Starting phenix.real_space_refine on Sun Oct 12 13:07:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8slp_40579/10_2025/8slp_40579.cif Found real_map, /net/cci-nas-00/data/ceres_data/8slp_40579/10_2025/8slp_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8slp_40579/10_2025/8slp_40579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8slp_40579/10_2025/8slp_40579.map" model { file = "/net/cci-nas-00/data/ceres_data/8slp_40579/10_2025/8slp_40579.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8slp_40579/10_2025/8slp_40579.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/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, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: A, B, C Time building chain proxies: 6.91, per 1000 atoms: 0.28 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: 2.37 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 1.2 microseconds 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: 1.12 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: 4.94 Time building geometry restraints manager: 3.10 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: 0.05 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: 3.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 25.540 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 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 aren 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 covalent geometry : bond 0.00286 (24864) covalent geometry : angle 0.56448 (34132) hydrogen bonds : bond 0.14762 ( 1788) hydrogen bonds : angle 5.56520 ( 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 : 0.968 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 339 LYS cc_start: 0.8909 (tmtt) cc_final: 0.8705 (tmtt) REVERT: D 557 MET cc_start: 0.8090 (mtp) cc_final: 0.7774 (tmm) REVERT: D 719 LEU cc_start: 0.7888 (tt) cc_final: 0.7687 (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: 0.8843 (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 557 MET cc_start: 0.8102 (mtp) cc_final: 0.7877 (tmm) REVERT: B 970 MET cc_start: 0.8916 (ptm) cc_final: 0.8692 (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: 0.1740 time to fit residues: 86.1944 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 : 0.954 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: D 115 HIS D 467 HIS D 855 HIS D 951 ASN A 115 HIS A 467 HIS A 855 HIS A 951 ASN B 115 HIS B 467 HIS B 629 GLN B 855 HIS B 951 ASN C 115 HIS C 467 HIS C 629 GLN C 855 HIS C 951 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.112959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.078864 restraints weight = 91907.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.081038 restraints weight = 47405.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.082332 restraints weight = 32445.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.083086 restraints weight = 26116.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.083446 restraints weight = 23114.472| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1567 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 : 0.504 9.247 34132 Z= 0.263 Chirality : 0.036 0.139 4132 Planarity : 0.005 0.092 4396 Dihedral : 3.702 19.976 3756 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.12 % Allowed : 12.15 % 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 aren not related in a simple way. whole: 0.63 (0.14), residues: 3528 helix: 1.38 (0.10), residues: 2448 sheet: -0.93 (0.37), residues: 192 loop : -1.99 (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 0.027 0.001 TRP A 773 HIS 0.003 0.001 HIS C 123 Details of bonding type rmsd covalent geometry : bond 0.00215 (24864) covalent geometry : angle 0.50366 (34132) hydrogen bonds : bond 0.03237 ( 1788) hydrogen bonds : angle 3.93946 ( 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: 19 poor density : 249 time to evaluate : 1.180 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: 0.7583 (t80) cc_final: 0.6022 (t80) REVERT: D 321 PHE cc_start: 0.7054 (m-10) cc_final: 0.6645 (m-80) REVERT: D 420 GLN cc_start: 0.9234 (mt0) cc_final: 0.8934 (mt0) REVERT: D 539 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7854 (mtt) REVERT: D 557 MET cc_start: 0.8392 (mtp) cc_final: 0.7908 (tmm) REVERT: A 319 TYR cc_start: 0.7599 (t80) cc_final: 0.6150 (t80) REVERT: A 420 GLN cc_start: 0.9237 (mt0) cc_final: 0.8857 (mt0) REVERT: A 539 MET cc_start: 0.8235 (mmt) cc_final: 0.7912 (mpp) REVERT: A 557 MET cc_start: 0.8292 (mtp) cc_final: 0.8040 (tmm) REVERT: A 598 LEU cc_start: 0.9091 (tp) cc_final: 0.8733 (tt) REVERT: A 719 LEU cc_start: 0.7895 (tt) cc_final: 0.7692 (mm) REVERT: A 773 TRP cc_start: 0.6596 (t60) cc_final: 0.6199 (t60) REVERT: A 970 MET cc_start: 0.9059 (ptm) cc_final: 0.8731 (mpp) REVERT: B 319 TYR cc_start: 0.7386 (t80) cc_final: 0.5971 (t80) REVERT: B 420 GLN cc_start: 0.9290 (mt0) cc_final: 0.9042 (mt0) REVERT: B 539 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7595 (mtt) REVERT: B 557 MET cc_start: 0.8326 (mtp) cc_final: 0.8024 (tmm) REVERT: C 319 TYR cc_start: 0.7562 (t80) cc_final: 0.6173 (t80) REVERT: C 321 PHE cc_start: 0.7067 (m-10) cc_final: 0.6778 (m-80) REVERT: C 354 GLU cc_start: 0.8283 (mt-10) cc_final: 0.8068 (mt-10) REVERT: C 539 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7721 (mtm) REVERT: C 737 ASN cc_start: 0.8106 (m110) cc_final: 0.7824 (t0) outliers start: 19 outliers final: 10 residues processed: 257 average time/residue: 0.1358 time to fit residues: 59.9220 Evaluate side-chains 237 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 224 time to evaluate : 0.878 ------------------------------------------------------------------------------- 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 329 LEU 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: 5.9990 chunk 343 optimal weight: 0.8980 chunk 11 optimal weight: 20.0000 chunk 1 optimal weight: 40.0000 chunk 61 optimal weight: 10.0000 chunk 194 optimal weight: 50.0000 chunk 161 optimal weight: 7.9990 chunk 180 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 328 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3909 r_free = 0.3909 target = 0.109490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.075181 restraints weight = 92588.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.077213 restraints weight = 48260.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.078400 restraints weight = 33408.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.078990 restraints weight = 27186.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.079443 restraints weight = 24383.130| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 24864 Z= 0.265 Angle : 0.644 8.262 34132 Z= 0.339 Chirality : 0.040 0.145 4132 Planarity : 0.005 0.091 4396 Dihedral : 4.219 19.670 3756 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.52 % Allowed : 14.96 % Favored : 82.51 % 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 aren not related in a simple way. whole: 0.72 (0.14), residues: 3528 helix: 1.37 (0.10), residues: 2488 sheet: -0.64 (0.40), residues: 152 loop : -1.88 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 443 TYR 0.014 0.002 TYR A 422 PHE 0.031 0.002 PHE A 744 TRP 0.013 0.002 TRP D 773 HIS 0.005 0.001 HIS C 423 Details of bonding type rmsd covalent geometry : bond 0.00563 (24864) covalent geometry : angle 0.64397 (34132) hydrogen bonds : bond 0.04381 ( 1788) hydrogen bonds : angle 4.52683 ( 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 262 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 219 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 319 TYR cc_start: 0.7768 (t80) cc_final: 0.7214 (t80) REVERT: D 420 GLN cc_start: 0.9195 (mt0) cc_final: 0.8931 (mt0) REVERT: A 319 TYR cc_start: 0.7638 (t80) cc_final: 0.6089 (t80) REVERT: A 409 MET cc_start: 0.8825 (mmp) cc_final: 0.8623 (mmm) REVERT: A 420 GLN cc_start: 0.9228 (mt0) cc_final: 0.8969 (mt0) REVERT: A 557 MET cc_start: 0.8431 (mtp) cc_final: 0.7820 (tmm) REVERT: B 319 TYR cc_start: 0.7672 (t80) cc_final: 0.6126 (t80) REVERT: B 420 GLN cc_start: 0.9243 (mt0) cc_final: 0.8993 (mt0) REVERT: B 557 MET cc_start: 0.8319 (mtp) cc_final: 0.7811 (tmm) outliers start: 43 outliers final: 28 residues processed: 238 average time/residue: 0.1322 time to fit residues: 55.1004 Evaluate side-chains 244 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 216 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 532 MET 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 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 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: 0.9980 chunk 71 optimal weight: 9.9990 chunk 232 optimal weight: 0.9990 chunk 164 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 35 optimal weight: 0.4980 chunk 255 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 137 optimal weight: 10.0000 chunk 76 optimal weight: 0.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.111150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.076699 restraints weight = 92073.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.078802 restraints weight = 47776.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.080041 restraints weight = 32936.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.080756 restraints weight = 26693.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.081030 restraints weight = 23737.207| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24864 Z= 0.137 Angle : 0.520 8.180 34132 Z= 0.270 Chirality : 0.037 0.134 4132 Planarity : 0.005 0.095 4396 Dihedral : 3.867 20.853 3756 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.29 % Allowed : 16.43 % Favored : 80.28 % 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 aren not related in a simple way. whole: 1.37 (0.15), residues: 3528 helix: 1.85 (0.11), residues: 2468 sheet: -0.11 (0.40), residues: 152 loop : -1.62 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 363 TYR 0.008 0.001 TYR B 997 PHE 0.017 0.001 PHE D 873 TRP 0.017 0.001 TRP C 727 HIS 0.003 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00291 (24864) covalent geometry : angle 0.52037 (34132) hydrogen bonds : bond 0.03265 ( 1788) hydrogen bonds : angle 3.91353 ( 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 282 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 226 time to evaluate : 0.941 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: 0.7538 (t80) cc_final: 0.6856 (t80) REVERT: D 409 MET cc_start: 0.8779 (mmp) cc_final: 0.8560 (mmp) REVERT: A 409 MET cc_start: 0.8737 (mmp) cc_final: 0.8401 (mmm) REVERT: A 420 GLN cc_start: 0.9155 (mt0) cc_final: 0.8877 (mt0) REVERT: A 557 MET cc_start: 0.8379 (mtp) cc_final: 0.7895 (tmm) REVERT: B 319 TYR cc_start: 0.7778 (t80) cc_final: 0.6274 (t80) REVERT: B 420 GLN cc_start: 0.9152 (mt0) cc_final: 0.8907 (mt0) REVERT: B 557 MET cc_start: 0.8319 (mtp) cc_final: 0.7866 (tmm) REVERT: B 970 MET cc_start: 0.8899 (ppp) cc_final: 0.8612 (mpp) REVERT: C 992 TRP cc_start: 0.9334 (t60) cc_final: 0.8807 (t60) outliers start: 56 outliers final: 37 residues processed: 261 average time/residue: 0.1294 time to fit residues: 59.4874 Evaluate side-chains 259 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 222 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 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 D residue 973 LEU 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 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 386 VAL 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 B residue 973 LEU 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 316 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 532 MET 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: 10.0000 chunk 321 optimal weight: 2.9990 chunk 198 optimal weight: 8.9990 chunk 347 optimal weight: 0.0170 chunk 199 optimal weight: 20.0000 chunk 312 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 176 optimal weight: 40.0000 chunk 221 optimal weight: 5.9990 chunk 202 optimal weight: 20.0000 chunk 331 optimal weight: 6.9990 overall best weight: 4.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 998 HIS ** C 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.108166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.073914 restraints weight = 91956.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.075912 restraints weight = 48051.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.077094 restraints weight = 33309.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.077780 restraints weight = 27052.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.078095 restraints weight = 24112.823| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 24864 Z= 0.296 Angle : 0.683 8.521 34132 Z= 0.361 Chirality : 0.041 0.141 4132 Planarity : 0.006 0.094 4396 Dihedral : 4.482 18.885 3756 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 4.58 % Allowed : 16.96 % Favored : 78.46 % 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 aren not related in a simple way. whole: 0.66 (0.14), residues: 3528 helix: 1.25 (0.10), residues: 2512 sheet: 0.58 (0.43), residues: 124 loop : -1.94 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 541 TYR 0.016 0.002 TYR C 422 PHE 0.015 0.002 PHE C 583 TRP 0.014 0.002 TRP D 773 HIS 0.007 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00630 (24864) covalent geometry : angle 0.68303 (34132) hydrogen bonds : bond 0.04627 ( 1788) hydrogen bonds : angle 4.70959 ( 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 294 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 216 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 420 GLN cc_start: 0.9140 (mt0) cc_final: 0.8892 (mt0) REVERT: D 532 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8243 (tpp) REVERT: D 970 MET cc_start: 0.8802 (ptm) cc_final: 0.8525 (mpp) REVERT: A 319 TYR cc_start: 0.7535 (t80) cc_final: 0.5964 (t80) REVERT: A 409 MET cc_start: 0.8825 (mmp) cc_final: 0.8466 (mmm) REVERT: A 420 GLN cc_start: 0.9141 (mt0) cc_final: 0.8916 (mt0) REVERT: A 532 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8228 (tpp) REVERT: A 557 MET cc_start: 0.8440 (mtp) cc_final: 0.7801 (tmm) REVERT: B 319 TYR cc_start: 0.7688 (t80) cc_final: 0.6054 (t80) REVERT: B 420 GLN cc_start: 0.9153 (mt0) cc_final: 0.8918 (mt0) REVERT: B 532 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8296 (tpp) REVERT: B 539 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7989 (mtt) REVERT: B 557 MET cc_start: 0.8309 (mtp) cc_final: 0.7753 (tmm) REVERT: C 319 TYR cc_start: 0.7348 (t80) cc_final: 0.5814 (t80) REVERT: C 354 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7946 (mt-10) REVERT: C 532 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8197 (tpp) outliers start: 78 outliers final: 56 residues processed: 264 average time/residue: 0.1335 time to fit residues: 61.9891 Evaluate side-chains 274 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 213 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 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 829 VAL 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 329 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 357 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 829 VAL 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 316 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 332 VAL 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 95 optimal weight: 30.0000 chunk 118 optimal weight: 8.9990 chunk 217 optimal weight: 0.8980 chunk 6 optimal weight: 30.0000 chunk 80 optimal weight: 10.0000 chunk 213 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 75 optimal weight: 40.0000 chunk 28 optimal weight: 2.9990 chunk 278 optimal weight: 20.0000 chunk 73 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.118181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.084502 restraints weight = 89956.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.087288 restraints weight = 51937.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.087596 restraints weight = 30296.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.087579 restraints weight = 31869.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.087633 restraints weight = 27813.049| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3350 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= 0.219 Angle : 0.599 9.665 34132 Z= 0.316 Chirality : 0.039 0.139 4132 Planarity : 0.005 0.096 4396 Dihedral : 4.195 20.432 3756 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.93 % Allowed : 18.08 % Favored : 77.99 % 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 aren not related in a simple way. whole: 0.91 (0.15), residues: 3528 helix: 1.47 (0.11), residues: 2516 sheet: -0.51 (0.35), residues: 208 loop : -1.88 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 363 TYR 0.013 0.001 TYR D 319 PHE 0.014 0.002 PHE D 873 TRP 0.016 0.002 TRP A 952 HIS 0.005 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00468 (24864) covalent geometry : angle 0.59950 (34132) hydrogen bonds : bond 0.03796 ( 1788) hydrogen bonds : angle 4.30825 ( 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 292 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 225 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 319 TYR cc_start: 0.7680 (t80) cc_final: 0.6908 (t80) REVERT: D 420 GLN cc_start: 0.9007 (mt0) cc_final: 0.8776 (mt0) REVERT: D 532 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.7849 (tpp) REVERT: D 773 TRP cc_start: 0.7532 (t60) cc_final: 0.7082 (t60) REVERT: A 319 TYR cc_start: 0.7613 (t80) cc_final: 0.5953 (t80) REVERT: A 409 MET cc_start: 0.8600 (mmp) cc_final: 0.8273 (mmm) REVERT: A 420 GLN cc_start: 0.9045 (mt0) cc_final: 0.8780 (mt0) REVERT: A 557 MET cc_start: 0.8284 (mtp) cc_final: 0.7816 (tmm) REVERT: B 319 TYR cc_start: 0.7720 (t80) cc_final: 0.6044 (t80) REVERT: B 557 MET cc_start: 0.8168 (mtp) cc_final: 0.7744 (tmm) REVERT: C 243 MET cc_start: 0.7641 (ppp) cc_final: 0.7095 (ppp) REVERT: C 319 TYR cc_start: 0.7496 (t80) cc_final: 0.5926 (t80) REVERT: C 409 MET cc_start: 0.8742 (mmm) cc_final: 0.8205 (mmm) outliers start: 67 outliers final: 56 residues processed: 266 average time/residue: 0.1332 time to fit residues: 62.5422 Evaluate side-chains 279 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 222 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 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 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 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 875 PHE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain B residue 210 HIS 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 357 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 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 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 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 1076 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 328 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 chunk 157 optimal weight: 10.0000 chunk 156 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 300 optimal weight: 0.9990 chunk 169 optimal weight: 0.9980 chunk 298 optimal weight: 5.9990 chunk 171 optimal weight: 8.9990 chunk 362 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.123140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.090391 restraints weight = 92423.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.092443 restraints weight = 49132.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.093461 restraints weight = 34340.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.094226 restraints weight = 28283.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.094549 restraints weight = 25225.689| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 24864 Z= 0.223 Angle : 0.620 10.529 34132 Z= 0.325 Chirality : 0.040 0.176 4132 Planarity : 0.005 0.094 4396 Dihedral : 4.240 19.720 3756 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.93 % Allowed : 19.07 % Favored : 77.00 % 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 aren not related in a simple way. whole: 0.93 (0.15), residues: 3528 helix: 1.53 (0.10), residues: 2480 sheet: -0.12 (0.40), residues: 152 loop : -1.87 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 541 TYR 0.012 0.001 TYR B 997 PHE 0.014 0.002 PHE D 873 TRP 0.016 0.002 TRP A 253 HIS 0.005 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00476 (24864) covalent geometry : angle 0.61963 (34132) hydrogen bonds : bond 0.04019 ( 1788) hydrogen bonds : angle 4.40261 ( 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: 67 poor density : 228 time to evaluate : 1.008 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: 0.7464 (t80) cc_final: 0.6693 (t80) REVERT: D 532 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.7927 (tpp) REVERT: D 773 TRP cc_start: 0.7526 (t60) cc_final: 0.7084 (t60) REVERT: A 319 TYR cc_start: 0.7439 (t80) cc_final: 0.5868 (t80) REVERT: A 409 MET cc_start: 0.8637 (mmp) cc_final: 0.8304 (mmm) REVERT: A 557 MET cc_start: 0.8300 (mtp) cc_final: 0.7709 (tmm) REVERT: B 319 TYR cc_start: 0.7718 (t80) cc_final: 0.6069 (t80) REVERT: B 557 MET cc_start: 0.8265 (mtp) cc_final: 0.7850 (tmm) REVERT: C 243 MET cc_start: 0.7681 (ppp) cc_final: 0.7466 (ppp) REVERT: C 319 TYR cc_start: 0.7352 (t80) cc_final: 0.5861 (t80) REVERT: C 409 MET cc_start: 0.8667 (mmm) cc_final: 0.8190 (mmm) outliers start: 67 outliers final: 54 residues processed: 267 average time/residue: 0.1292 time to fit residues: 61.2347 Evaluate side-chains 281 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 226 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 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 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 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 973 LEU Chi-restraints excluded: chain A residue 1076 VAL 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 357 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 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 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: 0.9980 chunk 11 optimal weight: 40.0000 chunk 183 optimal weight: 20.0000 chunk 37 optimal weight: 9.9990 chunk 176 optimal weight: 6.9990 chunk 328 optimal weight: 10.0000 chunk 202 optimal weight: 0.9990 chunk 180 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 201 optimal weight: 3.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 998 HIS C 998 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.122466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.090167 restraints weight = 92598.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.092144 restraints weight = 48492.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.093326 restraints weight = 33827.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.094033 restraints weight = 27508.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.094336 restraints weight = 24397.306| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 24864 Z= 0.272 Angle : 0.672 13.355 34132 Z= 0.355 Chirality : 0.041 0.233 4132 Planarity : 0.005 0.095 4396 Dihedral : 4.451 20.104 3756 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 4.28 % Allowed : 19.37 % 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 aren not related in a simple way. whole: 0.51 (0.14), residues: 3528 helix: 1.22 (0.10), residues: 2500 sheet: -0.38 (0.40), residues: 152 loop : -2.07 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 541 TYR 0.016 0.002 TYR B 351 PHE 0.015 0.002 PHE C 583 TRP 0.015 0.002 TRP C 952 HIS 0.006 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00577 (24864) covalent geometry : angle 0.67234 (34132) hydrogen bonds : bond 0.04362 ( 1788) hydrogen bonds : angle 4.71570 ( 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 296 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 223 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 319 TYR cc_start: 0.7602 (t80) cc_final: 0.6811 (t80) REVERT: D 420 GLN cc_start: 0.9004 (mt0) cc_final: 0.8773 (mt0) REVERT: D 532 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8022 (tpp) REVERT: A 103 ILE cc_start: 0.8653 (mm) cc_final: 0.8324 (mp) REVERT: B 532 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8086 (tpp) REVERT: B 557 MET cc_start: 0.8175 (mtp) cc_final: 0.7735 (tmm) REVERT: C 253 TRP cc_start: 0.7237 (m100) cc_final: 0.6991 (m100) REVERT: C 409 MET cc_start: 0.8673 (mmm) cc_final: 0.8466 (mmp) REVERT: C 532 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8038 (tpp) outliers start: 73 outliers final: 58 residues processed: 268 average time/residue: 0.1323 time to fit residues: 62.4117 Evaluate side-chains 279 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 218 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 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 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 732 THR Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain A residue 823 CYS Chi-restraints excluded: chain A residue 875 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 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 357 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 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 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 1076 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 38 optimal weight: 2.9990 chunk 245 optimal weight: 10.0000 chunk 336 optimal weight: 9.9990 chunk 231 optimal weight: 1.9990 chunk 201 optimal weight: 8.9990 chunk 194 optimal weight: 50.0000 chunk 28 optimal weight: 3.9990 chunk 316 optimal weight: 0.8980 chunk 242 optimal weight: 9.9990 chunk 264 optimal weight: 0.9990 chunk 109 optimal weight: 10.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.124843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.092601 restraints weight = 92985.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.094652 restraints weight = 48574.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.095914 restraints weight = 33551.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.096591 restraints weight = 26974.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.096915 restraints weight = 24023.037| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24864 Z= 0.155 Angle : 0.586 13.242 34132 Z= 0.299 Chirality : 0.038 0.201 4132 Planarity : 0.005 0.094 4396 Dihedral : 4.080 20.950 3756 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.52 % Allowed : 20.01 % Favored : 76.47 % 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 aren not related in a simple way. whole: 1.15 (0.15), residues: 3528 helix: 1.72 (0.11), residues: 2484 sheet: -0.30 (0.41), residues: 152 loop : -1.82 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 417 TYR 0.021 0.001 TYR B 351 PHE 0.016 0.001 PHE D 873 TRP 0.018 0.002 TRP C 952 HIS 0.003 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00334 (24864) covalent geometry : angle 0.58556 (34132) hydrogen bonds : bond 0.03470 ( 1788) hydrogen bonds : angle 4.14802 ( 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 289 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 229 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 319 TYR cc_start: 0.7569 (t80) cc_final: 0.6706 (t80) REVERT: D 420 GLN cc_start: 0.8939 (mt0) cc_final: 0.8724 (mt0) REVERT: D 773 TRP cc_start: 0.7458 (t60) cc_final: 0.7037 (t60) REVERT: A 103 ILE cc_start: 0.8654 (mm) cc_final: 0.8323 (mp) REVERT: A 319 TYR cc_start: 0.7547 (t80) cc_final: 0.5970 (t80) REVERT: A 420 GLN cc_start: 0.8989 (mt0) cc_final: 0.8681 (mp10) REVERT: B 319 TYR cc_start: 0.7829 (t80) cc_final: 0.6215 (t80) REVERT: B 557 MET cc_start: 0.8157 (mtp) cc_final: 0.7757 (tmm) REVERT: C 243 MET cc_start: 0.8218 (ppp) cc_final: 0.7448 (ppp) REVERT: C 319 TYR cc_start: 0.7493 (t80) cc_final: 0.5973 (t80) REVERT: C 409 MET cc_start: 0.8576 (mmm) cc_final: 0.8072 (mmm) REVERT: C 773 TRP cc_start: 0.7477 (t60) cc_final: 0.6995 (t60) REVERT: C 992 TRP cc_start: 0.9333 (t60) cc_final: 0.8829 (t60) outliers start: 60 outliers final: 55 residues processed: 266 average time/residue: 0.1273 time to fit residues: 60.2460 Evaluate side-chains 280 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 225 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 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 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 732 THR Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain A residue 823 CYS Chi-restraints excluded: chain A residue 875 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 270 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 357 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 745 LEU Chi-restraints excluded: chain B residue 822 THR Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 1076 VAL 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 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 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: 0.9980 chunk 206 optimal weight: 8.9990 chunk 142 optimal weight: 5.9990 chunk 271 optimal weight: 2.9990 chunk 345 optimal weight: 10.0000 chunk 167 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 998 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.124565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.092454 restraints weight = 93546.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.094529 restraints weight = 48355.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.095774 restraints weight = 32988.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.096541 restraints weight = 26330.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.096865 restraints weight = 23139.228| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 24864 Z= 0.269 Angle : 0.680 12.370 34132 Z= 0.356 Chirality : 0.041 0.190 4132 Planarity : 0.005 0.090 4396 Dihedral : 4.381 19.919 3756 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.87 % Allowed : 19.95 % 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 aren not related in a simple way. whole: 0.70 (0.15), residues: 3528 helix: 1.40 (0.11), residues: 2476 sheet: -0.58 (0.41), residues: 152 loop : -1.99 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 541 TYR 0.021 0.002 TYR B 351 PHE 0.021 0.002 PHE C 877 TRP 0.017 0.002 TRP D 952 HIS 0.006 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00570 (24864) covalent geometry : angle 0.67989 (34132) hydrogen bonds : bond 0.04341 ( 1788) hydrogen bonds : angle 4.66551 ( 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 289 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 223 time to evaluate : 0.812 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: 0.7579 (t80) cc_final: 0.6759 (t80) REVERT: D 532 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8143 (tpp) REVERT: A 420 GLN cc_start: 0.9045 (mt0) cc_final: 0.8736 (mp10) REVERT: B 532 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8212 (tpp) REVERT: B 557 MET cc_start: 0.8196 (mtp) cc_final: 0.7680 (tmm) REVERT: C 243 MET cc_start: 0.8324 (ppp) cc_final: 0.7696 (ppp) REVERT: C 253 TRP cc_start: 0.7038 (m100) cc_final: 0.6719 (m100) REVERT: C 319 TYR cc_start: 0.7578 (t80) cc_final: 0.5988 (t80) REVERT: C 532 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8081 (tpp) outliers start: 66 outliers final: 57 residues processed: 267 average time/residue: 0.1290 time to fit residues: 60.8517 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 : 0.952 ------------------------------------------------------------------------------- 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 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 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 732 THR Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain A residue 823 CYS Chi-restraints excluded: chain A residue 875 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 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 357 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 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 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 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: 6.9990 chunk 245 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 182 optimal weight: 50.0000 chunk 99 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 chunk 163 optimal weight: 10.0000 chunk 8 optimal weight: 30.0000 chunk 199 optimal weight: 30.0000 chunk 273 optimal weight: 50.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 998 HIS A 998 HIS B 629 GLN B 998 HIS ** C 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 998 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.122812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.090033 restraints weight = 95591.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.091954 restraints weight = 50567.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.093156 restraints weight = 35090.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.093675 restraints weight = 28458.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.094237 restraints weight = 25503.964| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.084 24864 Z= 0.451 Angle : 0.878 12.443 34132 Z= 0.467 Chirality : 0.047 0.236 4132 Planarity : 0.006 0.095 4396 Dihedral : 5.208 23.727 3756 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.99 % Allowed : 20.19 % Favored : 75.82 % 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 aren not related in a simple way. whole: -0.50 (0.14), residues: 3528 helix: 0.48 (0.10), residues: 2456 sheet: -0.95 (0.40), residues: 148 loop : -2.31 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 417 TYR 0.022 0.003 TYR B 351 PHE 0.020 0.003 PHE C 748 TRP 0.021 0.003 TRP A 253 HIS 0.011 0.002 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00947 (24864) covalent geometry : angle 0.87835 (34132) hydrogen bonds : bond 0.05593 ( 1788) hydrogen bonds : angle 5.68280 ( 5304) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4690.94 seconds wall clock time: 81 minutes 10.09 seconds (4870.09 seconds total)