Starting phenix.real_space_refine on Sat Jun 21 05:26:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8slp_40579/06_2025/8slp_40579.cif Found real_map, /net/cci-nas-00/data/ceres_data/8slp_40579/06_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_40579/06_2025/8slp_40579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8slp_40579/06_2025/8slp_40579.map" model { file = "/net/cci-nas-00/data/ceres_data/8slp_40579/06_2025/8slp_40579.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8slp_40579/06_2025/8slp_40579.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24356 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" 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: {'GLN:plan1': 23, 'ASP:plan': 31, 'TYR:plan': 9, 'ASN:plan1': 11, 'TRP:plan': 3, 'HIS:plan': 11, 'PHE:plan': 21, 'GLU:plan': 37, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 762 Chain: "A" 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: C, B, D Time building chain proxies: 15.75, per 1000 atoms: 0.65 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: 6.98 Conformation dependent library (CDL) restraints added in 3.5 seconds 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6976 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 16 sheets defined 71.5% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.17 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: 10.07 Time building geometry restraints manager: 8.17 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: 0.20 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.020 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 59.530 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.140 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.016 0.001 TRP D 727 HIS 0.002 0.001 HIS A 612 PHE 0.014 0.001 PHE B 53 TYR 0.011 0.001 TYR B 535 ARG 0.002 0.000 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.14762 ( 1788) hydrogen bonds : angle 5.56520 ( 5304) covalent geometry : bond 0.00286 (24864) covalent geometry : angle 0.56448 (34132) *********************** 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 : 2.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 339 LYS cc_start: 0.8909 (tmtt) cc_final: 0.8705 (tmtt) REVERT: D 420 GLN cc_start: 0.9077 (mt0) cc_final: 0.8841 (mt0) REVERT: D 557 MET cc_start: 0.8090 (mtp) cc_final: 0.7773 (tmm) REVERT: D 719 LEU cc_start: 0.7888 (tt) cc_final: 0.7686 (mm) REVERT: D 773 TRP cc_start: 0.7317 (t60) cc_final: 0.7026 (t60) REVERT: D 970 MET cc_start: 0.8963 (ptm) cc_final: 0.8735 (mpp) REVERT: A 253 TRP cc_start: 0.7241 (m100) cc_final: 0.7008 (m100) REVERT: A 339 LYS cc_start: 0.8935 (tmtt) cc_final: 0.8728 (tmtt) REVERT: A 420 GLN cc_start: 0.9079 (mt0) cc_final: 0.8842 (mt0) REVERT: A 557 MET cc_start: 0.8082 (mtp) cc_final: 0.7851 (tmm) REVERT: A 719 LEU cc_start: 0.7934 (tt) cc_final: 0.7687 (mm) REVERT: A 970 MET cc_start: 0.8974 (ptm) cc_final: 0.8707 (mpp) REVERT: B 420 GLN cc_start: 0.9130 (mt0) cc_final: 0.8859 (mt0) REVERT: B 557 MET cc_start: 0.8102 (mtp) cc_final: 0.7876 (tmm) REVERT: B 970 MET cc_start: 0.8916 (ptm) cc_final: 0.8691 (mpp) REVERT: C 339 LYS cc_start: 0.8898 (tmtt) cc_final: 0.8690 (tmtt) REVERT: C 401 LEU cc_start: 0.9413 (tp) cc_final: 0.9202 (tp) REVERT: C 737 ASN cc_start: 0.8219 (m110) cc_final: 0.7981 (t0) REVERT: C 970 MET cc_start: 0.8892 (ptm) cc_final: 0.8679 (mpp) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.3632 time to fit residues: 180.8125 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 : 4.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 307 optimal weight: 4.9990 chunk 275 optimal weight: 8.9990 chunk 153 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 186 optimal weight: 40.0000 chunk 147 optimal weight: 10.0000 chunk 285 optimal weight: 50.0000 chunk 110 optimal weight: 20.0000 chunk 173 optimal weight: 6.9990 chunk 212 optimal weight: 5.9990 chunk 330 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 D 998 HIS A 115 HIS A 467 HIS A 855 HIS A 951 ASN B 115 HIS B 467 HIS B 855 HIS B 951 ASN C 115 HIS ** C 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 467 HIS C 737 ASN C 855 HIS C 951 ASN C 998 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.106982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.072619 restraints weight = 93853.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.074570 restraints weight = 49527.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.075707 restraints weight = 34729.110| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.086 24864 Z= 0.435 Angle : 0.854 10.448 34132 Z= 0.452 Chirality : 0.046 0.162 4132 Planarity : 0.007 0.097 4396 Dihedral : 5.012 22.306 3756 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.46 % Allowed : 16.67 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.13), residues: 3528 helix: 0.05 (0.10), residues: 2496 sheet: -0.48 (0.44), residues: 124 loop : -2.43 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 102 HIS 0.008 0.002 HIS C 423 PHE 0.024 0.003 PHE B 412 TYR 0.021 0.002 TYR B 422 ARG 0.006 0.001 ARG D 443 Details of bonding type rmsd hydrogen bonds : bond 0.05529 ( 1788) hydrogen bonds : angle 5.56917 ( 5304) covalent geometry : bond 0.00911 (24864) covalent geometry : angle 0.85356 (34132) *********************** 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 275 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 216 time to evaluate : 2.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 319 TYR cc_start: 0.7722 (t80) cc_final: 0.7175 (t80) REVERT: D 420 GLN cc_start: 0.9214 (mt0) cc_final: 0.8941 (mt0) REVERT: D 532 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8418 (tpp) REVERT: D 539 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8293 (mtt) REVERT: A 253 TRP cc_start: 0.7417 (m100) cc_final: 0.7073 (m100) REVERT: A 319 TYR cc_start: 0.7830 (t80) cc_final: 0.6155 (t80) REVERT: A 420 GLN cc_start: 0.9219 (mt0) cc_final: 0.8933 (mt0) REVERT: A 532 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8530 (tpp) REVERT: A 557 MET cc_start: 0.8468 (mtp) cc_final: 0.7848 (tmm) REVERT: B 319 TYR cc_start: 0.7609 (t80) cc_final: 0.5958 (t80) REVERT: B 354 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8076 (mt-10) REVERT: B 420 GLN cc_start: 0.9229 (mt0) cc_final: 0.8926 (mt0) REVERT: B 532 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8470 (tpp) REVERT: B 539 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8212 (mtt) REVERT: B 557 MET cc_start: 0.8403 (mtp) cc_final: 0.7827 (tmm) REVERT: C 319 TYR cc_start: 0.7634 (t80) cc_final: 0.6064 (t80) REVERT: C 539 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8245 (mtt) outliers start: 59 outliers final: 39 residues processed: 248 average time/residue: 0.2836 time to fit residues: 121.3272 Evaluate side-chains 249 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 204 time to evaluate : 2.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 532 MET Chi-restraints excluded: chain D residue 539 MET Chi-restraints excluded: chain D residue 628 VAL 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 A residue 211 ILE 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 338 VAL Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain A residue 823 CYS Chi-restraints excluded: chain A residue 873 PHE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain B residue 211 ILE 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 338 VAL Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 539 MET Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 823 CYS Chi-restraints excluded: chain B residue 873 PHE Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 532 MET Chi-restraints excluded: chain C residue 539 MET Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain C residue 750 TYR Chi-restraints excluded: chain C residue 823 CYS Chi-restraints excluded: chain C residue 876 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 150 optimal weight: 0.7980 chunk 199 optimal weight: 5.9990 chunk 290 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 218 optimal weight: 1.9990 chunk 227 optimal weight: 0.7980 chunk 321 optimal weight: 0.7980 chunk 300 optimal weight: 0.9980 chunk 344 optimal weight: 0.0010 chunk 68 optimal weight: 5.9990 chunk 279 optimal weight: 20.0000 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 629 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.111456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.077256 restraints weight = 91394.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.079378 restraints weight = 47170.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.080634 restraints weight = 32496.660| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2456 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= 0.106 Angle : 0.527 8.577 34132 Z= 0.273 Chirality : 0.037 0.134 4132 Planarity : 0.005 0.096 4396 Dihedral : 4.059 20.640 3756 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.70 % Allowed : 18.02 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.14), residues: 3528 helix: 1.43 (0.11), residues: 2468 sheet: -0.80 (0.39), residues: 152 loop : -1.82 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 727 HIS 0.002 0.000 HIS C 612 PHE 0.016 0.001 PHE D 873 TYR 0.017 0.001 TYR A 660 ARG 0.004 0.000 ARG A 443 Details of bonding type rmsd hydrogen bonds : bond 0.03348 ( 1788) hydrogen bonds : angle 4.04116 ( 5304) covalent geometry : bond 0.00216 (24864) covalent geometry : angle 0.52743 (34132) *********************** 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 277 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 231 time to evaluate : 2.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 319 TYR cc_start: 0.7658 (t80) cc_final: 0.6994 (t80) REVERT: D 420 GLN cc_start: 0.9071 (mt0) cc_final: 0.8807 (mt0) REVERT: D 539 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.7959 (mtt) REVERT: D 557 MET cc_start: 0.8304 (mtm) cc_final: 0.7888 (tmm) REVERT: A 253 TRP cc_start: 0.7217 (m100) cc_final: 0.6907 (m100) REVERT: A 319 TYR cc_start: 0.7803 (t80) cc_final: 0.6171 (t80) REVERT: A 532 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8123 (tpp) REVERT: A 539 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8182 (mtm) REVERT: A 557 MET cc_start: 0.8390 (mtp) cc_final: 0.7937 (tmm) REVERT: B 319 TYR cc_start: 0.7680 (t80) cc_final: 0.6149 (t80) REVERT: B 354 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7926 (mt-10) REVERT: B 532 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8042 (tpp) REVERT: B 539 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.7970 (mtt) REVERT: B 557 MET cc_start: 0.8287 (mtp) cc_final: 0.7832 (tmm) REVERT: C 319 TYR cc_start: 0.7673 (t80) cc_final: 0.6136 (t80) REVERT: C 539 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.7807 (mtt) REVERT: C 773 TRP cc_start: 0.7378 (t60) cc_final: 0.6957 (t60) REVERT: C 970 MET cc_start: 0.8994 (ppp) cc_final: 0.8577 (mpp) outliers start: 46 outliers final: 26 residues processed: 254 average time/residue: 0.2830 time to fit residues: 123.7351 Evaluate side-chains 254 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 222 time to evaluate : 2.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 532 MET Chi-restraints excluded: chain D residue 539 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 A residue 40 PHE 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 539 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 532 MET Chi-restraints excluded: chain B residue 539 MET 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 211 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 532 MET Chi-restraints excluded: chain C residue 539 MET Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain C residue 823 CYS Chi-restraints excluded: chain C residue 973 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 178 optimal weight: 0.6980 chunk 253 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 346 optimal weight: 10.0000 chunk 274 optimal weight: 30.0000 chunk 142 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 165 optimal weight: 20.0000 chunk 205 optimal weight: 7.9990 chunk 184 optimal weight: 10.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.109679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.075407 restraints weight = 92318.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.077455 restraints weight = 48035.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.078654 restraints weight = 33220.237| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24864 Z= 0.187 Angle : 0.578 9.628 34132 Z= 0.300 Chirality : 0.038 0.140 4132 Planarity : 0.005 0.092 4396 Dihedral : 4.060 20.133 3756 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.34 % Allowed : 17.31 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.15), residues: 3528 helix: 1.55 (0.11), residues: 2488 sheet: -0.47 (0.39), residues: 152 loop : -1.85 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 727 HIS 0.004 0.001 HIS B 301 PHE 0.014 0.001 PHE D 873 TYR 0.011 0.001 TYR B 997 ARG 0.002 0.000 ARG C 346 Details of bonding type rmsd hydrogen bonds : bond 0.03780 ( 1788) hydrogen bonds : angle 4.20420 ( 5304) covalent geometry : bond 0.00402 (24864) covalent geometry : angle 0.57771 (34132) *********************** 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 300 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 226 time to evaluate : 2.556 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 539 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8154 (mtt) REVERT: A 319 TYR cc_start: 0.7804 (t80) cc_final: 0.6140 (t80) REVERT: A 557 MET cc_start: 0.8444 (mtp) cc_final: 0.7782 (tmm) REVERT: B 319 TYR cc_start: 0.7611 (t80) cc_final: 0.5995 (t80) REVERT: B 409 MET cc_start: 0.8914 (mmm) cc_final: 0.8359 (mmm) REVERT: B 539 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8128 (mtt) REVERT: B 557 MET cc_start: 0.8335 (mtp) cc_final: 0.7896 (tmm) REVERT: B 773 TRP cc_start: 0.7677 (t60) cc_final: 0.7229 (t60) REVERT: C 319 TYR cc_start: 0.7640 (t80) cc_final: 0.5998 (t80) REVERT: C 539 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8096 (mtt) REVERT: C 773 TRP cc_start: 0.7543 (t60) cc_final: 0.7045 (t60) REVERT: C 992 TRP cc_start: 0.9344 (t60) cc_final: 0.8808 (t60) outliers start: 74 outliers final: 53 residues processed: 270 average time/residue: 0.3220 time to fit residues: 152.0574 Evaluate side-chains 278 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 222 time to evaluate : 2.946 ------------------------------------------------------------------------------- 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 329 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 484 PHE Chi-restraints excluded: chain D residue 532 MET Chi-restraints excluded: chain D residue 539 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 976 MET 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 233 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain A residue 823 CYS Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1076 VAL 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 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 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 973 LEU Chi-restraints excluded: chain C residue 210 HIS Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 484 PHE Chi-restraints excluded: chain C residue 532 MET Chi-restraints excluded: chain C residue 539 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 300 optimal weight: 3.9990 chunk 352 optimal weight: 20.0000 chunk 241 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 169 optimal weight: 10.0000 chunk 208 optimal weight: 7.9990 chunk 99 optimal weight: 30.0000 chunk 20 optimal weight: 20.0000 chunk 228 optimal weight: 9.9990 chunk 115 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 = 0.3910 r_free = 0.3910 target = 0.107864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.074056 restraints weight = 93353.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.076036 restraints weight = 48520.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.077172 restraints weight = 33758.889| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 24864 Z= 0.330 Angle : 0.720 8.554 34132 Z= 0.382 Chirality : 0.042 0.150 4132 Planarity : 0.006 0.095 4396 Dihedral : 4.678 19.315 3756 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 5.16 % Allowed : 18.25 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.14), residues: 3528 helix: 0.94 (0.10), residues: 2496 sheet: -0.90 (0.33), residues: 208 loop : -2.13 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 253 HIS 0.009 0.001 HIS D 301 PHE 0.016 0.002 PHE C 748 TYR 0.018 0.002 TYR C 422 ARG 0.004 0.001 ARG C 541 Details of bonding type rmsd hydrogen bonds : bond 0.04821 ( 1788) hydrogen bonds : angle 4.96740 ( 5304) covalent geometry : bond 0.00696 (24864) covalent geometry : angle 0.71959 (34132) *********************** 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 306 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 218 time to evaluate : 3.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 420 GLN cc_start: 0.9142 (mt0) cc_final: 0.8897 (mt0) REVERT: D 532 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8259 (tpp) REVERT: D 539 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8079 (mpp) REVERT: A 409 MET cc_start: 0.8880 (mmm) cc_final: 0.8350 (mmm) REVERT: A 420 GLN cc_start: 0.9117 (mt0) cc_final: 0.8890 (mt0) REVERT: A 532 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8311 (tpp) REVERT: B 354 GLU cc_start: 0.8220 (mt-10) cc_final: 0.8016 (mt-10) REVERT: B 409 MET cc_start: 0.9007 (mmm) cc_final: 0.8753 (mmp) REVERT: B 420 GLN cc_start: 0.9126 (mt0) cc_final: 0.8827 (mt0) REVERT: B 532 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8307 (tpp) REVERT: B 539 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.7927 (mpp) REVERT: B 557 MET cc_start: 0.8317 (mtp) cc_final: 0.7755 (tmm) REVERT: C 532 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8159 (tpp) REVERT: C 539 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8015 (mpp) outliers start: 88 outliers final: 64 residues processed: 271 average time/residue: 0.3321 time to fit residues: 159.9596 Evaluate side-chains 286 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 215 time to evaluate : 2.559 ------------------------------------------------------------------------------- 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 329 LEU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 484 PHE Chi-restraints excluded: chain D residue 532 MET Chi-restraints excluded: chain D residue 539 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 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 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 A residue 1076 VAL 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 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 539 MET Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 822 THR Chi-restraints excluded: chain B residue 823 CYS Chi-restraints excluded: chain B residue 873 PHE Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 976 MET 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 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 331 THR 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 539 MET Chi-restraints excluded: chain C residue 719 LEU 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 829 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 138 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 257 optimal weight: 50.0000 chunk 178 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 176 optimal weight: 40.0000 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 = 0.4014 r_free = 0.4014 target = 0.117659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.084022 restraints weight = 90810.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.086100 restraints weight = 47642.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.087358 restraints weight = 33317.189| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3388 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= 0.124 Angle : 0.550 11.000 34132 Z= 0.283 Chirality : 0.038 0.187 4132 Planarity : 0.005 0.096 4396 Dihedral : 4.038 21.217 3756 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.64 % Allowed : 19.60 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.15), residues: 3528 helix: 1.64 (0.11), residues: 2508 sheet: -0.76 (0.33), residues: 208 loop : -1.86 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 727 HIS 0.002 0.000 HIS B 301 PHE 0.016 0.001 PHE D 873 TYR 0.010 0.001 TYR D 660 ARG 0.002 0.000 ARG D 363 Details of bonding type rmsd hydrogen bonds : bond 0.03280 ( 1788) hydrogen bonds : angle 3.99407 ( 5304) covalent geometry : bond 0.00261 (24864) covalent geometry : angle 0.55045 (34132) *********************** 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 296 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 234 time to evaluate : 3.749 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: 0.7703 (t80) cc_final: 0.6914 (t80) REVERT: D 539 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.7857 (mpp) REVERT: D 773 TRP cc_start: 0.7452 (t60) cc_final: 0.7158 (t60) REVERT: D 992 TRP cc_start: 0.9333 (t60) cc_final: 0.8805 (t60) REVERT: A 319 TYR cc_start: 0.7908 (t80) cc_final: 0.6265 (t80) REVERT: B 319 TYR cc_start: 0.7805 (t80) cc_final: 0.6194 (t80) REVERT: B 354 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7767 (mt-10) REVERT: B 539 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.7816 (mpp) REVERT: B 557 MET cc_start: 0.8205 (mtp) cc_final: 0.7799 (tmm) REVERT: C 319 TYR cc_start: 0.7765 (t80) cc_final: 0.6163 (t80) REVERT: C 539 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.7869 (mpp) REVERT: C 773 TRP cc_start: 0.7464 (t60) cc_final: 0.7072 (t60) REVERT: C 992 TRP cc_start: 0.9335 (t60) cc_final: 0.8883 (t60) outliers start: 62 outliers final: 51 residues processed: 270 average time/residue: 0.4320 time to fit residues: 202.7139 Evaluate side-chains 283 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 229 time to evaluate : 3.517 ------------------------------------------------------------------------------- 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 329 LEU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 532 MET Chi-restraints excluded: chain D residue 539 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 953 LEU Chi-restraints excluded: chain D residue 973 LEU Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 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 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 329 LEU Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 539 MET Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 822 THR Chi-restraints excluded: chain B residue 823 CYS Chi-restraints excluded: chain B residue 875 PHE Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain 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 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 539 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 875 PHE Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 973 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 160 optimal weight: 6.9990 chunk 138 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 287 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 144 optimal weight: 0.9980 chunk 232 optimal weight: 1.9990 chunk 351 optimal weight: 20.0000 chunk 105 optimal weight: 20.0000 chunk 163 optimal weight: 9.9990 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 420 GLN C 998 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.122576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.090249 restraints weight = 92110.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.092219 restraints weight = 48522.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.093366 restraints weight = 33912.042| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 24864 Z= 0.270 Angle : 0.663 10.238 34132 Z= 0.350 Chirality : 0.041 0.167 4132 Planarity : 0.005 0.092 4396 Dihedral : 4.382 19.639 3756 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 4.87 % Allowed : 19.54 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.15), residues: 3528 helix: 1.30 (0.11), residues: 2508 sheet: -0.40 (0.39), residues: 152 loop : -2.07 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 727 HIS 0.006 0.001 HIS B 301 PHE 0.016 0.002 PHE B 412 TYR 0.015 0.002 TYR C 422 ARG 0.006 0.001 ARG C 417 Details of bonding type rmsd hydrogen bonds : bond 0.04322 ( 1788) hydrogen bonds : angle 4.63299 ( 5304) covalent geometry : bond 0.00572 (24864) covalent geometry : angle 0.66302 (34132) *********************** 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 308 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 225 time to evaluate : 3.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 243 MET cc_start: 0.7795 (ppp) cc_final: 0.7392 (ppp) REVERT: D 420 GLN cc_start: 0.8958 (mt0) cc_final: 0.8733 (mt0) REVERT: D 532 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8018 (tpp) REVERT: D 539 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.7990 (mpp) REVERT: A 532 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8078 (tpp) REVERT: B 253 TRP cc_start: 0.6999 (m100) cc_final: 0.6728 (m100) REVERT: B 420 GLN cc_start: 0.8978 (mt0) cc_final: 0.8745 (mt0) REVERT: B 539 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.7980 (mpp) REVERT: B 557 MET cc_start: 0.8290 (mtp) cc_final: 0.7757 (tmm) REVERT: C 539 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.7918 (mpp) outliers start: 83 outliers final: 59 residues processed: 275 average time/residue: 0.2696 time to fit residues: 130.1001 Evaluate side-chains 282 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 218 time to evaluate : 2.724 ------------------------------------------------------------------------------- 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 329 LEU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 484 PHE Chi-restraints excluded: chain D residue 532 MET Chi-restraints excluded: chain D residue 539 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 875 PHE 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 316 LEU 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 973 LEU Chi-restraints excluded: chain A residue 1076 VAL 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 329 LEU Chi-restraints excluded: chain B residue 331 THR 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 875 PHE 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 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 331 THR Chi-restraints excluded: chain C residue 484 PHE Chi-restraints excluded: chain C residue 532 MET Chi-restraints excluded: chain C residue 539 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 294 optimal weight: 10.0000 chunk 138 optimal weight: 7.9990 chunk 322 optimal weight: 0.9980 chunk 190 optimal weight: 30.0000 chunk 314 optimal weight: 0.6980 chunk 171 optimal weight: 3.9990 chunk 306 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 186 optimal weight: 30.0000 chunk 23 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 420 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.118823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.084840 restraints weight = 89214.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.086855 restraints weight = 47613.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.088079 restraints weight = 33582.785| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24864 Z= 0.128 Angle : 0.555 10.759 34132 Z= 0.284 Chirality : 0.038 0.231 4132 Planarity : 0.005 0.095 4396 Dihedral : 3.951 21.161 3756 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.93 % Allowed : 20.48 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.15), residues: 3528 helix: 1.78 (0.11), residues: 2488 sheet: -0.19 (0.40), residues: 152 loop : -1.78 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 727 HIS 0.002 0.000 HIS B 301 PHE 0.017 0.001 PHE D 873 TYR 0.020 0.001 TYR D 351 ARG 0.002 0.000 ARG A1068 Details of bonding type rmsd hydrogen bonds : bond 0.03212 ( 1788) hydrogen bonds : angle 4.00174 ( 5304) covalent geometry : bond 0.00274 (24864) covalent geometry : angle 0.55505 (34132) *********************** 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 300 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 233 time to evaluate : 3.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 243 MET cc_start: 0.7871 (ppp) cc_final: 0.7371 (ppp) REVERT: D 539 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.7874 (mpp) REVERT: D 773 TRP cc_start: 0.7488 (t60) cc_final: 0.7161 (t60) REVERT: D 992 TRP cc_start: 0.9342 (t60) cc_final: 0.8825 (t60) REVERT: A 103 ILE cc_start: 0.8560 (mm) cc_final: 0.8214 (mp) REVERT: A 992 TRP cc_start: 0.9366 (t60) cc_final: 0.8842 (t60) REVERT: B 409 MET cc_start: 0.8676 (mmm) cc_final: 0.8327 (mmm) REVERT: B 539 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.7810 (mpp) REVERT: B 557 MET cc_start: 0.8218 (mtp) cc_final: 0.7795 (tmm) REVERT: C 539 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.7739 (mpp) REVERT: C 773 TRP cc_start: 0.7487 (t60) cc_final: 0.7080 (t60) REVERT: C 992 TRP cc_start: 0.9351 (t60) cc_final: 0.8884 (t60) outliers start: 67 outliers final: 56 residues processed: 273 average time/residue: 0.3439 time to fit residues: 167.0805 Evaluate side-chains 289 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 230 time to evaluate : 2.693 ------------------------------------------------------------------------------- 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 357 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 532 MET Chi-restraints excluded: chain D residue 539 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 875 PHE 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 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 973 LEU Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 539 MET Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 822 THR Chi-restraints excluded: chain B residue 823 CYS Chi-restraints excluded: chain B residue 875 PHE Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain 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 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 539 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 234 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 205 optimal weight: 4.9990 chunk 250 optimal weight: 3.9990 chunk 260 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 286 optimal weight: 50.0000 chunk 224 optimal weight: 3.9990 chunk 95 optimal weight: 40.0000 chunk 265 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 998 HIS ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 998 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.125369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.092655 restraints weight = 93394.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.094725 restraints weight = 48351.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.095891 restraints weight = 33004.355| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 24864 Z= 0.257 Angle : 0.656 12.340 34132 Z= 0.343 Chirality : 0.041 0.167 4132 Planarity : 0.005 0.091 4396 Dihedral : 4.277 19.797 3756 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 4.40 % Allowed : 20.01 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.15), residues: 3528 helix: 1.48 (0.11), residues: 2484 sheet: -0.40 (0.40), residues: 152 loop : -1.91 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 952 HIS 0.005 0.001 HIS B 301 PHE 0.021 0.002 PHE B 877 TYR 0.021 0.002 TYR D 351 ARG 0.002 0.000 ARG B 783 Details of bonding type rmsd hydrogen bonds : bond 0.04156 ( 1788) hydrogen bonds : angle 4.55390 ( 5304) covalent geometry : bond 0.00543 (24864) covalent geometry : angle 0.65603 (34132) *********************** 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 299 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 224 time to evaluate : 2.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 243 MET cc_start: 0.7945 (ppp) cc_final: 0.7412 (ppp) REVERT: D 420 GLN cc_start: 0.8993 (mt0) cc_final: 0.8744 (mt0) REVERT: D 532 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8049 (tpp) REVERT: D 539 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.7967 (mpp) REVERT: A 103 ILE cc_start: 0.8659 (mm) cc_final: 0.8335 (mp) REVERT: A 409 MET cc_start: 0.8734 (mmm) cc_final: 0.8138 (mmm) REVERT: A 532 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8064 (tpp) REVERT: B 253 TRP cc_start: 0.7142 (m100) cc_final: 0.6836 (m100) REVERT: B 420 GLN cc_start: 0.9026 (mt0) cc_final: 0.8787 (mt0) REVERT: B 539 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8030 (mpp) REVERT: B 557 MET cc_start: 0.8251 (mtp) cc_final: 0.7713 (tmm) REVERT: C 253 TRP cc_start: 0.7114 (m100) cc_final: 0.6902 (m100) REVERT: C 539 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.7777 (mpp) outliers start: 75 outliers final: 61 residues processed: 268 average time/residue: 0.2611 time to fit residues: 124.2067 Evaluate side-chains 287 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 221 time to evaluate : 2.548 ------------------------------------------------------------------------------- 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 357 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 532 MET Chi-restraints excluded: chain D residue 539 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 875 PHE 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 331 THR Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain A residue 823 CYS Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 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 539 MET Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 822 THR Chi-restraints excluded: chain B residue 823 CYS Chi-restraints excluded: chain B residue 875 PHE Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain 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 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 386 VAL Chi-restraints excluded: chain C residue 484 PHE Chi-restraints excluded: chain C residue 532 MET Chi-restraints excluded: chain C residue 539 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 30 optimal weight: 5.9990 chunk 267 optimal weight: 30.0000 chunk 189 optimal weight: 8.9990 chunk 124 optimal weight: 0.0870 chunk 128 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 325 optimal weight: 0.8980 chunk 190 optimal weight: 30.0000 chunk 354 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 342 optimal weight: 7.9990 overall best weight: 3.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.117873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.086075 restraints weight = 89230.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.086791 restraints weight = 51388.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.086882 restraints weight = 37435.181| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 24864 Z= 0.219 Angle : 0.630 15.129 34132 Z= 0.326 Chirality : 0.040 0.216 4132 Planarity : 0.005 0.092 4396 Dihedral : 4.168 20.508 3756 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.05 % Allowed : 20.54 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.15), residues: 3528 helix: 1.49 (0.11), residues: 2484 sheet: -0.47 (0.41), residues: 152 loop : -1.94 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 952 HIS 0.005 0.001 HIS B 301 PHE 0.015 0.002 PHE D 873 TYR 0.021 0.002 TYR D 351 ARG 0.003 0.000 ARG A 541 Details of bonding type rmsd hydrogen bonds : bond 0.03810 ( 1788) hydrogen bonds : angle 4.41514 ( 5304) covalent geometry : bond 0.00469 (24864) covalent geometry : angle 0.63048 (34132) ********************** 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 292 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 223 time to evaluate : 4.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 243 MET cc_start: 0.7979 (ppp) cc_final: 0.7684 (ppp) REVERT: D 420 GLN cc_start: 0.9046 (mt0) cc_final: 0.8778 (mt0) REVERT: D 539 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.7744 (mpp) REVERT: A 103 ILE cc_start: 0.8652 (mm) cc_final: 0.8321 (mp) REVERT: A 409 MET cc_start: 0.8754 (mmm) cc_final: 0.8106 (mmm) REVERT: B 420 GLN cc_start: 0.9021 (mt0) cc_final: 0.8766 (mt0) REVERT: B 539 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.7899 (mpp) REVERT: B 557 MET cc_start: 0.8217 (mtp) cc_final: 0.7778 (tmm) REVERT: C 539 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7551 (mpp) outliers start: 69 outliers final: 64 residues processed: 267 average time/residue: 0.3771 time to fit residues: 180.6655 Evaluate side-chains 286 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 219 time to evaluate : 3.796 ------------------------------------------------------------------------------- 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 357 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 484 PHE Chi-restraints excluded: chain D residue 532 MET Chi-restraints excluded: chain D residue 539 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 875 PHE 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 331 THR Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain A residue 823 CYS Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 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 539 MET Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 822 THR Chi-restraints excluded: chain B residue 823 CYS Chi-restraints excluded: chain B residue 875 PHE Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain 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 331 THR Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 484 PHE Chi-restraints excluded: chain C residue 532 MET Chi-restraints excluded: chain C residue 539 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 118 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 334 optimal weight: 1.9990 chunk 281 optimal weight: 40.0000 chunk 287 optimal weight: 9.9990 chunk 198 optimal weight: 5.9990 chunk 337 optimal weight: 9.9990 chunk 314 optimal weight: 0.9980 chunk 192 optimal weight: 50.0000 chunk 6 optimal weight: 10.0000 chunk 233 optimal weight: 4.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 998 HIS ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 998 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.124831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.092117 restraints weight = 92932.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.094159 restraints weight = 48088.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.095437 restraints weight = 33005.424| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 24864 Z= 0.280 Angle : 0.695 12.558 34132 Z= 0.362 Chirality : 0.042 0.199 4132 Planarity : 0.005 0.092 4396 Dihedral : 4.469 19.878 3756 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 4.28 % Allowed : 20.83 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.15), residues: 3528 helix: 1.18 (0.11), residues: 2504 sheet: -0.62 (0.41), residues: 148 loop : -2.20 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 253 HIS 0.006 0.001 HIS B 301 PHE 0.016 0.002 PHE D 484 TYR 0.021 0.002 TYR D 351 ARG 0.005 0.000 ARG A 541 Details of bonding type rmsd hydrogen bonds : bond 0.04457 ( 1788) hydrogen bonds : angle 4.79201 ( 5304) covalent geometry : bond 0.00592 (24864) covalent geometry : angle 0.69452 (34132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9045.23 seconds wall clock time: 164 minutes 23.89 seconds (9863.89 seconds total)