Starting phenix.real_space_refine on Mon Sep 14 14:49:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ui9_20783/09_2026/6ui9_20783.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ui9_20783/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6ui9_20783/09_2026/6ui9_20783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ui9_20783/09_2026/6ui9_20783.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6ui9_20783/09_2026/6ui9_20783.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ui9_20783/09_2026/6ui9_20783.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ui9_20783/09_2026/6ui9_20783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ui9_20783/09_2026/6ui9_20783.map" } 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): 0.24s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 11.40, per 1000 atoms: 0.36 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: 2.79 Conformation dependent library (CDL) restraints added in 2.3 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: 1.17 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: 8.51 Time building geometry restraints manager: 3.64 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: 17946 22.40 - 44.80: 1221 44.80 - 67.20: 181 67.20 - 89.60: 36 89.60 - 112.00: 4 Dihedral angle restraints: 19388 sinusoidal: 7748 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 19385 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 37.710 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 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 : 15.071 111.996 11996 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/Z covalent geometry : bond 0.00799 / 0.50 (32592) covalent geometry : angle 0.90563 / 0.54 (44156) hydrogen bonds : bond 0.14353 / 9.82 ( 1433) hydrogen bonds : angle 6.46793 / 4.56 ( 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 : 1.084 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: 0.1989 time to fit residues: 143.7061 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 : 1.085 ------------------------------------------------------------------------------- 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... ** 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 = 0.4374 r_free = 0.4374 target = 0.214698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.184931 restraints weight = 65926.073| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 2.18 r_work: 0.3524 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3478 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.3478 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 32592 Z= 0.134 Angle : 0.605 8.251 44156 Z= 0.316 Chirality : 0.046 0.227 4912 Planarity : 0.004 0.098 5652 Dihedral : 7.065 101.057 4556 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.83 % Allowed : 5.43 % Favored : 93.74 % 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: -0.87 (0.13), residues: 4068 helix: 0.21 (0.12), residues: 1836 sheet: -0.63 (0.22), residues: 596 loop : -1.38 (0.14), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 995 TYR 0.025 0.001 TYR B 124 PHE 0.015 0.002 PHE A 29 TRP 0.016 0.001 TRP B 40 HIS 0.005 0.001 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (32592) covalent geometry : angle 0.60501 / 0.32 (44156) hydrogen bonds : bond 0.03747 / 2.55 ( 1433) hydrogen bonds : angle 4.73676 / 3.32 ( 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: 24 poor density : 380 time to evaluate : 1.267 Fit side-chains revert: symmetry clash REVERT: A 547 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7405 (mm-30) REVERT: A 615 GLN cc_start: 0.8012 (tm-30) cc_final: 0.7688 (mt0) REVERT: A 691 ARG cc_start: 0.7596 (ptt90) cc_final: 0.7260 (ptt90) REVERT: A 847 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7614 (pt0) REVERT: C 494 SER cc_start: 0.8374 (m) cc_final: 0.8075 (p) REVERT: C 692 TYR cc_start: 0.7859 (m-10) cc_final: 0.7628 (m-10) REVERT: D 992 ASP cc_start: 0.7885 (m-30) cc_final: 0.7635 (m-30) outliers start: 24 outliers final: 16 residues processed: 392 average time/residue: 0.2055 time to fit residues: 131.4948 Evaluate side-chains 357 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 340 time to evaluate : 1.174 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 192 optimal weight: 0.0050 chunk 298 optimal weight: 7.9990 chunk 383 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 274 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 278 optimal weight: 0.0470 chunk 168 optimal weight: 5.9990 chunk 187 optimal weight: 0.7980 chunk 60 optimal weight: 20.0000 overall best weight: 0.7694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** 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 315 GLN ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1072 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.218108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.178845 restraints weight = 78394.253| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 3.23 r_work: 0.3203 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 32592 Z= 0.107 Angle : 0.547 6.772 44156 Z= 0.284 Chirality : 0.044 0.217 4912 Planarity : 0.004 0.088 5652 Dihedral : 6.052 89.657 4508 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.83 % Allowed : 7.54 % Favored : 91.63 % 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: -0.50 (0.13), residues: 4068 helix: 0.55 (0.13), residues: 1832 sheet: -0.51 (0.22), residues: 600 loop : -1.20 (0.14), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 995 TYR 0.025 0.001 TYR A 124 PHE 0.016 0.001 PHE D 785 TRP 0.011 0.001 TRP B 40 HIS 0.005 0.000 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (32592) covalent geometry : angle 0.54740 / 0.28 (44156) hydrogen bonds : bond 0.03324 / 2.26 ( 1433) hydrogen bonds : angle 4.37449 / 3.06 ( 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 402 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 378 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 615 GLN cc_start: 0.8010 (tm-30) cc_final: 0.7697 (mt0) REVERT: A 691 ARG cc_start: 0.7757 (ptt90) cc_final: 0.7371 (ptt90) REVERT: A 735 ARG cc_start: 0.7723 (tpt90) cc_final: 0.7449 (tpt-90) REVERT: A 847 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7928 (pt0) REVERT: B 327 MET cc_start: 0.6566 (mtm) cc_final: 0.6261 (mtm) REVERT: B 978 LYS cc_start: 0.7854 (mtpp) cc_final: 0.7149 (mtpp) REVERT: C 405 PHE cc_start: 0.8459 (m-80) cc_final: 0.7956 (m-80) REVERT: C 494 SER cc_start: 0.8399 (m) cc_final: 0.7995 (p) REVERT: D 327 MET cc_start: 0.6436 (mtm) cc_final: 0.6191 (mtm) REVERT: D 615 GLN cc_start: 0.8181 (tm-30) cc_final: 0.7615 (mt0) REVERT: D 735 ARG cc_start: 0.7209 (tpt-90) cc_final: 0.6985 (tpt170) outliers start: 24 outliers final: 18 residues processed: 387 average time/residue: 0.2029 time to fit residues: 128.2996 Evaluate side-chains 357 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 338 time to evaluate : 1.177 ------------------------------------------------------------------------------- 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 358 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 405 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 30 optimal weight: 30.0000 chunk 403 optimal weight: 0.6980 chunk 56 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 185 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 366 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 142 optimal weight: 3.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 HIS A 410 HIS ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1024 ASN A1081 GLN ** 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** ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1024 ASN D 315 GLN ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 981 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.212055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.182014 restraints weight = 71482.231| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 2.31 r_work: 0.3754 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work: 0.3708 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3722 r_free = 0.3722 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3722 r_free = 0.3722 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1601 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= 0.154 Angle : 0.570 8.094 44156 Z= 0.294 Chirality : 0.045 0.203 4912 Planarity : 0.004 0.082 5652 Dihedral : 5.951 89.859 4505 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.89 % Allowed : 8.70 % Favored : 90.41 % 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: -0.41 (0.13), residues: 4068 helix: 0.61 (0.13), residues: 1836 sheet: -0.53 (0.22), residues: 648 loop : -1.12 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 995 TYR 0.022 0.001 TYR A 124 PHE 0.016 0.001 PHE A 785 TRP 0.009 0.001 TRP B 40 HIS 0.006 0.001 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.15 (32592) covalent geometry : angle 0.57008 / 0.29 (44156) hydrogen bonds : bond 0.03570 / 2.43 ( 1433) hydrogen bonds : angle 4.38738 / 3.06 ( 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 383 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 357 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 494 SER cc_start: 0.8471 (m) cc_final: 0.8204 (t) REVERT: A 547 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7389 (mm-30) REVERT: A 847 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7765 (pt0) REVERT: B 1035 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7805 (m-30) REVERT: C 565 GLU cc_start: 0.7025 (tm-30) cc_final: 0.6733 (tm-30) REVERT: C 1035 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7822 (m-30) outliers start: 26 outliers final: 20 residues processed: 368 average time/residue: 0.2026 time to fit residues: 122.0282 Evaluate side-chains 363 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 340 time to evaluate : 1.346 ------------------------------------------------------------------------------- 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 358 VAL Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain B residue 1035 ASP 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 1035 ASP 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 73 optimal weight: 3.9990 chunk 29 optimal weight: 20.0000 chunk 382 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 121 optimal weight: 4.9990 chunk 389 optimal weight: 3.9990 chunk 115 optimal weight: 50.0000 chunk 235 optimal weight: 10.0000 chunk 298 optimal weight: 4.9990 chunk 318 optimal weight: 20.0000 chunk 272 optimal weight: 40.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 91 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 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 HIS ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 996 GLN D 997 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.208382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.178945 restraints weight = 75844.819| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 2.30 r_work: 0.3680 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3611 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3611 r_free = 0.3611 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3611 r_free = 0.3611 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3611 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 32592 Z= 0.247 Angle : 0.644 9.120 44156 Z= 0.330 Chirality : 0.048 0.219 4912 Planarity : 0.004 0.078 5652 Dihedral : 6.247 99.200 4505 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.31 % Allowed : 9.68 % Favored : 89.01 % 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: -0.54 (0.13), residues: 4068 helix: 0.45 (0.12), residues: 1828 sheet: -0.49 (0.23), residues: 608 loop : -1.14 (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 0.017 0.002 PHE C 405 TRP 0.008 0.001 TRP B 40 HIS 0.006 0.001 HIS A1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.25 (32592) covalent geometry : angle 0.64380 / 0.33 (44156) hydrogen bonds : bond 0.04178 / 2.85 ( 1433) hydrogen bonds : angle 4.57856 / 3.18 ( 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 405 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 365 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 547 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7385 (mm-30) REVERT: A 615 GLN cc_start: 0.8166 (tm-30) cc_final: 0.7885 (tm-30) REVERT: A 847 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8016 (pt0) REVERT: C 496 HIS cc_start: 0.8223 (m90) cc_final: 0.7940 (p-80) REVERT: C 1035 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7855 (m-30) outliers start: 40 outliers final: 30 residues processed: 385 average time/residue: 0.2033 time to fit residues: 128.8054 Evaluate side-chains 375 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 343 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 326 LEU 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 358 VAL Chi-restraints excluded: chain B residue 545 HIS 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 156 VAL Chi-restraints excluded: chain C residue 542 TYR Chi-restraints excluded: chain C residue 545 HIS Chi-restraints excluded: chain C residue 719 ILE 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 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 925 THR Chi-restraints excluded: chain D residue 977 VAL Chi-restraints excluded: chain D residue 1077 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 377 optimal weight: 10.0000 chunk 2 optimal weight: 0.0170 chunk 234 optimal weight: 20.0000 chunk 378 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 372 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 277 optimal weight: 20.0000 chunk 30 optimal weight: 30.0000 chunk 358 optimal weight: 0.7980 chunk 385 optimal weight: 0.6980 overall best weight: 1.5022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 ASN B 168 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.212680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.181683 restraints weight = 73477.600| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 2.43 r_work: 0.3720 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3667 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3659 r_free = 0.3659 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 = 0.3659 r_free = 0.3659 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1890 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= 0.121 Angle : 0.549 7.312 44156 Z= 0.283 Chirality : 0.044 0.244 4912 Planarity : 0.004 0.075 5652 Dihedral : 5.718 90.536 4503 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.10 % Allowed : 10.75 % Favored : 88.15 % 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: -0.28 (0.13), residues: 4068 helix: 0.66 (0.13), residues: 1832 sheet: -0.36 (0.22), residues: 648 loop : -1.01 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 995 TYR 0.020 0.001 TYR A 124 PHE 0.014 0.001 PHE C 405 TRP 0.007 0.001 TRP B 40 HIS 0.003 0.000 HIS A 900 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (32592) covalent geometry : angle 0.54948 / 0.28 (44156) hydrogen bonds : bond 0.03308 / 2.24 ( 1433) hydrogen bonds : angle 4.28966 / 2.98 ( 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 400 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 367 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 494 SER cc_start: 0.8488 (m) cc_final: 0.8233 (t) REVERT: A 547 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7419 (mm-30) REVERT: A 615 GLN cc_start: 0.8143 (tm-30) cc_final: 0.7856 (tm-30) REVERT: A 732 LYS cc_start: 0.7888 (mmpt) cc_final: 0.7650 (mmtp) REVERT: C 971 MET cc_start: 0.8745 (mmm) cc_final: 0.8543 (mmt) outliers start: 33 outliers final: 26 residues processed: 383 average time/residue: 0.2026 time to fit residues: 128.8862 Evaluate side-chains 374 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 348 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 326 LEU 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 156 VAL 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 10 THR 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 1035 ASP 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 384 optimal weight: 1.9990 chunk 344 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 105 optimal weight: 40.0000 chunk 221 optimal weight: 30.0000 chunk 382 optimal weight: 2.9990 chunk 157 optimal weight: 9.9990 chunk 397 optimal weight: 0.0870 chunk 57 optimal weight: 0.8980 chunk 23 optimal weight: 0.0670 chunk 109 optimal weight: 30.0000 overall best weight: 1.2100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 410 HIS ** 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 = 0.4362 r_free = 0.4362 target = 0.214353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.183883 restraints weight = 64138.624| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 2.31 r_work: 0.3788 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3742 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3739 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3739 r_free = 0.3739 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3739 r_free = 0.3739 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3739 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2069 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= 0.113 Angle : 0.537 7.220 44156 Z= 0.277 Chirality : 0.044 0.252 4912 Planarity : 0.004 0.072 5652 Dihedral : 5.435 81.730 4500 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.98 % Allowed : 11.43 % Favored : 87.59 % 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: -0.09 (0.13), residues: 4068 helix: 0.81 (0.13), residues: 1832 sheet: -0.25 (0.22), residues: 656 loop : -0.91 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 995 TYR 0.020 0.001 TYR B 124 PHE 0.014 0.001 PHE C 405 TRP 0.007 0.001 TRP B 827 HIS 0.002 0.000 HIS A 700 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (32592) covalent geometry : angle 0.53714 / 0.28 (44156) hydrogen bonds : bond 0.03195 / 2.16 ( 1433) hydrogen bonds : angle 4.20937 / 2.93 ( 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 391 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 362 time to evaluate : 1.205 Fit side-chains revert: symmetry clash REVERT: A 494 SER cc_start: 0.8308 (m) cc_final: 0.8083 (t) REVERT: A 547 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7373 (mm-30) REVERT: A 615 GLN cc_start: 0.8077 (tm-30) cc_final: 0.7856 (tm-30) outliers start: 29 outliers final: 26 residues processed: 375 average time/residue: 0.2034 time to fit residues: 125.7055 Evaluate side-chains 370 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 344 time to evaluate : 1.244 ------------------------------------------------------------------------------- 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 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 C residue 10 THR 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 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 279 VAL 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=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: 1.9990 chunk 200 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 378 optimal weight: 6.9990 chunk 226 optimal weight: 9.9990 chunk 292 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 283 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 638 ASN ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS ** 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 168 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.213218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.181854 restraints weight = 72257.202| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 2.49 r_work: 0.3706 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3655 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3663 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3663 r_free = 0.3663 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 = 0.3663 r_free = 0.3663 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3663 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32592 Z= 0.134 Angle : 0.552 7.994 44156 Z= 0.283 Chirality : 0.045 0.251 4912 Planarity : 0.004 0.071 5652 Dihedral : 5.406 80.160 4500 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.95 % Allowed : 11.67 % 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: -0.03 (0.13), residues: 4068 helix: 0.84 (0.13), residues: 1828 sheet: -0.21 (0.22), residues: 648 loop : -0.87 (0.15), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 691 TYR 0.020 0.001 TYR A 124 PHE 0.014 0.001 PHE C 405 TRP 0.007 0.001 TRP B 827 HIS 0.002 0.001 HIS A 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 (32592) covalent geometry : angle 0.55150 / 0.28 (44156) hydrogen bonds : bond 0.03336 / 2.27 ( 1433) hydrogen bonds : angle 4.24785 / 2.95 ( 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 381 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 353 time to evaluate : 1.198 Fit side-chains revert: symmetry clash REVERT: A 494 SER cc_start: 0.8411 (m) cc_final: 0.8165 (t) REVERT: A 615 GLN cc_start: 0.8164 (tm-30) cc_final: 0.7893 (tm-30) REVERT: A 971 MET cc_start: 0.8724 (mmm) cc_final: 0.8488 (mmt) REVERT: C 971 MET cc_start: 0.8817 (mmm) cc_final: 0.8587 (mmt) outliers start: 28 outliers final: 27 residues processed: 366 average time/residue: 0.1979 time to fit residues: 118.9943 Evaluate side-chains 372 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 345 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 123 ILE 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 C residue 10 THR 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 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 279 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 166 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 349 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 244 optimal weight: 30.0000 chunk 96 optimal weight: 0.0770 chunk 239 optimal weight: 9.9990 chunk 268 optimal weight: 6.9990 chunk 253 optimal weight: 9.9990 chunk 187 optimal weight: 0.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.210300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.179036 restraints weight = 56338.544| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 2.12 r_work: 0.3743 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3686 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 32592 Z= 0.181 Angle : 0.592 8.677 44156 Z= 0.303 Chirality : 0.046 0.241 4912 Planarity : 0.004 0.070 5652 Dihedral : 5.624 85.693 4500 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.10 % Allowed : 11.52 % 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: 0.71 (0.12), residues: 1828 sheet: -0.46 (0.22), residues: 624 loop : -0.89 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 691 TYR 0.019 0.002 TYR A 124 PHE 0.014 0.002 PHE A 405 TRP 0.007 0.001 TRP B 40 HIS 0.004 0.001 HIS A 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.18 (32592) covalent geometry : angle 0.59166 / 0.30 (44156) hydrogen bonds : bond 0.03723 / 2.53 ( 1433) hydrogen bonds : angle 4.38291 / 3.05 ( 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 386 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 353 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 494 SER cc_start: 0.8531 (m) cc_final: 0.8275 (t) REVERT: A 615 GLN cc_start: 0.8115 (tm-30) cc_final: 0.7891 (tm-30) outliers start: 33 outliers final: 27 residues processed: 369 average time/residue: 0.2108 time to fit residues: 128.0267 Evaluate side-chains 372 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 345 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 123 ILE 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 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 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 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 279 VAL 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: 0.9980 chunk 295 optimal weight: 3.9990 chunk 242 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 203 optimal weight: 0.0770 chunk 296 optimal weight: 0.0370 chunk 223 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 402 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.4220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.212969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.181409 restraints weight = 53656.371| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 2.09 r_work: 0.3795 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3750 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3758 r_free = 0.3758 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3758 r_free = 0.3758 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32592 Z= 0.120 Angle : 0.552 9.026 44156 Z= 0.284 Chirality : 0.044 0.270 4912 Planarity : 0.004 0.070 5652 Dihedral : 5.376 80.775 4500 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.89 % Allowed : 11.88 % Favored : 87.23 % 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: -0.05 (0.13), residues: 4068 helix: 0.82 (0.12), residues: 1828 sheet: -0.41 (0.22), residues: 632 loop : -0.77 (0.15), residues: 1608 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 0.018 0.001 PHE A 405 TRP 0.006 0.001 TRP B 827 HIS 0.002 0.001 HIS C 900 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (32592) covalent geometry : angle 0.55242 / 0.28 (44156) hydrogen bonds : bond 0.03254 / 2.20 ( 1433) hydrogen bonds : angle 4.24205 / 2.95 ( 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 377 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 351 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 494 SER cc_start: 0.8382 (m) cc_final: 0.8147 (t) REVERT: A 615 GLN cc_start: 0.8018 (tm-30) cc_final: 0.7806 (tm-30) outliers start: 26 outliers final: 25 residues processed: 363 average time/residue: 0.2035 time to fit residues: 121.0057 Evaluate side-chains 372 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 347 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 123 ILE 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 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 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 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 390 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 178 optimal weight: 0.0470 chunk 195 optimal weight: 3.9990 chunk 387 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 288 optimal weight: 0.7980 chunk 135 optimal weight: 0.0770 chunk 265 optimal weight: 10.0000 chunk 115 optimal weight: 0.0980 chunk 151 optimal weight: 4.9990 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1024 ASN C 671 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.216946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.186705 restraints weight = 65383.469| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 2.22 r_work: 0.3806 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3752 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3763 r_free = 0.3763 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3763 r_free = 0.3763 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 32592 Z= 0.098 Angle : 0.524 8.950 44156 Z= 0.270 Chirality : 0.044 0.260 4912 Planarity : 0.004 0.069 5652 Dihedral : 5.019 67.174 4500 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.53 % Allowed : 12.41 % 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: 0.21 (0.14), residues: 4068 helix: 1.05 (0.13), residues: 1836 sheet: -0.23 (0.22), residues: 672 loop : -0.68 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 691 TYR 0.019 0.001 TYR A 124 PHE 0.017 0.001 PHE A 405 TRP 0.008 0.001 TRP D 877 HIS 0.003 0.000 HIS A 700 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (32592) covalent geometry : angle 0.52368 / 0.27 (44156) hydrogen bonds : bond 0.02885 / 1.95 ( 1433) hydrogen bonds : angle 4.09109 / 2.84 ( 4125) =============================================================================== Job complete usr+sys time: 8861.92 seconds wall clock time: 152 minutes 31.81 seconds (9151.81 seconds total)