Starting phenix.real_space_refine on Fri Mar 6 13:19:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ui9_20783/03_2026/6ui9_20783.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ui9_20783/03_2026/6ui9_20783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ui9_20783/03_2026/6ui9_20783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ui9_20783/03_2026/6ui9_20783.map" model { file = "/net/cci-nas-00/data/ceres_data/6ui9_20783/03_2026/6ui9_20783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ui9_20783/03_2026/6ui9_20783.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.001 sd= 0.005 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 P 12 5.49 5 S 180 5.16 5 C 20380 2.51 5 N 5388 2.21 5 O 5952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31912 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 49, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 49, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Chain: "B" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 47, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 47, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Chain: "C" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Chain: "D" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 47, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 47, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Chain: "A" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 120 Unusual residues: {'ACO': 2, 'OAA': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'ACO': 1, 'OAA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'OAA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'ACO': 1, 'OAA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 12.90, per 1000 atoms: 0.40 Number of scatterers: 31912 At special positions: 0 Unit cell: (140.07, 162.69, 171.39, 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) S 180 16.00 P 12 15.00 O 5952 8.00 N 5388 7.00 C 20380 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 2.4 seconds 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7392 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 36 sheets defined 47.0% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 7 through 19 Processing helix chain 'A' and resid 40 through 47 removed outlier: 3.708A pdb=" N HIS A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 52 removed outlier: 4.209A pdb=" N LEU A 51 " --> pdb=" O PRO A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 70 removed outlier: 3.581A pdb=" N LEU A 69 " --> pdb=" O ARG A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 161 through 169 Processing helix chain 'A' and resid 177 through 195 Processing helix chain 'A' and resid 225 through 234 removed outlier: 6.733A pdb=" N VAL A 231 " --> pdb=" O TYR A 227 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LYS A 232 " --> pdb=" O ILE A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 259 removed outlier: 3.614A pdb=" N LYS A 259 " --> pdb=" O ASP A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 295 Processing helix chain 'A' and resid 312 through 326 Processing helix chain 'A' and resid 349 through 364 removed outlier: 3.752A pdb=" N THR A 353 " --> pdb=" O ASN A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.647A pdb=" N LEU A 368 " --> pdb=" O TYR A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 399 removed outlier: 3.564A pdb=" N GLY A 387 " --> pdb=" O ASN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 419 Processing helix chain 'A' and resid 505 through 519 Processing helix chain 'A' and resid 555 through 563 removed outlier: 3.803A pdb=" N ALA A 559 " --> pdb=" O ASN A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 587 removed outlier: 3.663A pdb=" N SER A 581 " --> pdb=" O SER A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 617 Processing helix chain 'A' and resid 642 through 649 Processing helix chain 'A' and resid 664 through 678 removed outlier: 4.220A pdb=" N ASN A 668 " --> pdb=" O GLY A 664 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLU A 669 " --> pdb=" O GLY A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 707 removed outlier: 3.767A pdb=" N HIS A 700 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG A 703 " --> pdb=" O ASP A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 734 removed outlier: 3.610A pdb=" N ILE A 727 " --> pdb=" O GLU A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 770 Processing helix chain 'A' and resid 771 through 783 Processing helix chain 'A' and resid 792 through 807 removed outlier: 4.112A pdb=" N ASN A 807 " --> pdb=" O ASP A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 831 Processing helix chain 'A' and resid 858 through 865 Processing helix chain 'A' and resid 868 through 877 Processing helix chain 'A' and resid 883 through 898 Processing helix chain 'A' and resid 904 through 915 Processing helix chain 'A' and resid 919 through 929 Processing helix chain 'A' and resid 937 through 952 Processing helix chain 'A' and resid 955 through 966 removed outlier: 3.587A pdb=" N ASN A 961 " --> pdb=" O MET A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 998 Processing helix chain 'A' and resid 1001 through 1018 removed outlier: 3.502A pdb=" N TYR A1006 " --> pdb=" O PRO A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1040 removed outlier: 3.816A pdb=" N GLY A1030 " --> pdb=" O ASP A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1055 removed outlier: 3.578A pdb=" N ILE A1052 " --> pdb=" O ALA A1048 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP A1053 " --> pdb=" O ASP A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1079 removed outlier: 4.034A pdb=" N MET A1067 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY A1068 " --> pdb=" O GLY A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1091 Processing helix chain 'B' and resid 7 through 19 Processing helix chain 'B' and resid 40 through 47 removed outlier: 3.659A pdb=" N HIS B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 52 removed outlier: 4.216A pdb=" N LEU B 51 " --> pdb=" O PRO B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 70 removed outlier: 3.585A pdb=" N LEU B 69 " --> pdb=" O ARG B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 86 Processing helix chain 'B' and resid 161 through 169 Processing helix chain 'B' and resid 177 through 195 removed outlier: 3.536A pdb=" N LEU B 195 " --> pdb=" O PHE B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 234 removed outlier: 6.659A pdb=" N VAL B 231 " --> pdb=" O TYR B 227 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N LYS B 232 " --> pdb=" O ILE B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 259 removed outlier: 3.618A pdb=" N LYS B 259 " --> pdb=" O ASP B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 295 Processing helix chain 'B' and resid 312 through 328 removed outlier: 3.565A pdb=" N MET B 327 " --> pdb=" O ILE B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 364 removed outlier: 3.728A pdb=" N THR B 353 " --> pdb=" O ASN B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.585A pdb=" N LEU B 368 " --> pdb=" O TYR B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 398 removed outlier: 3.596A pdb=" N GLY B 387 " --> pdb=" O ASN B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 419 Processing helix chain 'B' and resid 505 through 519 Processing helix chain 'B' and resid 555 through 563 removed outlier: 3.823A pdb=" N ALA B 559 " --> pdb=" O ASN B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 587 removed outlier: 3.717A pdb=" N SER B 581 " --> pdb=" O SER B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 617 Processing helix chain 'B' and resid 642 through 649 Processing helix chain 'B' and resid 664 through 678 removed outlier: 4.336A pdb=" N ASN B 668 " --> pdb=" O GLY B 664 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU B 669 " --> pdb=" O GLY B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 707 removed outlier: 3.748A pdb=" N HIS B 700 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG B 703 " --> pdb=" O ASP B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 734 removed outlier: 3.603A pdb=" N ILE B 727 " --> pdb=" O GLU B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 767 through 770 Processing helix chain 'B' and resid 771 through 783 Processing helix chain 'B' and resid 792 through 807 removed outlier: 4.016A pdb=" N ASN B 807 " --> pdb=" O ASP B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 831 Processing helix chain 'B' and resid 858 through 865 Processing helix chain 'B' and resid 868 through 877 Processing helix chain 'B' and resid 883 through 898 Processing helix chain 'B' and resid 904 through 915 Processing helix chain 'B' and resid 919 through 929 Processing helix chain 'B' and resid 937 through 952 Processing helix chain 'B' and resid 955 through 966 removed outlier: 3.577A pdb=" N ASN B 961 " --> pdb=" O MET B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 998 Processing helix chain 'B' and resid 1001 through 1018 Processing helix chain 'B' and resid 1024 through 1040 removed outlier: 3.825A pdb=" N GLY B1030 " --> pdb=" O ASP B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1047 through 1055 removed outlier: 3.593A pdb=" N ILE B1052 " --> pdb=" O ALA B1048 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP B1053 " --> pdb=" O ASP B1049 " (cutoff:3.500A) Processing helix chain 'B' and resid 1055 through 1079 removed outlier: 4.049A pdb=" N MET B1067 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY B1068 " --> pdb=" O GLY B1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 1087 through 1091 removed outlier: 3.595A pdb=" N ILE B1091 " --> pdb=" O TRP B1088 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 19 Processing helix chain 'C' and resid 40 through 47 removed outlier: 3.659A pdb=" N HIS C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 52 removed outlier: 4.246A pdb=" N LEU C 51 " --> pdb=" O PRO C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 70 removed outlier: 3.588A pdb=" N LEU C 69 " --> pdb=" O ARG C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 86 Processing helix chain 'C' and resid 161 through 169 Processing helix chain 'C' and resid 177 through 195 Processing helix chain 'C' and resid 225 through 234 removed outlier: 6.662A pdb=" N VAL C 231 " --> pdb=" O TYR C 227 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N LYS C 232 " --> pdb=" O ILE C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 259 removed outlier: 3.620A pdb=" N LYS C 259 " --> pdb=" O ASP C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 295 Processing helix chain 'C' and resid 312 through 326 Processing helix chain 'C' and resid 349 through 364 removed outlier: 3.742A pdb=" N THR C 353 " --> pdb=" O ASN C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.651A pdb=" N LEU C 368 " --> pdb=" O TYR C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 399 removed outlier: 3.569A pdb=" N GLY C 387 " --> pdb=" O ASN C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 419 Processing helix chain 'C' and resid 505 through 519 Processing helix chain 'C' and resid 555 through 563 removed outlier: 3.821A pdb=" N ALA C 559 " --> pdb=" O ASN C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 587 removed outlier: 3.702A pdb=" N SER C 581 " --> pdb=" O SER C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 617 Processing helix chain 'C' and resid 642 through 649 Processing helix chain 'C' and resid 664 through 678 removed outlier: 4.333A pdb=" N ASN C 668 " --> pdb=" O GLY C 664 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLU C 669 " --> pdb=" O GLY C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 707 removed outlier: 3.709A pdb=" N HIS C 700 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG C 703 " --> pdb=" O ASP C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 734 removed outlier: 3.598A pdb=" N ILE C 727 " --> pdb=" O GLU C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 767 through 770 Processing helix chain 'C' and resid 771 through 783 Processing helix chain 'C' and resid 792 through 807 removed outlier: 4.099A pdb=" N ASN C 807 " --> pdb=" O ASP C 803 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 831 Processing helix chain 'C' and resid 858 through 865 Processing helix chain 'C' and resid 868 through 877 Processing helix chain 'C' and resid 883 through 898 Processing helix chain 'C' and resid 904 through 915 Processing helix chain 'C' and resid 919 through 929 Processing helix chain 'C' and resid 937 through 952 removed outlier: 3.523A pdb=" N SER C 952 " --> pdb=" O LYS C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 955 through 966 removed outlier: 3.613A pdb=" N ASN C 961 " --> pdb=" O MET C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 998 Processing helix chain 'C' and resid 1001 through 1018 Processing helix chain 'C' and resid 1024 through 1040 removed outlier: 3.812A pdb=" N GLY C1030 " --> pdb=" O ASP C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1047 through 1055 removed outlier: 3.583A pdb=" N ILE C1052 " --> pdb=" O ALA C1048 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP C1053 " --> pdb=" O ASP C1049 " (cutoff:3.500A) Processing helix chain 'C' and resid 1055 through 1079 removed outlier: 4.038A pdb=" N MET C1067 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY C1068 " --> pdb=" O GLY C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1087 through 1091 removed outlier: 3.629A pdb=" N ILE C1091 " --> pdb=" O TRP C1088 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 19 Processing helix chain 'D' and resid 40 through 47 removed outlier: 3.659A pdb=" N HIS D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 52 removed outlier: 4.236A pdb=" N LEU D 51 " --> pdb=" O PRO D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 70 removed outlier: 3.576A pdb=" N LEU D 69 " --> pdb=" O ARG D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 86 Processing helix chain 'D' and resid 161 through 169 Processing helix chain 'D' and resid 177 through 195 removed outlier: 3.614A pdb=" N SER D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 195 " --> pdb=" O PHE D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 234 removed outlier: 6.619A pdb=" N VAL D 231 " --> pdb=" O TYR D 227 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N LYS D 232 " --> pdb=" O ILE D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 259 removed outlier: 3.500A pdb=" N ALA D 258 " --> pdb=" O ALA D 254 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS D 259 " --> pdb=" O ASP D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 295 Processing helix chain 'D' and resid 312 through 328 removed outlier: 3.554A pdb=" N MET D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 364 removed outlier: 3.747A pdb=" N THR D 353 " --> pdb=" O ASN D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 371 removed outlier: 3.596A pdb=" N LEU D 368 " --> pdb=" O TYR D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 398 removed outlier: 3.583A pdb=" N GLY D 387 " --> pdb=" O ASN D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 419 Processing helix chain 'D' and resid 505 through 519 Processing helix chain 'D' and resid 555 through 563 removed outlier: 3.826A pdb=" N ALA D 559 " --> pdb=" O ASN D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 587 removed outlier: 3.719A pdb=" N SER D 581 " --> pdb=" O SER D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 617 Processing helix chain 'D' and resid 642 through 649 Processing helix chain 'D' and resid 664 through 678 removed outlier: 4.375A pdb=" N ASN D 668 " --> pdb=" O GLY D 664 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU D 669 " --> pdb=" O GLY D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 696 through 707 removed outlier: 3.747A pdb=" N HIS D 700 " --> pdb=" O THR D 696 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 734 removed outlier: 3.602A pdb=" N ILE D 727 " --> pdb=" O GLU D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 767 through 770 Processing helix chain 'D' and resid 771 through 783 Processing helix chain 'D' and resid 792 through 807 removed outlier: 4.059A pdb=" N ASN D 807 " --> pdb=" O ASP D 803 " (cutoff:3.500A) Processing helix chain 'D' and resid 825 through 831 Processing helix chain 'D' and resid 858 through 865 Processing helix chain 'D' and resid 868 through 877 Processing helix chain 'D' and resid 883 through 898 Processing helix chain 'D' and resid 904 through 915 Processing helix chain 'D' and resid 919 through 931 removed outlier: 3.825A pdb=" N GLY D 927 " --> pdb=" O SER D 923 " (cutoff:3.500A) Processing helix chain 'D' and resid 937 through 951 removed outlier: 3.514A pdb=" N ALA D 941 " --> pdb=" O GLY D 937 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS D 948 " --> pdb=" O LYS D 944 " (cutoff:3.500A) Processing helix chain 'D' and resid 955 through 966 removed outlier: 3.595A pdb=" N ASN D 961 " --> pdb=" O MET D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 986 through 992 removed outlier: 3.624A pdb=" N LEU D 990 " --> pdb=" O ARG D 986 " (cutoff:3.500A) Processing helix chain 'D' and resid 992 through 997 removed outlier: 3.548A pdb=" N GLN D 996 " --> pdb=" O ASP D 992 " (cutoff:3.500A) Processing helix chain 'D' and resid 1001 through 1018 removed outlier: 4.159A pdb=" N LYS D1012 " --> pdb=" O LEU D1008 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS D1017 " --> pdb=" O ILE D1013 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS D1018 " --> pdb=" O THR D1014 " (cutoff:3.500A) Processing helix chain 'D' and resid 1024 through 1038 Processing helix chain 'D' and resid 1046 through 1049 Processing helix chain 'D' and resid 1050 through 1055 Processing helix chain 'D' and resid 1057 through 1072 removed outlier: 3.678A pdb=" N PHE D1061 " --> pdb=" O LEU D1057 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL D1062 " --> pdb=" O ASN D1058 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET D1067 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY D1068 " --> pdb=" O GLY D1064 " (cutoff:3.500A) Processing helix chain 'D' and resid 1087 through 1091 removed outlier: 3.542A pdb=" N ILE D1091 " --> pdb=" O TRP D1088 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 removed outlier: 4.819A pdb=" N ALA A 219 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ASP A 222 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE A 197 " --> pdb=" O ASP A 222 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N THR A 198 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 121 " --> pdb=" O ILE A 202 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 34 removed outlier: 6.671A pdb=" N LEU A 55 " --> pdb=" O ASN A 75 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN A 75 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 95 Processing sheet with id=AA4, first strand: chain 'A' and resid 205 through 207 Processing sheet with id=AA5, first strand: chain 'A' and resid 263 through 268 removed outlier: 3.533A pdb=" N THR A 267 " --> pdb=" O TYR A 304 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 275 through 277 removed outlier: 6.836A pdb=" N TRP A 276 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LYS A 336 " --> pdb=" O THR A 374 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N PHE A 376 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU A 338 " --> pdb=" O PHE A 376 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ARG A 378 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE A 340 " --> pdb=" O ARG A 378 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 537 through 543 removed outlier: 7.108A pdb=" N ALA A 527 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N PHE A 553 " --> pdb=" O ALA A 527 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N MET A 529 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ALA A 499 " --> pdb=" O ALA A 527 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N MET A 529 " --> pdb=" O ALA A 499 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL A 501 " --> pdb=" O MET A 529 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU A 569 " --> pdb=" O ALA A 595 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 634 through 635 removed outlier: 7.027A pdb=" N VAL A 657 " --> pdb=" O TYR A 682 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N GLY A 684 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TYR A 659 " --> pdb=" O GLY A 684 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ALA A 686 " --> pdb=" O TYR A 659 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N SER A 661 " --> pdb=" O ALA A 686 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ALA A 658 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N LEU A 716 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL A 660 " --> pdb=" O LEU A 716 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE A 713 " --> pdb=" O VAL A 741 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 823 through 824 removed outlier: 6.487A pdb=" N MET A 823 " --> pdb=" O ARG B 835 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 834 through 835 Processing sheet with id=AB2, first strand: chain 'B' and resid 3 through 5 removed outlier: 6.549A pdb=" N ALA B 218 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU B 200 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS B 220 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N THR B 198 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 32 through 34 removed outlier: 6.650A pdb=" N LEU B 55 " --> pdb=" O ASN B 75 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASN B 75 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 92 through 95 Processing sheet with id=AB5, first strand: chain 'B' and resid 205 through 207 Processing sheet with id=AB6, first strand: chain 'B' and resid 263 through 268 Processing sheet with id=AB7, first strand: chain 'B' and resid 275 through 277 removed outlier: 6.872A pdb=" N TRP B 276 " --> pdb=" O ILE B 339 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS B 336 " --> pdb=" O THR B 374 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N PHE B 376 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU B 338 " --> pdb=" O PHE B 376 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ARG B 378 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE B 340 " --> pdb=" O ARG B 378 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 537 through 543 removed outlier: 7.135A pdb=" N ALA B 527 " --> pdb=" O PRO B 551 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N PHE B 553 " --> pdb=" O ALA B 527 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N MET B 529 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ALA B 499 " --> pdb=" O ALA B 527 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N MET B 529 " --> pdb=" O ALA B 499 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL B 501 " --> pdb=" O MET B 529 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU B 569 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE B 594 " --> pdb=" O ILE B 621 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 634 through 635 removed outlier: 7.043A pdb=" N VAL B 657 " --> pdb=" O TYR B 682 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N GLY B 684 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N TYR B 659 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ALA B 686 " --> pdb=" O TYR B 659 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N SER B 661 " --> pdb=" O ALA B 686 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ALA B 658 " --> pdb=" O VAL B 714 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N LEU B 716 " --> pdb=" O ALA B 658 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL B 660 " --> pdb=" O LEU B 716 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE B 713 " --> pdb=" O VAL B 741 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 3 through 5 removed outlier: 5.749A pdb=" N ASP C 222 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE C 197 " --> pdb=" O ASP C 222 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N THR C 198 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL C 121 " --> pdb=" O ILE C 202 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY C 129 " --> pdb=" O THR C 126 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 32 through 34 removed outlier: 6.681A pdb=" N LEU C 55 " --> pdb=" O ASN C 75 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN C 75 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 92 through 95 Processing sheet with id=AC4, first strand: chain 'C' and resid 205 through 207 Processing sheet with id=AC5, first strand: chain 'C' and resid 263 through 268 Processing sheet with id=AC6, first strand: chain 'C' and resid 275 through 277 removed outlier: 6.536A pdb=" N LYS C 336 " --> pdb=" O THR C 374 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N PHE C 376 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU C 338 " --> pdb=" O PHE C 376 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ARG C 378 " --> pdb=" O LEU C 338 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE C 340 " --> pdb=" O ARG C 378 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 537 through 543 removed outlier: 7.111A pdb=" N ALA C 527 " --> pdb=" O PRO C 551 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N PHE C 553 " --> pdb=" O ALA C 527 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N MET C 529 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ALA C 499 " --> pdb=" O ALA C 527 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N MET C 529 " --> pdb=" O ALA C 499 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL C 501 " --> pdb=" O MET C 529 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU C 569 " --> pdb=" O ALA C 595 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE C 594 " --> pdb=" O ILE C 621 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 634 through 635 removed outlier: 4.326A pdb=" N GLY C 627 " --> pdb=" O ALA C 686 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL C 657 " --> pdb=" O TYR C 682 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N GLY C 684 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TYR C 659 " --> pdb=" O GLY C 684 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ALA C 686 " --> pdb=" O TYR C 659 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N SER C 661 " --> pdb=" O ALA C 686 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ALA C 658 " --> pdb=" O VAL C 714 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N LEU C 716 " --> pdb=" O ALA C 658 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL C 660 " --> pdb=" O LEU C 716 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE C 713 " --> pdb=" O VAL C 741 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 823 through 824 removed outlier: 6.432A pdb=" N MET C 823 " --> pdb=" O ARG D 835 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 834 through 835 Processing sheet with id=AD2, first strand: chain 'D' and resid 3 through 5 removed outlier: 6.556A pdb=" N ALA D 218 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU D 200 " --> pdb=" O ALA D 218 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LYS D 220 " --> pdb=" O THR D 198 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N THR D 198 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 32 through 34 removed outlier: 6.663A pdb=" N LEU D 55 " --> pdb=" O ASN D 75 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN D 75 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 92 through 95 Processing sheet with id=AD5, first strand: chain 'D' and resid 205 through 207 Processing sheet with id=AD6, first strand: chain 'D' and resid 263 through 268 Processing sheet with id=AD7, first strand: chain 'D' and resid 275 through 277 removed outlier: 6.863A pdb=" N TRP D 276 " --> pdb=" O ILE D 339 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LYS D 336 " --> pdb=" O THR D 374 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N PHE D 376 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU D 338 " --> pdb=" O PHE D 376 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ARG D 378 " --> pdb=" O LEU D 338 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE D 340 " --> pdb=" O ARG D 378 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 537 through 543 removed outlier: 7.123A pdb=" N ALA D 527 " --> pdb=" O PRO D 551 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N PHE D 553 " --> pdb=" O ALA D 527 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N MET D 529 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ALA D 499 " --> pdb=" O ALA D 527 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N MET D 529 " --> pdb=" O ALA D 499 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL D 501 " --> pdb=" O MET D 529 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU D 569 " --> pdb=" O ALA D 595 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE D 594 " --> pdb=" O ILE D 621 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 634 through 635 removed outlier: 7.044A pdb=" N VAL D 657 " --> pdb=" O TYR D 682 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLY D 684 " --> pdb=" O VAL D 657 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TYR D 659 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ALA D 686 " --> pdb=" O TYR D 659 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N SER D 661 " --> pdb=" O ALA D 686 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ALA D 658 " --> pdb=" O VAL D 714 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LEU D 716 " --> pdb=" O ALA D 658 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL D 660 " --> pdb=" O LEU D 716 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE D 713 " --> pdb=" O VAL D 741 " (cutoff:3.500A) 1433 hydrogen bonds defined for protein. 4125 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: 8.76 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 5300 1.27 - 1.41: 7824 1.41 - 1.54: 19093 1.54 - 1.68: 83 1.68 - 1.82: 292 Bond restraints: 32592 Sorted by residual: bond pdb=" CA TYR D1073 " pdb=" C TYR D1073 " ideal model delta sigma weight residual 1.524 1.426 0.098 1.16e-02 7.43e+03 7.10e+01 bond pdb=" CA MET D 945 " pdb=" C MET D 945 " ideal model delta sigma weight residual 1.525 1.425 0.100 1.29e-02 6.01e+03 5.99e+01 bond pdb=" C HIS D1072 " pdb=" O HIS D1072 " ideal model delta sigma weight residual 1.235 1.135 0.100 1.38e-02 5.25e+03 5.20e+01 bond pdb=" C PHE D 935 " pdb=" O PHE D 935 " ideal model delta sigma weight residual 1.236 1.153 0.083 1.17e-02 7.31e+03 5.01e+01 bond pdb=" CA ALA D 943 " pdb=" C ALA D 943 " ideal model delta sigma weight residual 1.523 1.426 0.097 1.37e-02 5.33e+03 4.97e+01 ... (remaining 32587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.73: 43721 3.73 - 7.46: 352 7.46 - 11.19: 67 11.19 - 14.92: 10 14.92 - 18.64: 6 Bond angle restraints: 44156 Sorted by residual: angle pdb=" N GLU D1046 " pdb=" CA GLU D1046 " pdb=" C GLU D1046 " ideal model delta sigma weight residual 114.62 97.53 17.09 1.14e+00 7.69e-01 2.25e+02 angle pdb=" N GLU D1050 " pdb=" CA GLU D1050 " pdb=" C GLU D1050 " ideal model delta sigma weight residual 113.55 97.55 16.00 1.26e+00 6.30e-01 1.61e+02 angle pdb=" P1A ACO B1203 " pdb=" O3A ACO B1203 " pdb=" P2A ACO B1203 " ideal model delta sigma weight residual 136.83 124.38 12.45 1.00e+00 1.00e+00 1.55e+02 angle pdb=" P1A ACO D1201 " pdb=" O3A ACO D1201 " pdb=" P2A ACO D1201 " ideal model delta sigma weight residual 136.83 124.50 12.33 1.00e+00 1.00e+00 1.52e+02 angle pdb=" P1A ACO A1204 " pdb=" O3A ACO A1204 " pdb=" P2A ACO A1204 " ideal model delta sigma weight residual 136.83 124.54 12.29 1.00e+00 1.00e+00 1.51e+02 ... (remaining 44151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.40: 18070 22.40 - 44.80: 1257 44.80 - 67.20: 185 67.20 - 89.60: 36 89.60 - 112.00: 4 Dihedral angle restraints: 19552 sinusoidal: 7912 harmonic: 11640 Sorted by residual: dihedral pdb=" C GLU D1050 " pdb=" N GLU D1050 " pdb=" CA GLU D1050 " pdb=" CB GLU D1050 " ideal model delta harmonic sigma weight residual -122.60 -108.89 -13.71 0 2.50e+00 1.60e-01 3.01e+01 dihedral pdb=" C ARG B 848 " pdb=" N ARG B 848 " pdb=" CA ARG B 848 " pdb=" CB ARG B 848 " ideal model delta harmonic sigma weight residual -122.60 -109.02 -13.58 0 2.50e+00 1.60e-01 2.95e+01 dihedral pdb=" CA ILE A 621 " pdb=" C ILE A 621 " pdb=" N GLY A 622 " pdb=" CA GLY A 622 " ideal model delta harmonic sigma weight residual 180.00 154.98 25.02 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 19549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 4388 0.084 - 0.169: 466 0.169 - 0.253: 36 0.253 - 0.337: 16 0.337 - 0.421: 6 Chirality restraints: 4912 Sorted by residual: chirality pdb=" CA ARG D1038 " pdb=" N ARG D1038 " pdb=" C ARG D1038 " pdb=" CB ARG D1038 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" CA MET D 985 " pdb=" N MET D 985 " pdb=" C MET D 985 " pdb=" CB MET D 985 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.38e+00 chirality pdb=" CA TYR D1051 " pdb=" N TYR D1051 " pdb=" C TYR D1051 " pdb=" CB TYR D1051 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.00e+00 ... (remaining 4909 not shown) Planarity restraints: 5652 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7P ACO A1204 " 0.173 2.00e-02 2.50e+03 1.41e-01 2.49e+02 pdb=" C9P ACO A1204 " -0.056 2.00e-02 2.50e+03 pdb=" CAP ACO A1204 " 0.130 2.00e-02 2.50e+03 pdb=" N8P ACO A1204 " -0.221 2.00e-02 2.50e+03 pdb=" O9P ACO A1204 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7P ACO D1201 " 0.164 2.00e-02 2.50e+03 1.34e-01 2.23e+02 pdb=" C9P ACO D1201 " -0.053 2.00e-02 2.50e+03 pdb=" CAP ACO D1201 " 0.123 2.00e-02 2.50e+03 pdb=" N8P ACO D1201 " -0.209 2.00e-02 2.50e+03 pdb=" O9P ACO D1201 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7P ACO B1203 " -0.164 2.00e-02 2.50e+03 1.33e-01 2.21e+02 pdb=" C9P ACO B1203 " 0.053 2.00e-02 2.50e+03 pdb=" CAP ACO B1203 " -0.123 2.00e-02 2.50e+03 pdb=" N8P ACO B1203 " 0.208 2.00e-02 2.50e+03 pdb=" O9P ACO B1203 " 0.026 2.00e-02 2.50e+03 ... (remaining 5649 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3080 2.74 - 3.28: 32180 3.28 - 3.82: 53933 3.82 - 4.36: 65802 4.36 - 4.90: 112913 Nonbonded interactions: 267908 Sorted by model distance: nonbonded pdb=" OG1 THR C 625 " pdb=" O ALA C 686 " model vdw 2.199 3.040 nonbonded pdb=" OE2 GLU B 306 " pdb=" OG SER B 308 " model vdw 2.208 3.040 nonbonded pdb=" O ALA C 838 " pdb=" NZ LYS D 540 " model vdw 2.246 3.120 nonbonded pdb=" NZ LYS A 540 " pdb=" O ALA B 838 " model vdw 2.255 3.120 nonbonded pdb=" O SER C 343 " pdb=" NH1 ARG C 379 " model vdw 2.256 3.120 ... (remaining 267903 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099 or resid 1202)) selection = (chain 'B' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099 or resid 1202)) selection = (chain 'C' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099 or resid 1202)) selection = (chain 'D' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099 or resid 1202)) } 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 39.370 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.100 32592 Z= 0.503 Angle : 0.906 18.644 44156 Z= 0.537 Chirality : 0.055 0.421 4912 Planarity : 0.006 0.141 5652 Dihedral : 15.162 111.996 12160 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.95 % Favored : 94.90 % Rotamer: Outliers : 1.51 % Allowed : 0.95 % Favored : 97.54 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.13), residues: 4068 helix: -0.25 (0.12), residues: 1788 sheet: -0.80 (0.21), residues: 604 loop : -1.59 (0.14), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 691 TYR 0.030 0.002 TYR A 542 PHE 0.021 0.002 PHE D1043 TRP 0.011 0.001 TRP C1088 HIS 0.012 0.001 HIS D1072 Details of bonding type rmsd covalent geometry : bond 0.00799 (32592) covalent geometry : angle 0.90563 (44156) hydrogen bonds : bond 0.14353 ( 1433) hydrogen bonds : angle 6.46793 ( 4125) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 409 time to evaluate : 1.109 Fit side-chains revert: symmetry clash REVERT: A 847 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.7565 (pt0) REVERT: C 847 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8283 (pt0) REVERT: D 847 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7985 (pt0) outliers start: 47 outliers final: 19 residues processed: 450 average time/residue: 0.1943 time to fit residues: 139.7508 Evaluate side-chains 365 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 343 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain D residue 847 GLU Chi-restraints excluded: chain D residue 924 LEU Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 926 SER Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 952 SER Chi-restraints excluded: chain D residue 954 ILE Chi-restraints excluded: chain D residue 965 LYS Chi-restraints excluded: chain D residue 971 MET Chi-restraints excluded: chain D residue 978 LYS Chi-restraints excluded: chain D residue 1011 GLU Chi-restraints excluded: chain D residue 1037 LEU Chi-restraints excluded: chain D residue 1038 ARG Chi-restraints excluded: chain D residue 1054 ILE Chi-restraints excluded: chain D residue 1060 ILE Chi-restraints excluded: chain D residue 1065 ARG Chi-restraints excluded: chain D residue 1078 ARG Chi-restraints excluded: chain D residue 1087 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 40.0000 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 40.0000 chunk 401 optimal weight: 0.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 10.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1081 GLN ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 ASN ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 GLN ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1020 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.214995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.186308 restraints weight = 65906.375| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 2.13 r_work: 0.3595 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3399 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3399 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 32592 Z= 0.134 Angle : 0.605 8.080 44156 Z= 0.315 Chirality : 0.046 0.219 4912 Planarity : 0.004 0.098 5652 Dihedral : 7.534 100.797 4720 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.86 % Allowed : 5.37 % Favored : 93.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.13), residues: 4068 helix: 0.22 (0.12), residues: 1836 sheet: -0.62 (0.22), residues: 596 loop : -1.37 (0.14), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 691 TYR 0.024 0.001 TYR B 124 PHE 0.015 0.002 PHE A 29 TRP 0.015 0.001 TRP B 40 HIS 0.005 0.001 HIS A 410 Details of bonding type rmsd covalent geometry : bond 0.00309 (32592) covalent geometry : angle 0.60516 (44156) hydrogen bonds : bond 0.03743 ( 1433) hydrogen bonds : angle 4.73157 ( 4125) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 379 time to evaluate : 1.110 Fit side-chains revert: symmetry clash REVERT: A 547 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7692 (mm-30) REVERT: A 615 GLN cc_start: 0.8191 (tm-30) cc_final: 0.7732 (mt0) REVERT: A 847 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7915 (pt0) REVERT: C 494 SER cc_start: 0.8522 (m) cc_final: 0.8242 (p) REVERT: C 547 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7703 (mm-30) REVERT: C 692 TYR cc_start: 0.7917 (m-10) cc_final: 0.7667 (m-10) REVERT: D 992 ASP cc_start: 0.8325 (m-30) cc_final: 0.8082 (m-30) outliers start: 25 outliers final: 17 residues processed: 392 average time/residue: 0.1850 time to fit residues: 117.7778 Evaluate side-chains 359 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 341 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain D residue 719 ILE Chi-restraints excluded: chain D residue 924 LEU Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 952 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 150 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 298 optimal weight: 7.9990 chunk 383 optimal weight: 0.0870 chunk 96 optimal weight: 7.9990 chunk 274 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 278 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 chunk 187 optimal weight: 0.7980 chunk 60 optimal weight: 20.0000 overall best weight: 2.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1081 GLN ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 638 ASN ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.211913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.181018 restraints weight = 78067.906| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 2.56 r_work: 0.3697 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3653 r_free = 0.3653 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3653 r_free = 0.3653 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 32592 Z= 0.147 Angle : 0.586 8.183 44156 Z= 0.303 Chirality : 0.046 0.219 4912 Planarity : 0.004 0.090 5652 Dihedral : 6.851 96.348 4672 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.86 % Allowed : 7.78 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.13), residues: 4068 helix: 0.42 (0.12), residues: 1836 sheet: -0.66 (0.21), residues: 648 loop : -1.21 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 995 TYR 0.024 0.001 TYR A 124 PHE 0.016 0.002 PHE D 785 TRP 0.011 0.001 TRP B 40 HIS 0.005 0.001 HIS A 410 Details of bonding type rmsd covalent geometry : bond 0.00354 (32592) covalent geometry : angle 0.58563 (44156) hydrogen bonds : bond 0.03689 ( 1433) hydrogen bonds : angle 4.51975 ( 4125) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 354 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 847 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7903 (pt0) REVERT: C 405 PHE cc_start: 0.8793 (m-80) cc_final: 0.8563 (m-80) REVERT: C 547 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7419 (mm-30) REVERT: D 615 GLN cc_start: 0.8020 (tm-30) cc_final: 0.7579 (mt0) outliers start: 25 outliers final: 20 residues processed: 366 average time/residue: 0.1842 time to fit residues: 110.5508 Evaluate side-chains 356 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 335 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain D residue 696 THR Chi-restraints excluded: chain D residue 719 ILE Chi-restraints excluded: chain D residue 924 LEU Chi-restraints excluded: chain D residue 925 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 405 optimal weight: 0.0370 chunk 180 optimal weight: 0.7980 chunk 30 optimal weight: 30.0000 chunk 403 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 185 optimal weight: 0.7980 chunk 27 optimal weight: 9.9990 chunk 366 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 ASN ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 HIS D 315 GLN ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 981 ASN D1072 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.216822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.188154 restraints weight = 71558.302| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 2.20 r_work: 0.3665 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3527 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3526 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 32592 Z= 0.106 Angle : 0.533 6.497 44156 Z= 0.275 Chirality : 0.044 0.224 4912 Planarity : 0.004 0.081 5652 Dihedral : 6.215 86.255 4669 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.98 % Allowed : 8.64 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.13), residues: 4068 helix: 0.71 (0.13), residues: 1832 sheet: -0.41 (0.23), residues: 600 loop : -1.12 (0.14), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 127 TYR 0.021 0.001 TYR A 124 PHE 0.013 0.001 PHE A1061 TRP 0.009 0.001 TRP B 40 HIS 0.006 0.000 HIS A 410 Details of bonding type rmsd covalent geometry : bond 0.00238 (32592) covalent geometry : angle 0.53294 (44156) hydrogen bonds : bond 0.03144 ( 1433) hydrogen bonds : angle 4.27404 ( 4125) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 381 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 847 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7809 (pt0) REVERT: B 978 LYS cc_start: 0.7983 (mtpp) cc_final: 0.7638 (mtpp) REVERT: C 547 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7650 (mm-30) REVERT: C 565 GLU cc_start: 0.7123 (tm-30) cc_final: 0.6836 (tm-30) REVERT: C 978 LYS cc_start: 0.8009 (mtpp) cc_final: 0.7763 (mtpp) outliers start: 29 outliers final: 20 residues processed: 396 average time/residue: 0.1868 time to fit residues: 119.9544 Evaluate side-chains 354 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 333 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 542 TYR Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 719 ILE Chi-restraints excluded: chain D residue 925 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 73 optimal weight: 7.9990 chunk 29 optimal weight: 20.0000 chunk 382 optimal weight: 6.9990 chunk 12 optimal weight: 20.0000 chunk 121 optimal weight: 4.9990 chunk 389 optimal weight: 0.7980 chunk 115 optimal weight: 40.0000 chunk 235 optimal weight: 30.0000 chunk 298 optimal weight: 4.9990 chunk 318 optimal weight: 20.0000 chunk 272 optimal weight: 4.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 HIS A1024 ASN ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1024 ASN ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1024 ASN D 168 HIS D 315 GLN ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.208989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.180122 restraints weight = 75949.351| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 2.27 r_work: 0.3700 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3640 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3636 r_free = 0.3636 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3636 r_free = 0.3636 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3636 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 32592 Z= 0.239 Angle : 0.633 8.619 44156 Z= 0.325 Chirality : 0.048 0.218 4912 Planarity : 0.004 0.078 5652 Dihedral : 6.514 95.572 4667 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.07 % Allowed : 10.18 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.13), residues: 4068 helix: 0.50 (0.12), residues: 1828 sheet: -0.48 (0.23), residues: 608 loop : -1.10 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 995 TYR 0.022 0.002 TYR B 124 PHE 0.018 0.002 PHE A 785 TRP 0.009 0.001 TRP C 276 HIS 0.006 0.001 HIS A1086 Details of bonding type rmsd covalent geometry : bond 0.00593 (32592) covalent geometry : angle 0.63340 (44156) hydrogen bonds : bond 0.04103 ( 1433) hydrogen bonds : angle 4.54224 ( 4125) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 362 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 547 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7487 (mm-30) REVERT: A 615 GLN cc_start: 0.8150 (tm-30) cc_final: 0.7862 (tm-30) REVERT: A 847 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7980 (pt0) REVERT: C 547 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7464 (mm-30) REVERT: D 924 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8461 (tp) outliers start: 32 outliers final: 23 residues processed: 379 average time/residue: 0.1814 time to fit residues: 112.8411 Evaluate side-chains 361 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 336 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 542 TYR Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 696 THR Chi-restraints excluded: chain D residue 719 ILE Chi-restraints excluded: chain D residue 924 LEU Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 985 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 377 optimal weight: 6.9990 chunk 2 optimal weight: 30.0000 chunk 234 optimal weight: 10.0000 chunk 378 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 372 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 277 optimal weight: 8.9990 chunk 30 optimal weight: 30.0000 chunk 358 optimal weight: 3.9990 chunk 385 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 ASN ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 HIS D 671 ASN ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.208437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.178994 restraints weight = 73138.808| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 2.28 r_work: 0.3683 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3626 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 32592 Z= 0.233 Angle : 0.635 8.593 44156 Z= 0.327 Chirality : 0.048 0.237 4912 Planarity : 0.004 0.076 5652 Dihedral : 6.570 99.497 4667 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.34 % Allowed : 10.87 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.13), residues: 4068 helix: 0.39 (0.12), residues: 1828 sheet: -0.46 (0.23), residues: 608 loop : -1.12 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 995 TYR 0.021 0.002 TYR B 124 PHE 0.016 0.002 PHE A 785 TRP 0.008 0.001 TRP B 40 HIS 0.005 0.001 HIS A1086 Details of bonding type rmsd covalent geometry : bond 0.00577 (32592) covalent geometry : angle 0.63468 (44156) hydrogen bonds : bond 0.04078 ( 1433) hydrogen bonds : angle 4.55388 ( 4125) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 354 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 547 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7410 (mm-30) REVERT: A 615 GLN cc_start: 0.8129 (tm-30) cc_final: 0.7863 (tm-30) REVERT: A 847 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.8014 (pt0) REVERT: C 547 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7509 (mm-30) REVERT: C 1035 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7871 (m-30) outliers start: 41 outliers final: 30 residues processed: 377 average time/residue: 0.1887 time to fit residues: 117.0498 Evaluate side-chains 377 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 345 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 545 HIS Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain B residue 1024 ASN Chi-restraints excluded: chain B residue 1060 ILE Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 542 TYR Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 1024 ASN Chi-restraints excluded: chain C residue 1035 ASP Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 696 THR Chi-restraints excluded: chain D residue 719 ILE Chi-restraints excluded: chain D residue 924 LEU Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 985 MET Chi-restraints excluded: chain D residue 1077 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 384 optimal weight: 0.5980 chunk 344 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 105 optimal weight: 0.0000 chunk 221 optimal weight: 8.9990 chunk 382 optimal weight: 0.8980 chunk 157 optimal weight: 7.9990 chunk 397 optimal weight: 0.2980 chunk 57 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 109 optimal weight: 20.0000 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 315 GLN ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.215309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.184707 restraints weight = 64303.948| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 2.24 r_work: 0.3761 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3702 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3711 r_free = 0.3711 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3711 r_free = 0.3711 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 32592 Z= 0.104 Angle : 0.538 7.683 44156 Z= 0.278 Chirality : 0.044 0.270 4912 Planarity : 0.004 0.072 5652 Dihedral : 6.019 85.992 4667 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.77 % Allowed : 11.85 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.13), residues: 4068 helix: 0.70 (0.12), residues: 1840 sheet: -0.32 (0.22), residues: 648 loop : -0.97 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 995 TYR 0.019 0.001 TYR A 124 PHE 0.015 0.001 PHE A1061 TRP 0.008 0.001 TRP B 49 HIS 0.003 0.000 HIS D1072 Details of bonding type rmsd covalent geometry : bond 0.00230 (32592) covalent geometry : angle 0.53758 (44156) hydrogen bonds : bond 0.03110 ( 1433) hydrogen bonds : angle 4.22305 ( 4125) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 364 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 494 SER cc_start: 0.8397 (m) cc_final: 0.8151 (t) REVERT: A 615 GLN cc_start: 0.8112 (tm-30) cc_final: 0.7824 (tm-30) REVERT: B 971 MET cc_start: 0.8597 (mmm) cc_final: 0.8394 (mmt) REVERT: D 327 MET cc_start: 0.5813 (mtm) cc_final: 0.5596 (mpp) outliers start: 22 outliers final: 20 residues processed: 373 average time/residue: 0.1906 time to fit residues: 117.3285 Evaluate side-chains 364 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 344 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain B residue 1024 ASN Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 542 TYR Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 1024 ASN Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 719 ILE Chi-restraints excluded: chain D residue 924 LEU Chi-restraints excluded: chain D residue 925 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 176 optimal weight: 7.9990 chunk 327 optimal weight: 30.0000 chunk 296 optimal weight: 2.9990 chunk 200 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 378 optimal weight: 8.9990 chunk 226 optimal weight: 10.0000 chunk 292 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 283 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 638 ASN ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 315 GLN ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 638 ASN ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.211902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.182514 restraints weight = 72062.994| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 2.30 r_work: 0.3748 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.3702 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3712 r_free = 0.3712 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3712 r_free = 0.3712 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32592 Z= 0.140 Angle : 0.557 7.748 44156 Z= 0.286 Chirality : 0.045 0.266 4912 Planarity : 0.004 0.071 5652 Dihedral : 5.987 84.664 4664 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.89 % Allowed : 11.94 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.13), residues: 4068 helix: 0.77 (0.12), residues: 1832 sheet: -0.30 (0.22), residues: 648 loop : -0.91 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 995 TYR 0.019 0.001 TYR A 124 PHE 0.013 0.001 PHE A 785 TRP 0.007 0.001 TRP D 827 HIS 0.003 0.001 HIS A1086 Details of bonding type rmsd covalent geometry : bond 0.00341 (32592) covalent geometry : angle 0.55715 (44156) hydrogen bonds : bond 0.03386 ( 1433) hydrogen bonds : angle 4.24793 ( 4125) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 361 time to evaluate : 1.246 Fit side-chains revert: symmetry clash REVERT: A 494 SER cc_start: 0.8515 (m) cc_final: 0.8264 (t) REVERT: C 405 PHE cc_start: 0.8783 (m-80) cc_final: 0.8516 (m-80) REVERT: C 547 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7550 (mm-30) outliers start: 26 outliers final: 23 residues processed: 372 average time/residue: 0.1879 time to fit residues: 114.3627 Evaluate side-chains 374 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 351 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 542 TYR Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain B residue 1024 ASN Chi-restraints excluded: chain B residue 1060 ILE Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 542 TYR Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 1024 ASN Chi-restraints excluded: chain C residue 1035 ASP Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 719 ILE Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 1077 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 166 optimal weight: 4.9990 chunk 3 optimal weight: 0.0980 chunk 349 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 244 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 239 optimal weight: 10.0000 chunk 268 optimal weight: 7.9990 chunk 253 optimal weight: 7.9990 chunk 187 optimal weight: 0.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 638 ASN ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.210823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.179840 restraints weight = 56293.276| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 2.10 r_work: 0.3753 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3690 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3686 r_free = 0.3686 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3686 r_free = 0.3686 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 32592 Z= 0.166 Angle : 0.586 8.623 44156 Z= 0.300 Chirality : 0.046 0.264 4912 Planarity : 0.004 0.071 5652 Dihedral : 6.076 86.575 4664 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.98 % Allowed : 11.97 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.13), residues: 4068 helix: 0.66 (0.12), residues: 1836 sheet: -0.53 (0.22), residues: 624 loop : -0.89 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 691 TYR 0.020 0.001 TYR B 124 PHE 0.013 0.001 PHE A 785 TRP 0.007 0.001 TRP B 40 HIS 0.003 0.001 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00408 (32592) covalent geometry : angle 0.58567 (44156) hydrogen bonds : bond 0.03616 ( 1433) hydrogen bonds : angle 4.33064 ( 4125) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 353 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: A 494 SER cc_start: 0.8518 (m) cc_final: 0.8267 (t) REVERT: C 405 PHE cc_start: 0.8816 (m-80) cc_final: 0.8577 (m-80) outliers start: 29 outliers final: 29 residues processed: 367 average time/residue: 0.1902 time to fit residues: 114.2184 Evaluate side-chains 375 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 346 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 1024 ASN Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 542 TYR Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain B residue 1024 ASN Chi-restraints excluded: chain B residue 1060 ILE Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 542 TYR Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 1024 ASN Chi-restraints excluded: chain C residue 1035 ASP Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 696 THR Chi-restraints excluded: chain D residue 719 ILE Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 1077 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 391 optimal weight: 1.9990 chunk 295 optimal weight: 0.9990 chunk 242 optimal weight: 6.9990 chunk 186 optimal weight: 0.9980 chunk 203 optimal weight: 4.9990 chunk 296 optimal weight: 1.9990 chunk 223 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 402 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 315 GLN ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.212948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.181243 restraints weight = 53616.251| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 2.12 r_work: 0.3773 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3717 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3711 r_free = 0.3711 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3711 r_free = 0.3711 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32592 Z= 0.118 Angle : 0.549 8.810 44156 Z= 0.282 Chirality : 0.044 0.268 4912 Planarity : 0.004 0.070 5652 Dihedral : 5.879 81.484 4664 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.98 % Allowed : 12.00 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.13), residues: 4068 helix: 0.80 (0.12), residues: 1828 sheet: -0.48 (0.22), residues: 632 loop : -0.81 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 691 TYR 0.019 0.001 TYR A 124 PHE 0.017 0.001 PHE A 405 TRP 0.006 0.001 TRP B 827 HIS 0.002 0.001 HIS A 900 Details of bonding type rmsd covalent geometry : bond 0.00279 (32592) covalent geometry : angle 0.54935 (44156) hydrogen bonds : bond 0.03227 ( 1433) hydrogen bonds : angle 4.20338 ( 4125) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 359 time to evaluate : 1.197 Fit side-chains revert: symmetry clash REVERT: A 494 SER cc_start: 0.8399 (m) cc_final: 0.8163 (t) REVERT: C 547 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7516 (mm-30) outliers start: 29 outliers final: 29 residues processed: 371 average time/residue: 0.1983 time to fit residues: 120.2466 Evaluate side-chains 383 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 354 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain B residue 1024 ASN Chi-restraints excluded: chain B residue 1060 ILE Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 542 TYR Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 1024 ASN Chi-restraints excluded: chain C residue 1035 ASP Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 542 TYR Chi-restraints excluded: chain D residue 696 THR Chi-restraints excluded: chain D residue 719 ILE Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 1077 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 390 optimal weight: 0.9990 chunk 190 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 387 optimal weight: 0.8980 chunk 33 optimal weight: 30.0000 chunk 288 optimal weight: 0.5980 chunk 135 optimal weight: 8.9990 chunk 265 optimal weight: 5.9990 chunk 115 optimal weight: 30.0000 chunk 151 optimal weight: 8.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 315 GLN ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.213922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.183558 restraints weight = 64895.044| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 2.24 r_work: 0.3740 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3669 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3666 r_free = 0.3666 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3666 r_free = 0.3666 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32592 Z= 0.123 Angle : 0.552 9.104 44156 Z= 0.283 Chirality : 0.044 0.259 4912 Planarity : 0.004 0.070 5652 Dihedral : 5.810 78.115 4664 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.07 % Allowed : 12.14 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.13), residues: 4068 helix: 0.82 (0.12), residues: 1836 sheet: -0.44 (0.22), residues: 632 loop : -0.79 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 691 TYR 0.020 0.001 TYR A 124 PHE 0.017 0.001 PHE A 405 TRP 0.007 0.001 TRP C 827 HIS 0.002 0.001 HIS C 168 Details of bonding type rmsd covalent geometry : bond 0.00293 (32592) covalent geometry : angle 0.55183 (44156) hydrogen bonds : bond 0.03232 ( 1433) hydrogen bonds : angle 4.18698 ( 4125) =============================================================================== Job complete usr+sys time: 8436.87 seconds wall clock time: 145 minutes 2.57 seconds (8702.57 seconds total)