=" O PRO D 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 793 through 804 removed outlier: 3.865A pdb=" N ASP D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 804 through 826 Processing helix chain 'D' and resid 829 through 847 Processing helix chain 'D' and resid 848 through 854 removed outlier: 3.703A pdb=" N ILE D 851 " --> pdb=" O LEU D 848 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA D 853 " --> pdb=" O HIS D 850 " (cutoff:3.500A) Processing helix chain 'D' and resid 857 through 868 removed outlier: 4.330A pdb=" N LYS D 861 " --> pdb=" O GLN D 857 " (cutoff:3.500A) Processing helix chain 'D' and resid 870 through 895 removed outlier: 3.732A pdb=" N PHE D 874 " --> pdb=" O LYS D 870 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA D 892 " --> pdb=" O VAL D 888 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS D 895 " --> pdb=" O GLN D 891 " (cutoff:3.500A) Processing helix chain 'D' and resid 900 through 918 removed outlier: 3.781A pdb=" N ILE D 904 " --> pdb=" O ARG D 900 " (cutoff:3.500A) Proline residue: D 912 - end of helix removed outlier: 4.449A pdb=" N ILE D 916 " --> pdb=" O PRO D 912 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N PHE D 917 " --> pdb=" O TYR D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 922 through 930 Processing helix chain 'D' and resid 950 through 983 removed outlier: 4.080A pdb=" N ASN D 966 " --> pdb=" O LEU D 962 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET D 970 " --> pdb=" O ASN D 966 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU D 973 " --> pdb=" O LEU D 969 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA D 975 " --> pdb=" O ASN D 971 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N MET D 976 " --> pdb=" O LEU D 972 " (cutoff:3.500A) Processing helix chain 'D' and resid 984 through 1005 removed outlier: 3.638A pdb=" N GLY D1005 " --> pdb=" O VAL D1001 " (cutoff:3.500A) Processing helix chain 'D' and resid 1013 through 1028 Processing helix chain 'D' and resid 1044 through 1071 removed outlier: 3.635A pdb=" N ASP D1071 " --> pdb=" O LYS D1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 1072 through 1092 Processing helix chain 'A' and resid 48 through 61 Processing helix chain 'A' and resid 81 through 98 Processing helix chain 'A' and resid 111 through 126 removed outlier: 4.364A pdb=" N HIS A 115 " --> pdb=" O GLY A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 202 through 212 Processing helix chain 'A' and resid 239 through 249 Processing helix chain 'A' and resid 262 through 269 Processing helix chain 'A' and resid 279 through 288 Processing helix chain 'A' and resid 295 through 311 Processing helix chain 'A' and resid 312 through 314 No H-bonds generated for 'chain 'A' and resid 312 through 314' Processing helix chain 'A' and resid 328 through 345 removed outlier: 3.504A pdb=" N SER A 343 " --> pdb=" O LYS A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 362 Processing helix chain 'A' and resid 364 through 370 Processing helix chain 'A' and resid 383 through 393 Processing helix chain 'A' and resid 395 through 405 removed outlier: 3.581A pdb=" N VAL A 399 " --> pdb=" O LYS A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 414 through 424 Processing helix chain 'A' and resid 429 through 443 removed outlier: 3.608A pdb=" N GLU A 433 " --> pdb=" O SER A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 477 Processing helix chain 'A' and resid 515 through 527 removed outlier: 3.570A pdb=" N GLN A 527 " --> pdb=" O TRP A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 539 Processing helix chain 'A' and resid 542 through 557 removed outlier: 3.505A pdb=" N ALA A 546 " --> pdb=" O GLU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 572 removed outlier: 3.746A pdb=" N THR A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 589 removed outlier: 4.339A pdb=" N ASN A 589 " --> pdb=" O GLU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 600 removed outlier: 3.804A pdb=" N ALA A 596 " --> pdb=" O ASP A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 617 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 625 through 637 Processing helix chain 'A' and resid 638 through 641 Processing helix chain 'A' and resid 645 through 655 Processing helix chain 'A' and resid 717 through 728 Processing helix chain 'A' and resid 729 through 754 removed outlier: 3.610A pdb=" N VAL A 733 " --> pdb=" O ALA A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 787 removed outlier: 3.711A pdb=" N SER A 764 " --> pdb=" O PRO A 760 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N SER A 766 " --> pdb=" O GLY A 762 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU A 767 " --> pdb=" O PRO A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 804 removed outlier: 3.865A pdb=" N ASP A 804 " --> pdb=" O LEU A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 826 Processing helix chain 'A' and resid 829 through 847 Processing helix chain 'A' and resid 848 through 854 removed outlier: 3.703A pdb=" N ILE A 851 " --> pdb=" O LEU A 848 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA A 853 " --> pdb=" O HIS A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 868 removed outlier: 4.329A pdb=" N LYS A 861 " --> pdb=" O GLN A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 895 removed outlier: 3.732A pdb=" N PHE A 874 " --> pdb=" O LYS A 870 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A 892 " --> pdb=" O VAL A 888 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS A 895 " --> pdb=" O GLN A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 918 removed outlier: 3.780A pdb=" N ILE A 904 " --> pdb=" O ARG A 900 " (cutoff:3.500A) Proline residue: A 912 - end of helix removed outlier: 4.449A pdb=" N ILE A 916 " --> pdb=" O PRO A 912 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE A 917 " --> pdb=" O TYR A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 930 Processing helix chain 'A' and resid 950 through 983 removed outlier: 4.080A pdb=" N ASN A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET A 970 " --> pdb=" O ASN A 966 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU A 973 " --> pdb=" O LEU A 969 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 975 " --> pdb=" O ASN A 971 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N MET A 976 " --> pdb=" O LEU A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 1005 removed outlier: 3.638A pdb=" N GLY A1005 " --> pdb=" O VAL A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1028 Processing helix chain 'A' and resid 1044 through 1071 removed outlier: 3.635A pdb=" N ASP A1071 " --> pdb=" O LYS A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1092 Processing helix chain 'B' and resid 48 through 61 Processing helix chain 'B' and resid 81 through 98 Processing helix chain 'B' and resid 111 through 126 removed outlier: 4.364A pdb=" N HIS B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 153 Processing helix chain 'B' and resid 202 through 212 Processing helix chain 'B' and resid 239 through 249 Processing helix chain 'B' and resid 262 through 269 Processing helix chain 'B' and resid 279 through 288 Processing helix chain 'B' and resid 295 through 311 Processing helix chain 'B' and resid 312 through 314 No H-bonds generated for 'chain 'B' and resid 312 through 314' Processing helix chain 'B' and resid 328 through 345 removed outlier: 3.504A pdb=" N SER B 343 " --> pdb=" O LYS B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 362 Processing helix chain 'B' and resid 364 through 370 Processing helix chain 'B' and resid 383 through 393 Processing helix chain 'B' and resid 395 through 405 removed outlier: 3.581A pdb=" N VAL B 399 " --> pdb=" O LYS B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 414 through 424 Processing helix chain 'B' and resid 429 through 443 removed outlier: 3.608A pdb=" N GLU B 433 " --> pdb=" O SER B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 477 Processing helix chain 'B' and resid 515 through 527 removed outlier: 3.571A pdb=" N GLN B 527 " --> pdb=" O TRP B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 539 Processing helix chain 'B' and resid 542 through 557 removed outlier: 3.504A pdb=" N ALA B 546 " --> pdb=" O GLU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 572 removed outlier: 3.746A pdb=" N THR B 569 " --> pdb=" O GLU B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 589 removed outlier: 4.339A pdb=" N ASN B 589 " --> pdb=" O GLU B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 600 removed outlier: 3.803A pdb=" N ALA B 596 " --> pdb=" O ASP B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 617 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 625 through 637 Processing helix chain 'B' and resid 638 through 641 Processing helix chain 'B' and resid 645 through 655 Processing helix chain 'B' and resid 717 through 728 Processing helix chain 'B' and resid 729 through 754 removed outlier: 3.610A pdb=" N VAL B 733 " --> pdb=" O ALA B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 787 removed outlier: 3.712A pdb=" N SER B 764 " --> pdb=" O PRO B 760 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N SER B 766 " --> pdb=" O GLY B 762 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU B 767 " --> pdb=" O PRO B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 804 removed outlier: 3.866A pdb=" N ASP B 804 " --> pdb=" O LEU B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 826 Processing helix chain 'B' and resid 829 through 847 Processing helix chain 'B' and resid 848 through 854 removed outlier: 3.702A pdb=" N ILE B 851 " --> pdb=" O LEU B 848 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA B 853 " --> pdb=" O HIS B 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 868 removed outlier: 4.330A pdb=" N LYS B 861 " --> pdb=" O GLN B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 895 removed outlier: 3.732A pdb=" N PHE B 874 " --> pdb=" O LYS B 870 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA B 892 " --> pdb=" O VAL B 888 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS B 895 " --> pdb=" O GLN B 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 918 removed outlier: 3.780A pdb=" N ILE B 904 " --> pdb=" O ARG B 900 " (cutoff:3.500A) Proline residue: B 912 - end of helix removed outlier: 4.449A pdb=" N ILE B 916 " --> pdb=" O PRO B 912 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE B 917 " --> pdb=" O TYR B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 930 Processing helix chain 'B' and resid 950 through 983 removed outlier: 4.080A pdb=" N ASN B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET B 970 " --> pdb=" O ASN B 966 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU B 973 " --> pdb=" O LEU B 969 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA B 975 " --> pdb=" O ASN B 971 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N MET B 976 " --> pdb=" O LEU B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 1005 removed outlier: 3.637A pdb=" N GLY B1005 " --> pdb=" O VAL B1001 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1028 Processing helix chain 'B' and resid 1044 through 1071 removed outlier: 3.634A pdb=" N ASP B1071 " --> pdb=" O LYS B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1072 through 1092 Processing helix chain 'C' and resid 48 through 61 Processing helix chain 'C' and resid 81 through 98 Processing helix chain 'C' and resid 111 through 126 removed outlier: 4.365A pdb=" N HIS C 115 " --> pdb=" O GLY C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 153 Processing helix chain 'C' and resid 202 through 212 Processing helix chain 'C' and resid 239 through 249 Processing helix chain 'C' and resid 262 through 269 Processing helix chain 'C' and resid 279 through 288 Processing helix chain 'C' and resid 295 through 311 Processing helix chain 'C' and resid 312 through 314 No H-bonds generated for 'chain 'C' and resid 312 through 314' Processing helix chain 'C' and resid 328 through 345 removed outlier: 3.504A pdb=" N SER C 343 " --> pdb=" O LYS C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 362 Processing helix chain 'C' and resid 364 through 370 Processing helix chain 'C' and resid 383 through 393 Processing helix chain 'C' and resid 395 through 405 removed outlier: 3.580A pdb=" N VAL C 399 " --> pdb=" O LYS C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'C' and resid 414 through 424 Processing helix chain 'C' and resid 429 through 443 removed outlier: 3.608A pdb=" N GLU C 433 " --> pdb=" O SER C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 477 Processing helix chain 'C' and resid 515 through 527 removed outlier: 3.570A pdb=" N GLN C 527 " --> pdb=" O TRP C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 539 Processing helix chain 'C' and resid 542 through 557 removed outlier: 3.505A pdb=" N ALA C 546 " --> pdb=" O GLU C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 572 removed outlier: 3.746A pdb=" N THR C 569 " --> pdb=" O GLU C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 589 removed outlier: 4.339A pdb=" N ASN C 589 " --> pdb=" O GLU C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 600 removed outlier: 3.804A pdb=" N ALA C 596 " --> pdb=" O ASP C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 617 Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 625 through 637 Processing helix chain 'C' and resid 638 through 641 Processing helix chain 'C' and resid 645 through 655 Processing helix chain 'C' and resid 717 through 728 Processing helix chain 'C' and resid 729 through 754 removed outlier: 3.610A pdb=" N VAL C 733 " --> pdb=" O ALA C 729 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 787 removed outlier: 3.712A pdb=" N SER C 764 " --> pdb=" O PRO C 760 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N SER C 766 " --> pdb=" O GLY C 762 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU C 767 " --> pdb=" O PRO C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 804 removed outlier: 3.865A pdb=" N ASP C 804 " --> pdb=" O LEU C 800 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 826 Processing helix chain 'C' and resid 829 through 847 Processing helix chain 'C' and resid 848 through 854 removed outlier: 3.703A pdb=" N ILE C 851 " --> pdb=" O LEU C 848 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA C 853 " --> pdb=" O HIS C 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 868 removed outlier: 4.329A pdb=" N LYS C 861 " --> pdb=" O GLN C 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 895 removed outlier: 3.732A pdb=" N PHE C 874 " --> pdb=" O LYS C 870 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA C 892 " --> pdb=" O VAL C 888 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS C 895 " --> pdb=" O GLN C 891 " (cutoff:3.500A) Processing helix chain 'C' and resid 900 through 918 removed outlier: 3.780A pdb=" N ILE C 904 " --> pdb=" O ARG C 900 " (cutoff:3.500A) Proline residue: C 912 - end of helix removed outlier: 4.450A pdb=" N ILE C 916 " --> pdb=" O PRO C 912 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE C 917 " --> pdb=" O TYR C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 922 through 930 Processing helix chain 'C' and resid 950 through 983 removed outlier: 4.080A pdb=" N ASN C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET C 970 " --> pdb=" O ASN C 966 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU C 973 " --> pdb=" O LEU C 969 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA C 975 " --> pdb=" O ASN C 971 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N MET C 976 " --> pdb=" O LEU C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 984 through 1005 removed outlier: 3.638A pdb=" N GLY C1005 " --> pdb=" O VAL C1001 " (cutoff:3.500A) Processing helix chain 'C' and resid 1013 through 1028 Processing helix chain 'C' and resid 1044 through 1071 removed outlier: 3.635A pdb=" N ASP C1071 " --> pdb=" O LYS C1067 " (cutoff:3.500A) Processing helix chain 'C' and resid 1072 through 1092 Processing sheet with id=AA1, first strand: chain 'D' and resid 25 through 28 Processing sheet with id=AA2, first strand: chain 'D' and resid 135 through 136 removed outlier: 7.592A pdb=" N VAL D 69 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL D 68 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU D 231 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N SER D 70 " --> pdb=" O LEU D 231 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N LEU D 254 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N CYS D 230 " --> pdb=" O LEU D 254 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 139 through 141 removed outlier: 3.568A pdb=" N VAL D 188 " --> pdb=" O ALA D 140 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 601 through 602 Processing sheet with id=AA5, first strand: chain 'A' and resid 25 through 28 Processing sheet with id=AA6, first strand: chain 'A' and resid 135 through 136 removed outlier: 7.592A pdb=" N VAL A 69 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL A 68 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU A 231 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N SER A 70 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N LEU A 254 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N CYS A 230 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 139 through 141 removed outlier: 3.569A pdb=" N VAL A 188 " --> pdb=" O ALA A 140 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 601 through 602 Processing sheet with id=AA9, first strand: chain 'B' and resid 25 through 28 Processing sheet with id=AB1, first strand: chain 'B' and resid 135 through 136 removed outlier: 7.592A pdb=" N VAL B 69 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL B 68 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU B 231 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N SER B 70 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N LEU B 254 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N CYS B 230 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 139 through 141 removed outlier: 3.569A pdb=" N VAL B 188 " --> pdb=" O ALA B 140 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 601 through 602 Processing sheet with id=AB4, first strand: chain 'C' and resid 25 through 28 Processing sheet with id=AB5, first strand: chain 'C' and resid 135 through 136 removed outlier: 7.592A pdb=" N VAL C 69 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL C 68 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU C 231 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N SER C 70 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N LEU C 254 " --> pdb=" O VAL C 228 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N CYS C 230 " --> pdb=" O LEU C 254 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 139 through 141 removed outlier: 3.569A pdb=" N VAL C 188 " --> pdb=" O ALA C 140 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 601 through 602 1788 hydrogen bonds defined for protein. 5304 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: 4.19 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8117 1.34 - 1.46: 4803 1.46 - 1.58: 11824 1.58 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 24864 Sorted by residual: bond pdb=" N HIS A 897 " pdb=" CA HIS A 897 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.29e-02 6.01e+03 2.41e+00 bond pdb=" N HIS D 897 " pdb=" CA HIS D 897 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.29e-02 6.01e+03 2.34e+00 bond pdb=" N HIS B 897 " pdb=" CA HIS B 897 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.29e-02 6.01e+03 2.34e+00 bond pdb=" N HIS C 897 " pdb=" CA HIS C 897 " ideal model delta sigma weight residual 1.457 1.477 -0.019 1.29e-02 6.01e+03 2.23e+00 bond pdb=" CA HIS A 897 " pdb=" C HIS A 897 " ideal model delta sigma weight residual 1.523 1.541 -0.018 1.34e-02 5.57e+03 1.71e+00 ... (remaining 24859 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 33363 1.60 - 3.20: 633 3.20 - 4.80: 96 4.80 - 6.39: 36 6.39 - 7.99: 4 Bond angle restraints: 34132 Sorted by residual: angle pdb=" N HIS A 895 " pdb=" CA HIS A 895 " pdb=" C HIS A 895 " ideal model delta sigma weight residual 108.07 111.81 -3.74 8.90e-01 1.26e+00 1.77e+01 angle pdb=" N HIS D 895 " pdb=" CA HIS D 895 " pdb=" C HIS D 895 " ideal model delta sigma weight residual 108.07 111.76 -3.69 8.90e-01 1.26e+00 1.72e+01 angle pdb=" N HIS C 895 " pdb=" CA HIS C 895 " pdb=" C HIS C 895 " ideal model delta sigma weight residual 108.07 111.72 -3.65 8.90e-01 1.26e+00 1.68e+01 angle pdb=" N HIS B 895 " pdb=" CA HIS B 895 " pdb=" C HIS B 895 " ideal model delta sigma weight residual 108.07 111.72 -3.65 8.90e-01 1.26e+00 1.68e+01 angle pdb=" N VAL D 888 " pdb=" CA VAL D 888 " pdb=" CB VAL D 888 " ideal model delta sigma weight residual 110.54 115.10 -4.56 1.36e+00 5.41e-01 1.12e+01 ... (remaining 34127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 13628 17.51 - 35.03: 634 35.03 - 52.54: 86 52.54 - 70.06: 4 70.06 - 87.57: 4 Dihedral angle restraints: 14356 sinusoidal: 3740 harmonic: 10616 Sorted by residual: dihedral pdb=" CA PRO C 759 " pdb=" C PRO C 759 " pdb=" N PRO C 760 " pdb=" CA PRO C 760 " ideal model delta harmonic sigma weight residual 180.00 159.04 20.96 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA PRO D 759 " pdb=" C PRO D 759 " pdb=" N PRO D 760 " pdb=" CA PRO D 760 " ideal model delta harmonic sigma weight residual 180.00 159.05 20.95 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA PRO B 759 " pdb=" C PRO B 759 " pdb=" N PRO B 760 " pdb=" CA PRO B 760 " ideal model delta harmonic sigma weight residual 180.00 159.05 20.95 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 14353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3557 0.053 - 0.106: 533 0.106 - 0.159: 31 0.159 - 0.212: 3 0.212 - 0.264: 8 Chirality restraints: 4132 Sorted by residual: chirality pdb=" CA HIS C 897 " pdb=" N HIS C 897 " pdb=" C HIS C 897 " pdb=" CB HIS C 897 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA HIS B 897 " pdb=" N HIS B 897 " pdb=" C HIS B 897 " pdb=" CB HIS B 897 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA HIS A 897 " pdb=" N HIS A 897 " pdb=" C HIS A 897 " pdb=" CB HIS A 897 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 4129 not shown) Planarity restraints: 4396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 759 " -0.061 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO D 760 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO D 760 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO D 760 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 759 " 0.061 5.00e-02 4.00e+02 9.12e-02 1.33e+01 pdb=" N PRO A 760 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO A 760 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 760 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 759 " -0.061 5.00e-02 4.00e+02 9.12e-02 1.33e+01 pdb=" N PRO C 760 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO C 760 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO C 760 " -0.051 5.00e-02 4.00e+02 ... (remaining 4393 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 28 2.25 - 2.91: 10384 2.91 - 3.58: 37652 3.58 - 4.24: 49004 4.24 - 4.90: 81254 Nonbonded interactions: 178322 Sorted by model distance: nonbonded pdb=" O GLN D 919 " pdb=" NE2 GLN A 919 " model vdw 1.591 3.120 nonbonded pdb=" NE2 GLN D 919 " pdb=" O GLN C 919 " model vdw 1.627 3.120 nonbonded pdb=" O GLN A 919 " pdb=" NE2 GLN B 919 " model vdw 1.695 3.120 nonbonded pdb=" O GLN B 919 " pdb=" NE2 GLN C 919 " model vdw 1.705 3.120 nonbonded pdb=" SG CYS C 586 " pdb=" CH2 TRP C1053 " model vdw 2.080 3.700 ... (remaining 178317 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 'D' selection = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 3.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 22.800 Find NCS groups from input model: 0.330 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: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24864 Z= 0.154 Angle : 0.564 7.993 34132 Z= 0.345 Chirality : 0.038 0.264 4132 Planarity : 0.005 0.091 4396 Dihedral : 10.538 87.569 7380 Min Nonbonded Distance : 1.591 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.50 (0.13), residues: 3528 helix: -0.29 (0.10), residues: 2396 sheet: -1.66 (0.37), residues: 152 loop : -2.45 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 600 TYR 0.011 0.001 TYR B 535 PHE 0.014 0.001 PHE B 53 TRP 0.016 0.001 TRP D 727 HIS 0.002 0.001 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (24864) covalent geometry : angle 0.56448 / 0.35 (34132) hydrogen bonds : bond 0.14762 / 10.42 ( 1788) hydrogen bonds : angle 5.56520 / 4.03 ( 5304) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 339 LYS cc_start: 0.8909 (tmtt) cc_final: 0.8705 (tmtt) REVERT: D 420 GLN cc_start: 0.9077 (mt0) cc_final: 0.8841 (mt0) REVERT: D 557 MET cc_start: 0.8090 (mtp) cc_final: 0.7773 (tmm) REVERT: D 719 LEU cc_start: 0.7888 (tt) cc_final: 0.7686 (mm) REVERT: D 773 TRP cc_start: 0.7317 (t60) cc_final: 0.7026 (t60) REVERT: D 970 MET cc_start: 0.8963 (ptm) cc_final: 0.8735 (mpp) REVERT: A 253 TRP cc_start: 0.7241 (m100) cc_final: 0.7008 (m100) REVERT: A 339 LYS cc_start: 0.8935 (tmtt) cc_final: 0.8728 (tmtt) REVERT: A 420 GLN cc_start: 0.9079 (mt0) cc_final: 0.8842 (mt0) REVERT: A 557 MET cc_start: 0.8082 (mtp) cc_final: 0.7851 (tmm) REVERT: A 719 LEU cc_start: 0.7934 (tt) cc_final: 0.7687 (mm) REVERT: A 970 MET cc_start: 0.8974 (ptm) cc_final: 0.8707 (mpp) REVERT: B 420 GLN cc_start: 0.9130 (mt0) cc_final: 0.8859 (mt0) REVERT: B 557 MET cc_start: 0.8102 (mtp) cc_final: 0.7876 (tmm) REVERT: B 970 MET cc_start: 0.8916 (ptm) cc_final: 0.8691 (mpp) REVERT: C 339 LYS cc_start: 0.8898 (tmtt) cc_final: 0.8690 (tmtt) REVERT: C 401 LEU cc_start: 0.9413 (tp) cc_final: 0.9202 (tp) REVERT: C 737 ASN cc_start: 0.8219 (m110) cc_final: 0.7981 (t0) REVERT: C 970 MET cc_start: 0.8892 (ptm) cc_final: 0.8679 (mpp) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.1483 time to fit residues: 73.8744 Evaluate side-chains 238 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 197 optimal weight: 0.4980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.3980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.0040 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 6.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 115 HIS D 225 GLN D 467 HIS D 855 HIS D 951 ASN A 115 HIS A 225 GLN A 467 HIS A 855 HIS A 951 ASN B 115 HIS B 225 GLN B 467 HIS B 855 HIS B 951 ASN C 115 HIS C 225 GLN C 467 HIS C 629 GLN C 855 HIS C 951 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.112955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.078783 restraints weight = 91818.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.080964 restraints weight = 47265.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.082257 restraints weight = 32315.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.083005 restraints weight = 26055.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.083373 restraints weight = 23093.183| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24864 Z= 0.105 Angle : 0.505 9.180 34132 Z= 0.263 Chirality : 0.036 0.139 4132 Planarity : 0.005 0.092 4396 Dihedral : 3.692 19.790 3756 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.06 % Allowed : 12.21 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.65 (0.14), residues: 3528 helix: 1.39 (0.10), residues: 2448 sheet: -0.94 (0.37), residues: 192 loop : -1.98 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 89 TYR 0.013 0.001 TYR C 535 PHE 0.018 0.001 PHE D 873 TRP 0.028 0.001 TRP A 773 HIS 0.003 0.001 HIS C 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (24864) covalent geometry : angle 0.50476 / 0.26 (34132) hydrogen bonds : bond 0.03209 / 2.26 ( 1788) hydrogen bonds : angle 3.93095 / 2.83 ( 5304) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 250 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 319 TYR cc_start: 0.7580 (t80) cc_final: 0.6023 (t80) REVERT: D 321 PHE cc_start: 0.7032 (m-10) cc_final: 0.6574 (m-80) REVERT: D 539 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7653 (mtt) REVERT: D 557 MET cc_start: 0.8391 (mtp) cc_final: 0.7906 (tmm) REVERT: A 319 TYR cc_start: 0.7584 (t80) cc_final: 0.6179 (t80) REVERT: A 539 MET cc_start: 0.8287 (mmt) cc_final: 0.7946 (mpp) REVERT: A 557 MET cc_start: 0.8293 (mtp) cc_final: 0.8040 (tmm) REVERT: A 598 LEU cc_start: 0.9094 (tp) cc_final: 0.8734 (tt) REVERT: A 719 LEU cc_start: 0.7894 (tt) cc_final: 0.7691 (mm) REVERT: A 773 TRP cc_start: 0.6625 (t60) cc_final: 0.6189 (t60) REVERT: A 970 MET cc_start: 0.9058 (ptm) cc_final: 0.8732 (mpp) REVERT: B 319 TYR cc_start: 0.7382 (t80) cc_final: 0.5968 (t80) REVERT: B 539 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7624 (mtt) REVERT: B 557 MET cc_start: 0.8328 (mtp) cc_final: 0.8025 (tmm) REVERT: C 319 TYR cc_start: 0.7560 (t80) cc_final: 0.6171 (t80) REVERT: C 321 PHE cc_start: 0.7061 (m-10) cc_final: 0.6771 (m-80) REVERT: C 539 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7840 (mtt) REVERT: C 737 ASN cc_start: 0.8105 (m110) cc_final: 0.7820 (t0) outliers start: 18 outliers final: 9 residues processed: 258 average time/residue: 0.1238 time to fit residues: 54.7179 Evaluate side-chains 236 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 224 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 532 MET Chi-restraints excluded: chain D residue 539 MET Chi-restraints excluded: chain D residue 823 CYS Chi-restraints excluded: chain A residue 823 CYS Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 539 MET Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 823 CYS Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 532 MET Chi-restraints excluded: chain C residue 539 MET Chi-restraints excluded: chain C residue 823 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 297 optimal weight: 4.9990 chunk 343 optimal weight: 7.9990 chunk 11 optimal weight: 20.0000 chunk 1 optimal weight: 40.0000 chunk 61 optimal weight: 0.5980 chunk 194 optimal weight: 50.0000 chunk 161 optimal weight: 4.9990 chunk 180 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 328 optimal weight: 7.9990 chunk 129 optimal weight: 0.7980 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 737 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.109850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.075370 restraints weight = 92912.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.077420 restraints weight = 48283.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.078618 restraints weight = 33417.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.079310 restraints weight = 27205.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.079676 restraints weight = 24275.537| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 24864 Z= 0.240 Angle : 0.626 8.153 34132 Z= 0.328 Chirality : 0.040 0.142 4132 Planarity : 0.005 0.091 4396 Dihedral : 4.155 19.697 3756 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.64 % Allowed : 14.73 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.80 (0.14), residues: 3528 helix: 1.43 (0.11), residues: 2488 sheet: -0.65 (0.40), residues: 152 loop : -1.86 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 443 TYR 0.013 0.002 TYR A 422 PHE 0.032 0.002 PHE A 744 TRP 0.013 0.002 TRP D 773 HIS 0.004 0.001 HIS C 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.24 (24864) covalent geometry : angle 0.62565 / 0.33 (34132) hydrogen bonds : bond 0.04317 / 3.07 ( 1788) hydrogen bonds : angle 4.44117 / 3.21 ( 5304) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 221 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 319 TYR cc_start: 0.7743 (t80) cc_final: 0.7182 (t80) REVERT: D 420 GLN cc_start: 0.9170 (mt0) cc_final: 0.8913 (mt0) REVERT: A 319 TYR cc_start: 0.7616 (t80) cc_final: 0.6072 (t80) REVERT: A 420 GLN cc_start: 0.9185 (mt0) cc_final: 0.8933 (mt0) REVERT: A 557 MET cc_start: 0.8393 (mtp) cc_final: 0.7799 (tmm) REVERT: B 319 TYR cc_start: 0.7659 (t80) cc_final: 0.6116 (t80) REVERT: B 409 MET cc_start: 0.8847 (mmp) cc_final: 0.8620 (mmm) REVERT: B 420 GLN cc_start: 0.9209 (mt0) cc_final: 0.8977 (mt0) REVERT: B 557 MET cc_start: 0.8278 (mtp) cc_final: 0.7790 (tmm) REVERT: C 354 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7808 (mt-10) outliers start: 45 outliers final: 32 residues processed: 241 average time/residue: 0.1277 time to fit residues: 53.8459 Evaluate side-chains 247 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 215 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 532 MET Chi-restraints excluded: chain D residue 823 CYS Chi-restraints excluded: chain D residue 876 LEU Chi-restraints excluded: chain D residue 953 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain A residue 823 CYS Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 823 CYS Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 532 MET Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain C residue 823 CYS Chi-restraints excluded: chain C residue 876 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 182 optimal weight: 50.0000 chunk 304 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 232 optimal weight: 0.8980 chunk 164 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 35 optimal weight: 0.5980 chunk 255 optimal weight: 4.9990 chunk 156 optimal weight: 9.9990 chunk 137 optimal weight: 9.9990 chunk 76 optimal weight: 0.6980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.111124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.076664 restraints weight = 91803.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.078771 restraints weight = 47545.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.080002 restraints weight = 32837.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.080720 restraints weight = 26597.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.081128 restraints weight = 23637.597| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24864 Z= 0.143 Angle : 0.526 9.437 34132 Z= 0.272 Chirality : 0.037 0.135 4132 Planarity : 0.005 0.095 4396 Dihedral : 3.852 21.206 3756 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.52 % Allowed : 16.31 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.41 (0.15), residues: 3528 helix: 1.92 (0.11), residues: 2444 sheet: -0.10 (0.40), residues: 152 loop : -1.61 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 541 TYR 0.009 0.001 TYR A 535 PHE 0.016 0.001 PHE C 873 TRP 0.016 0.001 TRP C 727 HIS 0.003 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (24864) covalent geometry : angle 0.52599 / 0.27 (34132) hydrogen bonds : bond 0.03291 / 2.33 ( 1788) hydrogen bonds : angle 3.91513 / 2.82 ( 5304) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 223 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 319 TYR cc_start: 0.7534 (t80) cc_final: 0.6845 (t80) REVERT: D 409 MET cc_start: 0.8733 (mmp) cc_final: 0.8514 (mmp) REVERT: A 557 MET cc_start: 0.8390 (mtp) cc_final: 0.7910 (tmm) REVERT: B 319 TYR cc_start: 0.7808 (t80) cc_final: 0.6329 (t80) REVERT: B 420 GLN cc_start: 0.9122 (mt0) cc_final: 0.8896 (mt0) REVERT: B 557 MET cc_start: 0.8337 (mtp) cc_final: 0.7880 (tmm) REVERT: B 970 MET cc_start: 0.8886 (ppp) cc_final: 0.8602 (mpp) REVERT: C 354 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7943 (mt-10) REVERT: C 992 TRP cc_start: 0.9337 (t60) cc_final: 0.8803 (t60) outliers start: 60 outliers final: 35 residues processed: 257 average time/residue: 0.1219 time to fit residues: 55.2820 Evaluate side-chains 252 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 217 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 532 MET Chi-restraints excluded: chain D residue 742 PHE Chi-restraints excluded: chain D residue 823 CYS Chi-restraints excluded: chain D residue 953 LEU Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain A residue 823 CYS Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 823 CYS Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 532 MET Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain C residue 823 CYS Chi-restraints excluded: chain C residue 876 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 239 optimal weight: 0.6980 chunk 321 optimal weight: 2.9990 chunk 198 optimal weight: 9.9990 chunk 347 optimal weight: 0.6980 chunk 199 optimal weight: 20.0000 chunk 312 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 176 optimal weight: 40.0000 chunk 221 optimal weight: 6.9990 chunk 202 optimal weight: 20.0000 chunk 331 optimal weight: 5.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.109351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.074918 restraints weight = 91815.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.076939 restraints weight = 47995.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.078141 restraints weight = 33358.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.078838 restraints weight = 27093.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.079218 restraints weight = 24146.064| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 24864 Z= 0.226 Angle : 0.605 9.873 34132 Z= 0.317 Chirality : 0.039 0.134 4132 Planarity : 0.005 0.092 4396 Dihedral : 4.125 19.462 3756 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.05 % Allowed : 17.19 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.17 (0.15), residues: 3528 helix: 1.71 (0.11), residues: 2464 sheet: -0.49 (0.36), residues: 200 loop : -1.68 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 541 TYR 0.012 0.001 TYR B 997 PHE 0.014 0.002 PHE C 873 TRP 0.014 0.002 TRP A 727 HIS 0.005 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.23 (24864) covalent geometry : angle 0.60466 / 0.32 (34132) hydrogen bonds : bond 0.03995 / 2.84 ( 1788) hydrogen bonds : angle 4.27953 / 3.08 ( 5304) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 218 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 532 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8000 (tpp) REVERT: D 970 MET cc_start: 0.8870 (ptm) cc_final: 0.8607 (mpp) REVERT: A 319 TYR cc_start: 0.7469 (t80) cc_final: 0.5939 (t80) REVERT: A 557 MET cc_start: 0.8409 (mtp) cc_final: 0.7824 (tmm) REVERT: B 319 TYR cc_start: 0.7768 (t80) cc_final: 0.6153 (t80) REVERT: B 539 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7771 (mtt) REVERT: B 557 MET cc_start: 0.8289 (mtp) cc_final: 0.7872 (tmm) REVERT: B 773 TRP cc_start: 0.7729 (t60) cc_final: 0.7191 (t60) REVERT: C 319 TYR cc_start: 0.7413 (t80) cc_final: 0.5921 (t80) REVERT: C 354 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7918 (mt-10) REVERT: C 420 GLN cc_start: 0.9042 (mt0) cc_final: 0.8760 (mp10) outliers start: 69 outliers final: 53 residues processed: 260 average time/residue: 0.1230 time to fit residues: 56.6139 Evaluate side-chains 270 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 215 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 484 PHE Chi-restraints excluded: chain D residue 532 MET Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 742 PHE Chi-restraints excluded: chain D residue 823 CYS Chi-restraints excluded: chain D residue 876 LEU Chi-restraints excluded: chain D residue 953 LEU Chi-restraints excluded: chain D residue 973 LEU Chi-restraints excluded: chain D residue 976 MET Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain A residue 823 CYS Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 484 PHE Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 539 MET Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 822 THR Chi-restraints excluded: chain B residue 823 CYS Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 484 PHE Chi-restraints excluded: chain C residue 532 MET Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain C residue 823 CYS Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 976 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 95 optimal weight: 40.0000 chunk 118 optimal weight: 9.9990 chunk 217 optimal weight: 1.9990 chunk 6 optimal weight: 30.0000 chunk 80 optimal weight: 9.9990 chunk 213 optimal weight: 4.9990 chunk 227 optimal weight: 3.9990 chunk 75 optimal weight: 30.0000 chunk 28 optimal weight: 0.8980 chunk 278 optimal weight: 20.0000 chunk 73 optimal weight: 7.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 998 HIS D1060 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.109922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.076316 restraints weight = 91600.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.078253 restraints weight = 47932.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.079393 restraints weight = 33348.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.080066 restraints weight = 27281.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.080353 restraints weight = 24365.535| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 24864 Z= 0.255 Angle : 0.642 10.711 34132 Z= 0.339 Chirality : 0.040 0.137 4132 Planarity : 0.005 0.095 4396 Dihedral : 4.334 20.645 3756 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.58 % Allowed : 17.78 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.83 (0.15), residues: 3528 helix: 1.42 (0.10), residues: 2508 sheet: -0.53 (0.35), residues: 208 loop : -1.89 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 541 TYR 0.014 0.002 TYR A 422 PHE 0.014 0.002 PHE C 873 TRP 0.015 0.002 TRP A 253 HIS 0.006 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.25 (24864) covalent geometry : angle 0.64216 / 0.34 (34132) hydrogen bonds : bond 0.04141 / 2.95 ( 1788) hydrogen bonds : angle 4.48464 / 3.23 ( 5304) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 220 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 319 TYR cc_start: 0.7615 (t80) cc_final: 0.6883 (t80) REVERT: D 420 GLN cc_start: 0.9025 (mt0) cc_final: 0.8797 (mt0) REVERT: D 532 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.7977 (tpp) REVERT: A 319 TYR cc_start: 0.7481 (t80) cc_final: 0.5864 (t80) REVERT: A 420 GLN cc_start: 0.9043 (mt0) cc_final: 0.8786 (mt0) REVERT: A 557 MET cc_start: 0.8251 (mtp) cc_final: 0.7782 (tmm) REVERT: B 319 TYR cc_start: 0.7715 (t80) cc_final: 0.6020 (t80) REVERT: B 532 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8043 (tpp) REVERT: B 539 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7634 (mtt) REVERT: B 557 MET cc_start: 0.8204 (mtp) cc_final: 0.7761 (tmm) REVERT: C 243 MET cc_start: 0.7632 (ppp) cc_final: 0.7081 (ppp) REVERT: C 319 TYR cc_start: 0.7415 (t80) cc_final: 0.5914 (t80) REVERT: C 354 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7745 (mt-10) REVERT: C 532 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.7993 (tpp) outliers start: 78 outliers final: 56 residues processed: 268 average time/residue: 0.1277 time to fit residues: 59.9169 Evaluate side-chains 279 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 219 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 210 HIS Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 484 PHE Chi-restraints excluded: chain D residue 532 MET Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 742 PHE Chi-restraints excluded: chain D residue 823 CYS Chi-restraints excluded: chain D residue 876 LEU Chi-restraints excluded: chain D residue 973 LEU Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain A residue 823 CYS Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 484 PHE Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 539 MET Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 822 THR Chi-restraints excluded: chain B residue 823 CYS Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 210 HIS Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 484 PHE Chi-restraints excluded: chain C residue 532 MET Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain C residue 823 CYS Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 976 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 328 optimal weight: 7.9990 chunk 164 optimal weight: 9.9990 chunk 157 optimal weight: 4.9990 chunk 156 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 300 optimal weight: 9.9990 chunk 169 optimal weight: 1.9990 chunk 298 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 362 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 998 HIS A 225 GLN C 225 GLN C 998 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.118339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.084453 restraints weight = 88829.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.087045 restraints weight = 51866.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.087109 restraints weight = 31438.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.087288 restraints weight = 33508.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.087386 restraints weight = 29390.109| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 24864 Z= 0.257 Angle : 0.651 11.858 34132 Z= 0.342 Chirality : 0.040 0.148 4132 Planarity : 0.005 0.093 4396 Dihedral : 4.374 19.778 3756 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 4.23 % Allowed : 18.96 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.72 (0.15), residues: 3528 helix: 1.37 (0.10), residues: 2500 sheet: -0.25 (0.40), residues: 152 loop : -2.02 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 541 TYR 0.014 0.002 TYR A 422 PHE 0.015 0.002 PHE C 873 TRP 0.016 0.002 TRP A 253 HIS 0.005 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.26 (24864) covalent geometry : angle 0.65135 / 0.34 (34132) hydrogen bonds : bond 0.04189 / 2.97 ( 1788) hydrogen bonds : angle 4.55120 / 3.27 ( 5304) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 223 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 319 TYR cc_start: 0.7527 (t80) cc_final: 0.6730 (t80) REVERT: D 420 GLN cc_start: 0.9079 (mt0) cc_final: 0.8834 (mt0) REVERT: D 532 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.7984 (tpp) REVERT: A 420 GLN cc_start: 0.9078 (mt0) cc_final: 0.8816 (mt0) REVERT: A 557 MET cc_start: 0.8222 (mtp) cc_final: 0.7674 (tmm) REVERT: B 225 GLN cc_start: 0.7139 (OUTLIER) cc_final: 0.6937 (mt0) REVERT: B 253 TRP cc_start: 0.7091 (m100) cc_final: 0.6794 (m100) REVERT: B 319 TYR cc_start: 0.7770 (t80) cc_final: 0.6106 (t80) REVERT: B 532 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.7908 (tpp) REVERT: B 539 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7738 (mtt) REVERT: B 557 MET cc_start: 0.8224 (mtp) cc_final: 0.7807 (tmm) REVERT: C 319 TYR cc_start: 0.7448 (t80) cc_final: 0.5910 (t80) REVERT: C 420 GLN cc_start: 0.8974 (mt0) cc_final: 0.8733 (mp10) REVERT: C 532 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8018 (tpp) outliers start: 72 outliers final: 51 residues processed: 267 average time/residue: 0.1269 time to fit residues: 59.3870 Evaluate side-chains 278 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 222 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 484 PHE Chi-restraints excluded: chain D residue 532 MET Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 742 PHE Chi-restraints excluded: chain D residue 823 CYS Chi-restraints excluded: chain D residue 876 LEU Chi-restraints excluded: chain D residue 973 LEU Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain A residue 823 CYS Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 484 PHE Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 539 MET Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 822 THR Chi-restraints excluded: chain B residue 823 CYS Chi-restraints excluded: chain B residue 875 PHE Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 484 PHE Chi-restraints excluded: chain C residue 532 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain C residue 823 CYS Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 976 MET Chi-restraints excluded: chain C residue 1076 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 124 optimal weight: 0.5980 chunk 11 optimal weight: 30.0000 chunk 183 optimal weight: 20.0000 chunk 37 optimal weight: 9.9990 chunk 176 optimal weight: 30.0000 chunk 328 optimal weight: 10.0000 chunk 202 optimal weight: 30.0000 chunk 180 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 201 optimal weight: 0.9990 overall best weight: 5.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 998 HIS ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 998 HIS ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 998 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.122227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.090094 restraints weight = 93429.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.092029 restraints weight = 48971.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.093181 restraints weight = 33909.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.093875 restraints weight = 27561.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.094001 restraints weight = 24467.827| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 24864 Z= 0.359 Angle : 0.772 13.031 34132 Z= 0.409 Chirality : 0.044 0.206 4132 Planarity : 0.006 0.095 4396 Dihedral : 4.834 20.200 3756 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 4.75 % Allowed : 18.90 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.03 (0.14), residues: 3528 helix: 0.82 (0.10), residues: 2496 sheet: -0.64 (0.41), residues: 152 loop : -2.26 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 346 TYR 0.019 0.002 TYR A 422 PHE 0.018 0.002 PHE C 583 TRP 0.016 0.002 TRP A 773 HIS 0.009 0.002 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00759 / 0.36 (24864) covalent geometry : angle 0.77189 / 0.41 (34132) hydrogen bonds : bond 0.05006 / 3.56 ( 1788) hydrogen bonds : angle 5.18399 / 3.73 ( 5304) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 217 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 420 GLN cc_start: 0.9053 (mt0) cc_final: 0.8831 (mt0) REVERT: D 532 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8365 (tpp) REVERT: B 225 GLN cc_start: 0.7230 (OUTLIER) cc_final: 0.6942 (mt0) REVERT: B 253 TRP cc_start: 0.7267 (m100) cc_final: 0.6976 (m100) REVERT: B 532 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8374 (tpp) REVERT: B 557 MET cc_start: 0.8204 (mtp) cc_final: 0.7649 (tmm) REVERT: B 744 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.7716 (t80) REVERT: C 532 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8243 (tpp) outliers start: 81 outliers final: 59 residues processed: 268 average time/residue: 0.1287 time to fit residues: 60.7117 Evaluate side-chains 276 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 212 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 484 PHE Chi-restraints excluded: chain D residue 532 MET Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 742 PHE Chi-restraints excluded: chain D residue 823 CYS Chi-restraints excluded: chain D residue 876 LEU Chi-restraints excluded: chain D residue 973 LEU Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain A residue 823 CYS Chi-restraints excluded: chain A residue 873 PHE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 484 PHE Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 822 THR Chi-restraints excluded: chain B residue 823 CYS Chi-restraints excluded: chain B residue 875 PHE Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 210 HIS Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 484 PHE Chi-restraints excluded: chain C residue 532 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain C residue 823 CYS Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 976 MET Chi-restraints excluded: chain C residue 1076 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 38 optimal weight: 0.7980 chunk 245 optimal weight: 7.9990 chunk 336 optimal weight: 10.0000 chunk 231 optimal weight: 0.8980 chunk 201 optimal weight: 20.0000 chunk 194 optimal weight: 50.0000 chunk 28 optimal weight: 2.9990 chunk 316 optimal weight: 0.9980 chunk 242 optimal weight: 8.9990 chunk 264 optimal weight: 0.8980 chunk 109 optimal weight: 9.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.119750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.085778 restraints weight = 88822.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.087755 restraints weight = 47434.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.088988 restraints weight = 33565.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.089664 restraints weight = 27607.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.089962 restraints weight = 24847.462| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24864 Z= 0.120 Angle : 0.570 12.414 34132 Z= 0.289 Chirality : 0.038 0.249 4132 Planarity : 0.005 0.096 4396 Dihedral : 4.095 21.728 3756 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.05 % Allowed : 20.77 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.13 (0.15), residues: 3528 helix: 1.71 (0.11), residues: 2480 sheet: -0.36 (0.41), residues: 152 loop : -1.84 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 417 TYR 0.019 0.001 TYR B 351 PHE 0.020 0.001 PHE C 873 TRP 0.020 0.002 TRP A 727 HIS 0.003 0.001 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (24864) covalent geometry : angle 0.56966 / 0.29 (34132) hydrogen bonds : bond 0.03264 / 2.31 ( 1788) hydrogen bonds : angle 4.05712 / 2.92 ( 5304) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 233 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 319 TYR cc_start: 0.7650 (t80) cc_final: 0.6813 (t80) REVERT: D 773 TRP cc_start: 0.7410 (t60) cc_final: 0.7090 (t60) REVERT: A 319 TYR cc_start: 0.7619 (t80) cc_final: 0.6020 (t80) REVERT: A 420 GLN cc_start: 0.9040 (mt0) cc_final: 0.8721 (mp10) REVERT: A 557 MET cc_start: 0.8076 (mtm) cc_final: 0.7792 (tmm) REVERT: B 253 TRP cc_start: 0.7068 (m100) cc_final: 0.6841 (m100) REVERT: B 319 TYR cc_start: 0.7873 (t80) cc_final: 0.6261 (t80) REVERT: B 557 MET cc_start: 0.8139 (mtp) cc_final: 0.7747 (tmm) REVERT: C 243 MET cc_start: 0.8207 (ppp) cc_final: 0.7611 (ppp) REVERT: C 319 TYR cc_start: 0.7608 (t80) cc_final: 0.6074 (t80) REVERT: C 420 GLN cc_start: 0.8910 (mt0) cc_final: 0.8574 (mp10) REVERT: C 557 MET cc_start: 0.8152 (mtm) cc_final: 0.7873 (tmm) REVERT: C 992 TRP cc_start: 0.9329 (t60) cc_final: 0.8889 (t60) outliers start: 52 outliers final: 43 residues processed: 263 average time/residue: 0.1276 time to fit residues: 59.4470 Evaluate side-chains 273 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 230 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 210 HIS Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 484 PHE Chi-restraints excluded: chain D residue 532 MET Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 742 PHE Chi-restraints excluded: chain D residue 823 CYS Chi-restraints excluded: chain D residue 973 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 484 PHE Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 822 THR Chi-restraints excluded: chain B residue 875 PHE Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 210 HIS Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 532 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain C residue 823 CYS Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 1076 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 305 optimal weight: 4.9990 chunk 355 optimal weight: 5.9990 chunk 196 optimal weight: 20.0000 chunk 208 optimal weight: 8.9990 chunk 206 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 271 optimal weight: 2.9990 chunk 345 optimal weight: 10.0000 chunk 167 optimal weight: 40.0000 chunk 5 optimal weight: 20.0000 chunk 23 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.116600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.083062 restraints weight = 90477.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.085020 restraints weight = 47833.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.086238 restraints weight = 33576.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.086906 restraints weight = 27480.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.087324 restraints weight = 24691.764| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24864 Z= 0.178 Angle : 0.605 12.123 34132 Z= 0.309 Chirality : 0.039 0.242 4132 Planarity : 0.005 0.092 4396 Dihedral : 4.085 21.144 3756 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.76 % Allowed : 21.24 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.18 (0.15), residues: 3528 helix: 1.74 (0.11), residues: 2480 sheet: -0.44 (0.41), residues: 152 loop : -1.80 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 242 TYR 0.020 0.001 TYR B 351 PHE 0.018 0.001 PHE C 873 TRP 0.019 0.002 TRP D 952 HIS 0.004 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 (24864) covalent geometry : angle 0.60482 / 0.31 (34132) hydrogen bonds : bond 0.03649 / 2.59 ( 1788) hydrogen bonds : angle 4.19952 / 3.03 ( 5304) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 228 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 319 TYR cc_start: 0.7634 (t80) cc_final: 0.6800 (t80) REVERT: D 532 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.7788 (tpp) REVERT: D 773 TRP cc_start: 0.7559 (t60) cc_final: 0.7140 (t60) REVERT: A 319 TYR cc_start: 0.7645 (t80) cc_final: 0.6043 (t80) REVERT: A 420 GLN cc_start: 0.9065 (mt0) cc_final: 0.8766 (mp10) REVERT: B 557 MET cc_start: 0.8169 (mtp) cc_final: 0.7782 (tmm) REVERT: C 243 MET cc_start: 0.8315 (ppp) cc_final: 0.7681 (ppp) REVERT: C 319 TYR cc_start: 0.7656 (t80) cc_final: 0.6111 (t80) REVERT: C 420 GLN cc_start: 0.8930 (mt0) cc_final: 0.8601 (mp10) REVERT: C 557 MET cc_start: 0.8189 (mtm) cc_final: 0.7882 (tmm) REVERT: C 992 TRP cc_start: 0.9311 (t60) cc_final: 0.8869 (t60) outliers start: 47 outliers final: 43 residues processed: 259 average time/residue: 0.1259 time to fit residues: 57.9330 Evaluate side-chains 270 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 226 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 210 HIS Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 484 PHE Chi-restraints excluded: chain D residue 532 MET Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 742 PHE Chi-restraints excluded: chain D residue 823 CYS Chi-restraints excluded: chain D residue 973 LEU Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 484 PHE Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 822 THR Chi-restraints excluded: chain B residue 875 PHE Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 210 HIS Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 532 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain C residue 823 CYS Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 1076 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 65 optimal weight: 5.9990 chunk 245 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 182 optimal weight: 50.0000 chunk 99 optimal weight: 30.0000 chunk 46 optimal weight: 9.9990 chunk 163 optimal weight: 10.0000 chunk 8 optimal weight: 0.0000 chunk 199 optimal weight: 0.2980 chunk 273 optimal weight: 50.0000 overall best weight: 3.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 998 HIS ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 GLN C 998 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.118811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.084862 restraints weight = 87967.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.086778 restraints weight = 47853.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.087914 restraints weight = 34208.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.088536 restraints weight = 28356.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.088806 restraints weight = 25629.870| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 24864 Z= 0.248 Angle : 0.663 12.284 34132 Z= 0.345 Chirality : 0.041 0.238 4132 Planarity : 0.005 0.091 4396 Dihedral : 4.358 20.371 3756 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.52 % Allowed : 20.60 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.79 (0.15), residues: 3528 helix: 1.45 (0.11), residues: 2496 sheet: -0.55 (0.41), residues: 148 loop : -2.00 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 541 TYR 0.020 0.002 TYR B 351 PHE 0.016 0.002 PHE C 873 TRP 0.017 0.002 TRP D 952 HIS 0.005 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.25 (24864) covalent geometry : angle 0.66277 / 0.34 (34132) hydrogen bonds : bond 0.04226 / 3.00 ( 1788) hydrogen bonds : angle 4.58289 / 3.30 ( 5304) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4477.00 seconds wall clock time: 77 minutes 32.49 seconds (4652.49 seconds total)