Starting phenix.real_space_refine on Sat Jul 4 03:39:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gn7_34156/07_2026/8gn7_34156.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gn7_34156/07_2026/8gn7_34156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gn7_34156/07_2026/8gn7_34156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gn7_34156/07_2026/8gn7_34156.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8gn7_34156/07_2026/8gn7_34156.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gn7_34156/07_2026/8gn7_34156.cif" model { file = "/net/cci-nas-00/data/ceres_data/8gn7_34156/07_2026/8gn7_34156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gn7_34156/07_2026/8gn7_34156.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.103 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 20 5.49 5 S 140 5.16 5 C 11900 2.51 5 N 2710 2.21 5 O 2760 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17530 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1588 Classifications: {'peptide': 203} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 190} Chain breaks: 1 Chain: "B" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1588 Classifications: {'peptide': 203} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 190} Chain breaks: 1 Chain: "G" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1588 Classifications: {'peptide': 203} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 190} Chain breaks: 1 Chain: "J" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1588 Classifications: {'peptide': 203} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 190} Chain breaks: 1 Chain: "M" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1588 Classifications: {'peptide': 203} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 190} Chain breaks: 1 Chain: "P" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1588 Classifications: {'peptide': 203} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 190} Chain breaks: 1 Chain: "S" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1588 Classifications: {'peptide': 203} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 190} Chain breaks: 1 Chain: "V" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1588 Classifications: {'peptide': 203} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 190} Chain breaks: 1 Chain: "Y" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1588 Classifications: {'peptide': 203} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 190} Chain breaks: 1 Chain: "b" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1588 Classifications: {'peptide': 203} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 190} Chain breaks: 1 Chain: "A" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 165 Unusual residues: {'3PE': 1, 'CLR': 3, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "B" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 165 Unusual residues: {'3PE': 1, 'CLR': 3, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "G" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 165 Unusual residues: {'3PE': 1, 'CLR': 3, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "J" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 137 Unusual residues: {'3PE': 1, 'CLR': 2, 'PTY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "M" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 193 Unusual residues: {'3PE': 1, 'CLR': 4, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "P" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 137 Unusual residues: {'3PE': 1, 'CLR': 2, 'PTY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "S" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 193 Unusual residues: {'3PE': 1, 'CLR': 4, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "V" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 137 Unusual residues: {'3PE': 1, 'CLR': 2, 'PTY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "Y" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 193 Unusual residues: {'3PE': 1, 'CLR': 4, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "b" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 165 Unusual residues: {'3PE': 1, 'CLR': 3, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Time building chain proxies: 4.54, per 1000 atoms: 0.26 Number of scatterers: 17530 At special positions: 0 Unit cell: (92.92, 91.08, 179.4, 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 140 16.00 P 20 15.00 O 2760 8.00 N 2710 7.00 C 11900 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 186 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 180 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 186 " distance=2.03 Simple disulfide: pdb=" SG CYS G 61 " - pdb=" SG CYS G 180 " distance=2.03 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 175 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 186 " distance=2.03 Simple disulfide: pdb=" SG CYS J 61 " - pdb=" SG CYS J 180 " distance=2.03 Simple disulfide: pdb=" SG CYS J 65 " - pdb=" SG CYS J 175 " distance=2.03 Simple disulfide: pdb=" SG CYS M 54 " - pdb=" SG CYS M 186 " distance=2.03 Simple disulfide: pdb=" SG CYS M 61 " - pdb=" SG CYS M 180 " distance=2.03 Simple disulfide: pdb=" SG CYS M 65 " - pdb=" SG CYS M 175 " distance=2.03 Simple disulfide: pdb=" SG CYS P 54 " - pdb=" SG CYS P 186 " distance=2.03 Simple disulfide: pdb=" SG CYS P 61 " - pdb=" SG CYS P 180 " distance=2.03 Simple disulfide: pdb=" SG CYS P 65 " - pdb=" SG CYS P 175 " distance=2.03 Simple disulfide: pdb=" SG CYS S 54 " - pdb=" SG CYS S 186 " distance=2.03 Simple disulfide: pdb=" SG CYS S 61 " - pdb=" SG CYS S 180 " distance=2.03 Simple disulfide: pdb=" SG CYS S 65 " - pdb=" SG CYS S 175 " distance=2.03 Simple disulfide: pdb=" SG CYS V 54 " - pdb=" SG CYS V 186 " distance=2.03 Simple disulfide: pdb=" SG CYS V 61 " - pdb=" SG CYS V 180 " distance=2.03 Simple disulfide: pdb=" SG CYS V 65 " - pdb=" SG CYS V 175 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 54 " - pdb=" SG CYS Y 186 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 61 " - pdb=" SG CYS Y 180 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 65 " - pdb=" SG CYS Y 175 " distance=2.03 Simple disulfide: pdb=" SG CYS b 54 " - pdb=" SG CYS b 186 " distance=2.03 Simple disulfide: pdb=" SG CYS b 61 " - pdb=" SG CYS b 180 " distance=2.03 Simple disulfide: pdb=" SG CYS b 65 " - pdb=" SG CYS b 175 " distance=2.03 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: 1.73 Conformation dependent library (CDL) restraints added in 699.8 milliseconds 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3760 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 10 sheets defined 66.4% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 8 through 13 Processing helix chain 'A' and resid 14 through 17 removed outlier: 3.878A pdb=" N ASN A 17 " --> pdb=" O LEU A 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 14 through 17' Processing helix chain 'A' and resid 19 through 32 removed outlier: 3.598A pdb=" N MET A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 31 " --> pdb=" O VAL A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 40 removed outlier: 3.834A pdb=" N VAL A 38 " --> pdb=" O MET A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 removed outlier: 4.060A pdb=" N VAL A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 70 Processing helix chain 'A' and resid 73 through 86 removed outlier: 3.525A pdb=" N VAL A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 86 " --> pdb=" O GLY A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 102 removed outlier: 3.540A pdb=" N PHE A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A 102 " --> pdb=" O HIS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 166 removed outlier: 3.849A pdb=" N ILE A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N HIS A 146 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 155 " --> pdb=" O THR A 151 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 226 removed outlier: 3.627A pdb=" N LEU A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 213 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N CYS A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG A 221 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG A 225 " --> pdb=" O ARG A 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 13 removed outlier: 3.513A pdb=" N THR B 13 " --> pdb=" O PHE B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 32 removed outlier: 3.641A pdb=" N MET B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 40 removed outlier: 3.846A pdb=" N VAL B 38 " --> pdb=" O MET B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 70 Processing helix chain 'B' and resid 73 through 86 removed outlier: 3.518A pdb=" N VAL B 85 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU B 86 " --> pdb=" O GLY B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 102 removed outlier: 3.573A pdb=" N PHE B 92 " --> pdb=" O PRO B 88 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER B 93 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B 102 " --> pdb=" O HIS B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 166 removed outlier: 3.977A pdb=" N ILE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N HIS B 146 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU B 154 " --> pdb=" O ARG B 150 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA B 155 " --> pdb=" O THR B 151 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE B 157 " --> pdb=" O LEU B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 226 removed outlier: 3.606A pdb=" N LEU B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 211 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 213 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N CYS B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG B 221 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG B 225 " --> pdb=" O ARG B 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 13 Processing helix chain 'G' and resid 14 through 17 removed outlier: 3.808A pdb=" N ASN G 17 " --> pdb=" O LEU G 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 14 through 17' Processing helix chain 'G' and resid 19 through 32 removed outlier: 3.539A pdb=" N VAL G 27 " --> pdb=" O LYS G 23 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET G 30 " --> pdb=" O PHE G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 40 removed outlier: 3.835A pdb=" N VAL G 38 " --> pdb=" O MET G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 70 Processing helix chain 'G' and resid 73 through 87 removed outlier: 3.508A pdb=" N VAL G 85 " --> pdb=" O GLN G 81 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU G 86 " --> pdb=" O GLY G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 102 removed outlier: 3.584A pdb=" N PHE G 92 " --> pdb=" O PRO G 88 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER G 93 " --> pdb=" O SER G 89 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR G 102 " --> pdb=" O HIS G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 165 removed outlier: 3.840A pdb=" N ILE G 144 " --> pdb=" O SER G 140 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE G 145 " --> pdb=" O ALA G 141 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N HIS G 146 " --> pdb=" O GLY G 142 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA G 155 " --> pdb=" O THR G 151 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA G 156 " --> pdb=" O LEU G 152 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE G 157 " --> pdb=" O LEU G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 192 through 212 removed outlier: 3.596A pdb=" N LEU G 199 " --> pdb=" O SER G 195 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE G 200 " --> pdb=" O LEU G 196 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU G 210 " --> pdb=" O ALA G 206 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU G 211 " --> pdb=" O LEU G 207 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 226 removed outlier: 3.598A pdb=" N VAL G 217 " --> pdb=" O LEU G 213 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N CYS G 218 " --> pdb=" O ALA G 214 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG G 221 " --> pdb=" O VAL G 217 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG G 225 " --> pdb=" O ARG G 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 13 Processing helix chain 'J' and resid 14 through 17 removed outlier: 3.671A pdb=" N ASN J 17 " --> pdb=" O LEU J 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 14 through 17' Processing helix chain 'J' and resid 19 through 32 removed outlier: 3.791A pdb=" N MET J 30 " --> pdb=" O PHE J 26 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU J 31 " --> pdb=" O VAL J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 33 through 40 removed outlier: 3.852A pdb=" N VAL J 38 " --> pdb=" O MET J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 70 Processing helix chain 'J' and resid 73 through 102 removed outlier: 3.506A pdb=" N VAL J 85 " --> pdb=" O GLN J 81 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU J 86 " --> pdb=" O GLY J 82 " (cutoff:3.500A) Proline residue: J 88 - end of helix removed outlier: 3.590A pdb=" N PHE J 92 " --> pdb=" O PRO J 88 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER J 93 " --> pdb=" O SER J 89 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR J 102 " --> pdb=" O HIS J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 165 removed outlier: 3.805A pdb=" N ILE J 144 " --> pdb=" O SER J 140 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE J 145 " --> pdb=" O ALA J 141 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N HIS J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU J 154 " --> pdb=" O ARG J 150 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA J 155 " --> pdb=" O THR J 151 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA J 156 " --> pdb=" O LEU J 152 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE J 157 " --> pdb=" O LEU J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 192 through 226 removed outlier: 3.626A pdb=" N LEU J 199 " --> pdb=" O SER J 195 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU J 210 " --> pdb=" O ALA J 206 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU J 211 " --> pdb=" O LEU J 207 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY J 212 " --> pdb=" O SER J 208 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU J 213 " --> pdb=" O PHE J 209 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL J 217 " --> pdb=" O LEU J 213 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N CYS J 218 " --> pdb=" O ALA J 214 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG J 221 " --> pdb=" O VAL J 217 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG J 225 " --> pdb=" O ARG J 221 " (cutoff:3.500A) Processing helix chain 'M' and resid 8 through 13 Processing helix chain 'M' and resid 19 through 32 removed outlier: 3.809A pdb=" N MET M 30 " --> pdb=" O PHE M 26 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU M 31 " --> pdb=" O VAL M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 33 through 40 removed outlier: 3.809A pdb=" N VAL M 38 " --> pdb=" O MET M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 70 Processing helix chain 'M' and resid 73 through 86 removed outlier: 3.676A pdb=" N LEU M 86 " --> pdb=" O GLY M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 102 removed outlier: 3.556A pdb=" N PHE M 92 " --> pdb=" O PRO M 88 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER M 93 " --> pdb=" O SER M 89 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR M 102 " --> pdb=" O HIS M 98 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 166 removed outlier: 3.828A pdb=" N ILE M 144 " --> pdb=" O SER M 140 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE M 145 " --> pdb=" O ALA M 141 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N HIS M 146 " --> pdb=" O GLY M 142 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA M 155 " --> pdb=" O THR M 151 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA M 156 " --> pdb=" O LEU M 152 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE M 157 " --> pdb=" O LEU M 153 " (cutoff:3.500A) Processing helix chain 'M' and resid 192 through 226 removed outlier: 3.597A pdb=" N LEU M 199 " --> pdb=" O SER M 195 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU M 210 " --> pdb=" O ALA M 206 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU M 211 " --> pdb=" O LEU M 207 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY M 212 " --> pdb=" O SER M 208 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU M 213 " --> pdb=" O PHE M 209 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL M 217 " --> pdb=" O LEU M 213 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N CYS M 218 " --> pdb=" O ALA M 214 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG M 221 " --> pdb=" O VAL M 217 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG M 225 " --> pdb=" O ARG M 221 " (cutoff:3.500A) Processing helix chain 'P' and resid 8 through 13 removed outlier: 3.530A pdb=" N THR P 13 " --> pdb=" O PHE P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 19 through 32 removed outlier: 3.584A pdb=" N MET P 30 " --> pdb=" O PHE P 26 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU P 31 " --> pdb=" O VAL P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 33 through 40 removed outlier: 3.839A pdb=" N VAL P 38 " --> pdb=" O MET P 34 " (cutoff:3.500A) Processing helix chain 'P' and resid 60 through 70 Processing helix chain 'P' and resid 73 through 86 removed outlier: 3.513A pdb=" N VAL P 85 " --> pdb=" O GLN P 81 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU P 86 " --> pdb=" O GLY P 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 102 removed outlier: 3.566A pdb=" N PHE P 92 " --> pdb=" O PRO P 88 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER P 93 " --> pdb=" O SER P 89 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR P 102 " --> pdb=" O HIS P 98 " (cutoff:3.500A) Processing helix chain 'P' and resid 140 through 166 removed outlier: 3.984A pdb=" N ILE P 144 " --> pdb=" O SER P 140 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE P 145 " --> pdb=" O ALA P 141 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N HIS P 146 " --> pdb=" O GLY P 142 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU P 154 " --> pdb=" O ARG P 150 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA P 155 " --> pdb=" O THR P 151 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA P 156 " --> pdb=" O LEU P 152 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE P 157 " --> pdb=" O LEU P 153 " (cutoff:3.500A) Processing helix chain 'P' and resid 192 through 226 removed outlier: 3.601A pdb=" N LEU P 199 " --> pdb=" O SER P 195 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU P 210 " --> pdb=" O ALA P 206 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU P 211 " --> pdb=" O LEU P 207 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY P 212 " --> pdb=" O SER P 208 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU P 213 " --> pdb=" O PHE P 209 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL P 217 " --> pdb=" O LEU P 213 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N CYS P 218 " --> pdb=" O ALA P 214 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG P 221 " --> pdb=" O VAL P 217 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG P 225 " --> pdb=" O ARG P 221 " (cutoff:3.500A) Processing helix chain 'S' and resid 8 through 13 Processing helix chain 'S' and resid 19 through 32 removed outlier: 3.536A pdb=" N MET S 30 " --> pdb=" O PHE S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 33 through 42 removed outlier: 3.842A pdb=" N VAL S 38 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG S 42 " --> pdb=" O VAL S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 70 Processing helix chain 'S' and resid 73 through 86 removed outlier: 3.514A pdb=" N VAL S 85 " --> pdb=" O GLN S 81 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU S 86 " --> pdb=" O GLY S 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 86 through 102 removed outlier: 3.547A pdb=" N PHE S 92 " --> pdb=" O PRO S 88 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER S 93 " --> pdb=" O SER S 89 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR S 102 " --> pdb=" O HIS S 98 " (cutoff:3.500A) Processing helix chain 'S' and resid 140 through 165 removed outlier: 3.844A pdb=" N ILE S 144 " --> pdb=" O SER S 140 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE S 145 " --> pdb=" O ALA S 141 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N HIS S 146 " --> pdb=" O GLY S 142 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA S 155 " --> pdb=" O THR S 151 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA S 156 " --> pdb=" O LEU S 152 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE S 157 " --> pdb=" O LEU S 153 " (cutoff:3.500A) Processing helix chain 'S' and resid 192 through 212 removed outlier: 3.591A pdb=" N LEU S 199 " --> pdb=" O SER S 195 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE S 200 " --> pdb=" O LEU S 196 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU S 210 " --> pdb=" O ALA S 206 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU S 211 " --> pdb=" O LEU S 207 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY S 212 " --> pdb=" O SER S 208 " (cutoff:3.500A) Processing helix chain 'S' and resid 212 through 226 removed outlier: 3.612A pdb=" N VAL S 217 " --> pdb=" O LEU S 213 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N CYS S 218 " --> pdb=" O ALA S 214 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG S 221 " --> pdb=" O VAL S 217 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG S 225 " --> pdb=" O ARG S 221 " (cutoff:3.500A) Processing helix chain 'V' and resid 8 through 13 Processing helix chain 'V' and resid 14 through 17 removed outlier: 3.825A pdb=" N ASN V 17 " --> pdb=" O LEU V 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 14 through 17' Processing helix chain 'V' and resid 19 through 32 removed outlier: 3.781A pdb=" N MET V 30 " --> pdb=" O PHE V 26 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU V 31 " --> pdb=" O VAL V 27 " (cutoff:3.500A) Processing helix chain 'V' and resid 33 through 40 removed outlier: 3.848A pdb=" N VAL V 38 " --> pdb=" O MET V 34 " (cutoff:3.500A) Processing helix chain 'V' and resid 60 through 70 Processing helix chain 'V' and resid 73 through 86 removed outlier: 3.517A pdb=" N VAL V 85 " --> pdb=" O GLN V 81 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU V 86 " --> pdb=" O GLY V 82 " (cutoff:3.500A) Processing helix chain 'V' and resid 87 through 102 removed outlier: 3.583A pdb=" N PHE V 92 " --> pdb=" O PRO V 88 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER V 93 " --> pdb=" O SER V 89 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR V 102 " --> pdb=" O HIS V 98 " (cutoff:3.500A) Processing helix chain 'V' and resid 140 through 166 removed outlier: 3.822A pdb=" N ILE V 144 " --> pdb=" O SER V 140 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE V 145 " --> pdb=" O ALA V 141 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N HIS V 146 " --> pdb=" O GLY V 142 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU V 154 " --> pdb=" O ARG V 150 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA V 155 " --> pdb=" O THR V 151 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA V 156 " --> pdb=" O LEU V 152 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE V 157 " --> pdb=" O LEU V 153 " (cutoff:3.500A) Processing helix chain 'V' and resid 192 through 226 removed outlier: 3.634A pdb=" N LEU V 199 " --> pdb=" O SER V 195 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU V 210 " --> pdb=" O ALA V 206 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU V 211 " --> pdb=" O LEU V 207 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY V 212 " --> pdb=" O SER V 208 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU V 213 " --> pdb=" O PHE V 209 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL V 217 " --> pdb=" O LEU V 213 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N CYS V 218 " --> pdb=" O ALA V 214 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG V 221 " --> pdb=" O VAL V 217 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG V 225 " --> pdb=" O ARG V 221 " (cutoff:3.500A) Processing helix chain 'Y' and resid 8 through 13 removed outlier: 3.511A pdb=" N THR Y 13 " --> pdb=" O PHE Y 9 " (cutoff:3.500A) Processing helix chain 'Y' and resid 19 through 32 removed outlier: 3.768A pdb=" N MET Y 30 " --> pdb=" O PHE Y 26 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU Y 31 " --> pdb=" O VAL Y 27 " (cutoff:3.500A) Processing helix chain 'Y' and resid 33 through 40 removed outlier: 3.817A pdb=" N VAL Y 38 " --> pdb=" O MET Y 34 " (cutoff:3.500A) Processing helix chain 'Y' and resid 60 through 70 Processing helix chain 'Y' and resid 73 through 86 removed outlier: 3.675A pdb=" N LEU Y 86 " --> pdb=" O GLY Y 82 " (cutoff:3.500A) Processing helix chain 'Y' and resid 87 through 102 removed outlier: 3.589A pdb=" N PHE Y 92 " --> pdb=" O PRO Y 88 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER Y 93 " --> pdb=" O SER Y 89 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR Y 102 " --> pdb=" O HIS Y 98 " (cutoff:3.500A) Processing helix chain 'Y' and resid 140 through 165 removed outlier: 3.836A pdb=" N ILE Y 144 " --> pdb=" O SER Y 140 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE Y 145 " --> pdb=" O ALA Y 141 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N HIS Y 146 " --> pdb=" O GLY Y 142 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA Y 155 " --> pdb=" O THR Y 151 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA Y 156 " --> pdb=" O LEU Y 152 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE Y 157 " --> pdb=" O LEU Y 153 " (cutoff:3.500A) Processing helix chain 'Y' and resid 192 through 212 removed outlier: 3.575A pdb=" N LEU Y 199 " --> pdb=" O SER Y 195 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU Y 210 " --> pdb=" O ALA Y 206 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU Y 211 " --> pdb=" O LEU Y 207 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY Y 212 " --> pdb=" O SER Y 208 " (cutoff:3.500A) Processing helix chain 'Y' and resid 212 through 226 removed outlier: 3.589A pdb=" N VAL Y 217 " --> pdb=" O LEU Y 213 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N CYS Y 218 " --> pdb=" O ALA Y 214 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG Y 221 " --> pdb=" O VAL Y 217 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG Y 225 " --> pdb=" O ARG Y 221 " (cutoff:3.500A) Processing helix chain 'b' and resid 8 through 13 Processing helix chain 'b' and resid 14 through 17 removed outlier: 3.882A pdb=" N ASN b 17 " --> pdb=" O LEU b 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 14 through 17' Processing helix chain 'b' and resid 19 through 32 removed outlier: 3.602A pdb=" N MET b 30 " --> pdb=" O PHE b 26 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU b 31 " --> pdb=" O VAL b 27 " (cutoff:3.500A) Processing helix chain 'b' and resid 33 through 40 removed outlier: 3.834A pdb=" N VAL b 38 " --> pdb=" O MET b 34 " (cutoff:3.500A) Processing helix chain 'b' and resid 40 through 45 removed outlier: 4.035A pdb=" N VAL b 44 " --> pdb=" O ALA b 40 " (cutoff:3.500A) Processing helix chain 'b' and resid 60 through 70 Processing helix chain 'b' and resid 73 through 86 removed outlier: 3.516A pdb=" N VAL b 85 " --> pdb=" O GLN b 81 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU b 86 " --> pdb=" O GLY b 82 " (cutoff:3.500A) Processing helix chain 'b' and resid 86 through 102 removed outlier: 3.540A pdb=" N PHE b 92 " --> pdb=" O PRO b 88 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER b 93 " --> pdb=" O SER b 89 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR b 102 " --> pdb=" O HIS b 98 " (cutoff:3.500A) Processing helix chain 'b' and resid 140 through 166 removed outlier: 3.844A pdb=" N ILE b 144 " --> pdb=" O SER b 140 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE b 145 " --> pdb=" O ALA b 141 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N HIS b 146 " --> pdb=" O GLY b 142 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA b 155 " --> pdb=" O THR b 151 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA b 156 " --> pdb=" O LEU b 152 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE b 157 " --> pdb=" O LEU b 153 " (cutoff:3.500A) Processing helix chain 'b' and resid 192 through 226 removed outlier: 3.609A pdb=" N LEU b 199 " --> pdb=" O SER b 195 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU b 210 " --> pdb=" O ALA b 206 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU b 211 " --> pdb=" O LEU b 207 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY b 212 " --> pdb=" O SER b 208 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU b 213 " --> pdb=" O PHE b 209 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL b 217 " --> pdb=" O LEU b 213 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N CYS b 218 " --> pdb=" O ALA b 214 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG b 221 " --> pdb=" O VAL b 217 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG b 225 " --> pdb=" O ARG b 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.614A pdb=" N VAL A 53 " --> pdb=" O TYR A 187 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.603A pdb=" N VAL B 53 " --> pdb=" O TYR B 187 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 53 through 54 removed outlier: 3.628A pdb=" N VAL G 53 " --> pdb=" O TYR G 187 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.657A pdb=" N VAL J 53 " --> pdb=" O TYR J 187 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 53 through 54 removed outlier: 3.620A pdb=" N VAL M 53 " --> pdb=" O TYR M 187 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 53 through 54 removed outlier: 3.608A pdb=" N VAL P 53 " --> pdb=" O TYR P 187 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'S' and resid 53 through 54 removed outlier: 3.632A pdb=" N VAL S 53 " --> pdb=" O TYR S 187 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'V' and resid 53 through 54 removed outlier: 3.660A pdb=" N VAL V 53 " --> pdb=" O TYR V 187 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Y' and resid 53 through 54 removed outlier: 3.648A pdb=" N VAL Y 53 " --> pdb=" O TYR Y 187 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'b' and resid 53 through 54 removed outlier: 3.613A pdb=" N VAL b 53 " --> pdb=" O TYR b 187 " (cutoff:3.500A) 804 hydrogen bonds defined for protein. 2382 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: 2.50 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2630 1.33 - 1.45: 4410 1.45 - 1.57: 10730 1.57 - 1.69: 40 1.69 - 1.81: 190 Bond restraints: 18000 Sorted by residual: bond pdb=" CB ASN M 15 " pdb=" CG ASN M 15 " ideal model delta sigma weight residual 1.516 1.559 -0.043 2.50e-02 1.60e+03 2.90e+00 bond pdb=" CB ASN Y 15 " pdb=" CG ASN Y 15 " ideal model delta sigma weight residual 1.516 1.558 -0.042 2.50e-02 1.60e+03 2.83e+00 bond pdb=" CB ASN G 15 " pdb=" CG ASN G 15 " ideal model delta sigma weight residual 1.516 1.558 -0.042 2.50e-02 1.60e+03 2.78e+00 bond pdb=" CB ASN V 15 " pdb=" CG ASN V 15 " ideal model delta sigma weight residual 1.516 1.557 -0.041 2.50e-02 1.60e+03 2.74e+00 bond pdb=" CB ASN J 15 " pdb=" CG ASN J 15 " ideal model delta sigma weight residual 1.516 1.556 -0.040 2.50e-02 1.60e+03 2.54e+00 ... (remaining 17995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 24179 2.51 - 5.03: 269 5.03 - 7.54: 17 7.54 - 10.05: 8 10.05 - 12.56: 7 Bond angle restraints: 24480 Sorted by residual: angle pdb=" CA ASN J 15 " pdb=" CB ASN J 15 " pdb=" CG ASN J 15 " ideal model delta sigma weight residual 112.60 116.23 -3.63 1.00e+00 1.00e+00 1.32e+01 angle pdb=" CA ASN M 15 " pdb=" CB ASN M 15 " pdb=" CG ASN M 15 " ideal model delta sigma weight residual 112.60 116.22 -3.62 1.00e+00 1.00e+00 1.31e+01 angle pdb=" CA ASN b 15 " pdb=" CB ASN b 15 " pdb=" CG ASN b 15 " ideal model delta sigma weight residual 112.60 116.22 -3.62 1.00e+00 1.00e+00 1.31e+01 angle pdb=" CA LEU M 24 " pdb=" CB LEU M 24 " pdb=" CG LEU M 24 " ideal model delta sigma weight residual 116.30 128.86 -12.56 3.50e+00 8.16e-02 1.29e+01 angle pdb=" CA ASN G 15 " pdb=" CB ASN G 15 " pdb=" CG ASN G 15 " ideal model delta sigma weight residual 112.60 116.16 -3.56 1.00e+00 1.00e+00 1.27e+01 ... (remaining 24475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 8586 17.35 - 34.69: 1303 34.69 - 52.04: 464 52.04 - 69.38: 100 69.38 - 86.73: 7 Dihedral angle restraints: 10460 sinusoidal: 4630 harmonic: 5830 Sorted by residual: dihedral pdb=" CA THR Y 29 " pdb=" C THR Y 29 " pdb=" N MET Y 30 " pdb=" CA MET Y 30 " ideal model delta harmonic sigma weight residual 180.00 159.62 20.38 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA THR M 29 " pdb=" C THR M 29 " pdb=" N MET M 30 " pdb=" CA MET M 30 " ideal model delta harmonic sigma weight residual 180.00 159.83 20.17 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA THR V 29 " pdb=" C THR V 29 " pdb=" N MET V 30 " pdb=" CA MET V 30 " ideal model delta harmonic sigma weight residual 180.00 160.74 19.26 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 10457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2065 0.041 - 0.082: 629 0.082 - 0.123: 150 0.123 - 0.164: 23 0.164 - 0.205: 13 Chirality restraints: 2880 Sorted by residual: chirality pdb=" CB THR A 29 " pdb=" CA THR A 29 " pdb=" OG1 THR A 29 " pdb=" CG2 THR A 29 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB THR b 29 " pdb=" CA THR b 29 " pdb=" OG1 THR b 29 " pdb=" CG2 THR b 29 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB THR S 29 " pdb=" CA THR S 29 " pdb=" OG1 THR S 29 " pdb=" CG2 THR S 29 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 2877 not shown) Planarity restraints: 2770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN V 15 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C ASN V 15 " 0.060 2.00e-02 2.50e+03 pdb=" O ASN V 15 " -0.023 2.00e-02 2.50e+03 pdb=" N CYS V 16 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN Y 15 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C ASN Y 15 " 0.060 2.00e-02 2.50e+03 pdb=" O ASN Y 15 " -0.023 2.00e-02 2.50e+03 pdb=" N CYS Y 16 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN M 15 " 0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C ASN M 15 " -0.059 2.00e-02 2.50e+03 pdb=" O ASN M 15 " 0.023 2.00e-02 2.50e+03 pdb=" N CYS M 16 " 0.019 2.00e-02 2.50e+03 ... (remaining 2767 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 69 2.58 - 3.16: 12239 3.16 - 3.74: 24074 3.74 - 4.32: 32835 4.32 - 4.90: 57093 Nonbonded interactions: 126310 Sorted by model distance: nonbonded pdb=" O ASN b 15 " pdb=" ND2 ASN b 15 " model vdw 2.001 3.120 nonbonded pdb=" O ASN A 15 " pdb=" ND2 ASN A 15 " model vdw 2.017 3.120 nonbonded pdb=" O ASN S 15 " pdb=" ND2 ASN S 15 " model vdw 2.090 3.120 nonbonded pdb=" O ASN P 15 " pdb=" ND2 ASN P 15 " model vdw 2.195 3.120 nonbonded pdb=" O ASN B 15 " pdb=" ND2 ASN B 15 " model vdw 2.205 3.120 ... (remaining 126305 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 3 through 229) selection = (chain 'B' and resid 3 through 229) selection = (chain 'G' and resid 3 through 229) selection = (chain 'J' and resid 3 through 229) selection = (chain 'M' and resid 3 through 229) selection = (chain 'P' and resid 3 through 229) selection = (chain 'S' and resid 3 through 229) selection = (chain 'V' and resid 3 through 229) selection = (chain 'Y' and resid 3 through 229) selection = (chain 'b' and resid 3 through 229) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.260 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18030 Z= 0.132 Angle : 0.699 12.564 24540 Z= 0.375 Chirality : 0.042 0.205 2880 Planarity : 0.005 0.039 2770 Dihedral : 18.403 86.726 6610 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 8.33 % Allowed : 26.95 % Favored : 64.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.11 (0.19), residues: 1990 helix: -0.36 (0.15), residues: 1340 sheet: -0.17 (0.50), residues: 110 loop : -1.47 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 76 TYR 0.010 0.001 TYR B 143 PHE 0.009 0.001 PHE P 200 TRP 0.010 0.001 TRP P 25 HIS 0.004 0.001 HIS M 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (18000) covalent geometry : angle 0.69943 / 0.38 (24480) SS BOND : bond 0.00113 / 0.07 ( 30) SS BOND : angle 0.47225 / 0.32 ( 60) hydrogen bonds : bond 0.24064 / 16.19 ( 804) hydrogen bonds : angle 7.01881 / 4.98 ( 2382) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 308 time to evaluate : 0.696 Fit side-chains REVERT: A 11 ILE cc_start: 0.7783 (mt) cc_final: 0.7578 (mt) REVERT: A 28 LEU cc_start: 0.7950 (mt) cc_final: 0.7579 (tp) REVERT: A 79 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8424 (tp) REVERT: B 28 LEU cc_start: 0.7944 (mt) cc_final: 0.7461 (tp) REVERT: B 47 ASP cc_start: 0.8904 (p0) cc_final: 0.8613 (p0) REVERT: G 28 LEU cc_start: 0.7950 (mt) cc_final: 0.7495 (tp) REVERT: J 28 LEU cc_start: 0.8026 (mt) cc_final: 0.7543 (tp) REVERT: M 28 LEU cc_start: 0.7952 (mt) cc_final: 0.7468 (tp) REVERT: P 28 LEU cc_start: 0.7926 (mt) cc_final: 0.7455 (tp) REVERT: P 47 ASP cc_start: 0.8881 (p0) cc_final: 0.8594 (p0) REVERT: S 28 LEU cc_start: 0.7900 (mt) cc_final: 0.7539 (tp) REVERT: V 28 LEU cc_start: 0.8029 (mt) cc_final: 0.7572 (tp) REVERT: Y 28 LEU cc_start: 0.7988 (mt) cc_final: 0.7527 (tp) REVERT: b 28 LEU cc_start: 0.7929 (mt) cc_final: 0.7539 (tp) REVERT: b 79 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8391 (tp) outliers start: 145 outliers final: 80 residues processed: 411 average time/residue: 0.4460 time to fit residues: 211.2123 Evaluate side-chains 311 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 229 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 74 HIS Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 146 HIS Chi-restraints excluded: chain G residue 151 THR Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain J residue 74 HIS Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 146 HIS Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain J residue 176 THR Chi-restraints excluded: chain M residue 7 LEU Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 74 HIS Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 146 HIS Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 189 SER Chi-restraints excluded: chain P residue 70 SER Chi-restraints excluded: chain P residue 74 HIS Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 140 SER Chi-restraints excluded: chain P residue 146 HIS Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain P residue 176 THR Chi-restraints excluded: chain P residue 189 SER Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 74 HIS Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain S residue 146 HIS Chi-restraints excluded: chain S residue 176 THR Chi-restraints excluded: chain S residue 189 SER Chi-restraints excluded: chain V residue 70 SER Chi-restraints excluded: chain V residue 72 VAL Chi-restraints excluded: chain V residue 74 HIS Chi-restraints excluded: chain V residue 94 VAL Chi-restraints excluded: chain V residue 146 HIS Chi-restraints excluded: chain V residue 151 THR Chi-restraints excluded: chain V residue 176 THR Chi-restraints excluded: chain Y residue 7 LEU Chi-restraints excluded: chain Y residue 70 SER Chi-restraints excluded: chain Y residue 74 HIS Chi-restraints excluded: chain Y residue 76 ARG Chi-restraints excluded: chain Y residue 80 ILE Chi-restraints excluded: chain Y residue 94 VAL Chi-restraints excluded: chain Y residue 146 HIS Chi-restraints excluded: chain Y residue 176 THR Chi-restraints excluded: chain Y residue 189 SER Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 74 HIS Chi-restraints excluded: chain b residue 76 ARG Chi-restraints excluded: chain b residue 79 LEU Chi-restraints excluded: chain b residue 94 VAL Chi-restraints excluded: chain b residue 146 HIS Chi-restraints excluded: chain b residue 151 THR Chi-restraints excluded: chain b residue 176 THR Chi-restraints excluded: chain b residue 189 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.0050 chunk 66 optimal weight: 0.0070 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 overall best weight: 0.5012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 46 GLN ** b 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.144686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.117189 restraints weight = 17247.886| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.09 r_work: 0.3062 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18030 Z= 0.125 Angle : 0.587 8.553 24540 Z= 0.282 Chirality : 0.040 0.165 2880 Planarity : 0.005 0.039 2770 Dihedral : 12.595 67.546 3134 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 5.52 % Allowed : 25.57 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.20), residues: 1990 helix: 0.34 (0.15), residues: 1360 sheet: 0.06 (0.52), residues: 110 loop : -1.34 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 76 TYR 0.005 0.001 TYR V 143 PHE 0.009 0.001 PHE B 139 TRP 0.006 0.001 TRP P 25 HIS 0.009 0.002 HIS G 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.13 (18000) covalent geometry : angle 0.58753 / 0.28 (24480) SS BOND : bond 0.00171 / 0.11 ( 30) SS BOND : angle 0.55368 / 0.37 ( 60) hydrogen bonds : bond 0.05329 / 3.57 ( 804) hydrogen bonds : angle 4.46998 / 3.17 ( 2382) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 250 time to evaluate : 0.552 Fit side-chains REVERT: A 74 HIS cc_start: 0.6777 (OUTLIER) cc_final: 0.6252 (p90) REVERT: A 227 ARG cc_start: 0.4354 (OUTLIER) cc_final: 0.3810 (tpm-80) REVERT: B 47 ASP cc_start: 0.8981 (p0) cc_final: 0.8698 (p0) REVERT: B 74 HIS cc_start: 0.6770 (OUTLIER) cc_final: 0.6275 (p90) REVERT: B 80 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8864 (mm) REVERT: B 176 THR cc_start: 0.8725 (p) cc_final: 0.8454 (t) REVERT: B 227 ARG cc_start: 0.4739 (OUTLIER) cc_final: 0.4196 (tpm-80) REVERT: G 74 HIS cc_start: 0.6842 (OUTLIER) cc_final: 0.6381 (p90) REVERT: G 227 ARG cc_start: 0.4301 (OUTLIER) cc_final: 0.3804 (tpm-80) REVERT: J 74 HIS cc_start: 0.6997 (OUTLIER) cc_final: 0.6360 (p90) REVERT: M 74 HIS cc_start: 0.6728 (OUTLIER) cc_final: 0.6227 (p90) REVERT: P 47 ASP cc_start: 0.8923 (p0) cc_final: 0.8657 (p0) REVERT: P 74 HIS cc_start: 0.6812 (OUTLIER) cc_final: 0.6329 (p90) REVERT: P 80 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8851 (mm) REVERT: P 176 THR cc_start: 0.8708 (p) cc_final: 0.8449 (t) REVERT: S 74 HIS cc_start: 0.6866 (OUTLIER) cc_final: 0.6464 (p90) REVERT: S 80 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8782 (mm) REVERT: S 227 ARG cc_start: 0.4715 (OUTLIER) cc_final: 0.4004 (tpm-80) REVERT: V 74 HIS cc_start: 0.6954 (OUTLIER) cc_final: 0.6401 (p90) REVERT: V 227 ARG cc_start: 0.4178 (OUTLIER) cc_final: 0.3923 (tpm-80) REVERT: Y 74 HIS cc_start: 0.6884 (OUTLIER) cc_final: 0.6296 (p90) REVERT: b 74 HIS cc_start: 0.6731 (OUTLIER) cc_final: 0.6179 (p90) REVERT: b 227 ARG cc_start: 0.4364 (OUTLIER) cc_final: 0.3861 (tpm-80) outliers start: 96 outliers final: 47 residues processed: 322 average time/residue: 0.4666 time to fit residues: 171.4665 Evaluate side-chains 298 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 232 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain G residue 74 HIS Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 146 HIS Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 74 HIS Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 146 HIS Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 205 SER Chi-restraints excluded: chain M residue 7 LEU Chi-restraints excluded: chain M residue 74 HIS Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 146 HIS Chi-restraints excluded: chain M residue 205 SER Chi-restraints excluded: chain P residue 74 HIS Chi-restraints excluded: chain P residue 80 ILE Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 146 HIS Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 189 SER Chi-restraints excluded: chain S residue 74 HIS Chi-restraints excluded: chain S residue 80 ILE Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain S residue 146 HIS Chi-restraints excluded: chain S residue 189 SER Chi-restraints excluded: chain S residue 227 ARG Chi-restraints excluded: chain V residue 74 HIS Chi-restraints excluded: chain V residue 79 LEU Chi-restraints excluded: chain V residue 94 VAL Chi-restraints excluded: chain V residue 146 HIS Chi-restraints excluded: chain V residue 205 SER Chi-restraints excluded: chain V residue 227 ARG Chi-restraints excluded: chain Y residue 74 HIS Chi-restraints excluded: chain Y residue 76 ARG Chi-restraints excluded: chain Y residue 94 VAL Chi-restraints excluded: chain Y residue 103 LEU Chi-restraints excluded: chain Y residue 146 HIS Chi-restraints excluded: chain Y residue 205 SER Chi-restraints excluded: chain b residue 74 HIS Chi-restraints excluded: chain b residue 76 ARG Chi-restraints excluded: chain b residue 94 VAL Chi-restraints excluded: chain b residue 146 HIS Chi-restraints excluded: chain b residue 189 SER Chi-restraints excluded: chain b residue 205 SER Chi-restraints excluded: chain b residue 227 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 57 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 176 optimal weight: 0.8980 chunk 120 optimal weight: 0.0980 chunk 12 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 ASN ** b 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.140505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.111868 restraints weight = 17381.279| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.08 r_work: 0.2999 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18030 Z= 0.116 Angle : 0.565 7.759 24540 Z= 0.268 Chirality : 0.040 0.161 2880 Planarity : 0.005 0.048 2770 Dihedral : 11.932 65.703 3091 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.57 % Allowed : 22.47 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.08 (0.19), residues: 1990 helix: 0.74 (0.15), residues: 1360 sheet: -0.10 (0.50), residues: 110 loop : -1.64 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y 177 TYR 0.005 0.001 TYR S 162 PHE 0.010 0.001 PHE S 9 TRP 0.005 0.001 TRP M 202 HIS 0.006 0.002 HIS J 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (18000) covalent geometry : angle 0.56513 / 0.27 (24480) SS BOND : bond 0.00237 / 0.15 ( 30) SS BOND : angle 0.60100 / 0.40 ( 60) hydrogen bonds : bond 0.05053 / 3.42 ( 804) hydrogen bonds : angle 3.84007 / 2.71 ( 2382) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 256 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: A 221 ARG cc_start: 0.8379 (ttm170) cc_final: 0.8163 (ttp-170) REVERT: A 227 ARG cc_start: 0.4613 (OUTLIER) cc_final: 0.3974 (tpm-80) REVERT: B 47 ASP cc_start: 0.8977 (p0) cc_final: 0.8699 (p0) REVERT: B 80 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8885 (mm) REVERT: B 227 ARG cc_start: 0.4797 (OUTLIER) cc_final: 0.4222 (tpm-80) REVERT: G 224 MET cc_start: 0.7253 (mtm) cc_final: 0.6769 (mpm) REVERT: G 227 ARG cc_start: 0.4625 (OUTLIER) cc_final: 0.4133 (tpm-80) REVERT: J 24 LEU cc_start: 0.8754 (tp) cc_final: 0.8389 (mt) REVERT: J 213 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8925 (mt) REVERT: J 227 ARG cc_start: 0.4741 (OUTLIER) cc_final: 0.4128 (tpm-80) REVERT: M 24 LEU cc_start: 0.8887 (tp) cc_final: 0.8527 (mt) REVERT: M 213 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.9011 (mt) REVERT: P 47 ASP cc_start: 0.8937 (p0) cc_final: 0.8673 (p0) REVERT: P 80 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8882 (mm) REVERT: P 176 THR cc_start: 0.8809 (p) cc_final: 0.8519 (t) REVERT: P 213 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8997 (mt) REVERT: S 227 ARG cc_start: 0.4883 (OUTLIER) cc_final: 0.4148 (tpm-80) REVERT: V 24 LEU cc_start: 0.8765 (tp) cc_final: 0.8413 (mt) REVERT: V 74 HIS cc_start: 0.7128 (OUTLIER) cc_final: 0.6117 (p90) REVERT: V 213 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8937 (mt) REVERT: Y 103 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8081 (tp) outliers start: 97 outliers final: 59 residues processed: 323 average time/residue: 0.5302 time to fit residues: 193.8819 Evaluate side-chains 302 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 230 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 74 HIS Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 146 HIS Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 74 HIS Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 146 HIS Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain J residue 227 ARG Chi-restraints excluded: chain M residue 74 HIS Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 146 HIS Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain M residue 213 LEU Chi-restraints excluded: chain P residue 74 HIS Chi-restraints excluded: chain P residue 80 ILE Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 146 HIS Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 213 LEU Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 74 HIS Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain S residue 146 HIS Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 181 THR Chi-restraints excluded: chain S residue 227 ARG Chi-restraints excluded: chain V residue 28 LEU Chi-restraints excluded: chain V residue 74 HIS Chi-restraints excluded: chain V residue 94 VAL Chi-restraints excluded: chain V residue 146 HIS Chi-restraints excluded: chain V residue 148 LEU Chi-restraints excluded: chain V residue 181 THR Chi-restraints excluded: chain V residue 213 LEU Chi-restraints excluded: chain Y residue 28 LEU Chi-restraints excluded: chain Y residue 74 HIS Chi-restraints excluded: chain Y residue 76 ARG Chi-restraints excluded: chain Y residue 94 VAL Chi-restraints excluded: chain Y residue 103 LEU Chi-restraints excluded: chain Y residue 146 HIS Chi-restraints excluded: chain Y residue 181 THR Chi-restraints excluded: chain b residue 74 HIS Chi-restraints excluded: chain b residue 76 ARG Chi-restraints excluded: chain b residue 83 VAL Chi-restraints excluded: chain b residue 94 VAL Chi-restraints excluded: chain b residue 146 HIS Chi-restraints excluded: chain b residue 227 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 80 optimal weight: 0.2980 chunk 21 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 55 optimal weight: 0.4980 chunk 184 optimal weight: 0.0040 chunk 30 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 ASN P 15 ASN Y 15 ASN b 15 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.139910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.111549 restraints weight = 17396.109| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 0.94 r_work: 0.2918 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 18030 Z= 0.108 Angle : 0.536 7.549 24540 Z= 0.252 Chirality : 0.040 0.161 2880 Planarity : 0.005 0.065 2770 Dihedral : 11.390 64.575 3083 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 5.29 % Allowed : 22.82 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.35 (0.19), residues: 1990 helix: 1.08 (0.14), residues: 1380 sheet: -0.03 (0.51), residues: 110 loop : -2.09 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 227 TYR 0.008 0.001 TYR J 66 PHE 0.009 0.001 PHE S 9 TRP 0.005 0.001 TRP b 202 HIS 0.005 0.002 HIS J 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (18000) covalent geometry : angle 0.53552 / 0.25 (24480) SS BOND : bond 0.00205 / 0.13 ( 30) SS BOND : angle 0.53145 / 0.35 ( 60) hydrogen bonds : bond 0.04390 / 2.97 ( 804) hydrogen bonds : angle 3.65139 / 2.58 ( 2382) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 241 time to evaluate : 0.677 Fit side-chains REVERT: A 227 ARG cc_start: 0.4747 (OUTLIER) cc_final: 0.3969 (tpm-80) REVERT: B 47 ASP cc_start: 0.9025 (p0) cc_final: 0.8751 (p0) REVERT: B 76 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8781 (mpp-170) REVERT: B 80 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8934 (mm) REVERT: B 176 THR cc_start: 0.8761 (p) cc_final: 0.8490 (t) REVERT: B 227 ARG cc_start: 0.4653 (OUTLIER) cc_final: 0.4123 (tpm-80) REVERT: G 224 MET cc_start: 0.7259 (mtm) cc_final: 0.6855 (mpm) REVERT: G 227 ARG cc_start: 0.4567 (OUTLIER) cc_final: 0.4086 (tpm-80) REVERT: J 24 LEU cc_start: 0.8819 (tp) cc_final: 0.8579 (mt) REVERT: J 221 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8197 (ttp80) REVERT: J 227 ARG cc_start: 0.4736 (OUTLIER) cc_final: 0.4038 (tpm-80) REVERT: M 24 LEU cc_start: 0.8901 (tp) cc_final: 0.8659 (mt) REVERT: P 24 LEU cc_start: 0.8980 (tp) cc_final: 0.8554 (mt) REVERT: P 47 ASP cc_start: 0.9000 (p0) cc_final: 0.8751 (p0) REVERT: P 80 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8933 (mm) REVERT: P 176 THR cc_start: 0.8813 (p) cc_final: 0.8539 (t) REVERT: S 227 ARG cc_start: 0.4798 (OUTLIER) cc_final: 0.4045 (tpm-80) REVERT: V 24 LEU cc_start: 0.8805 (tp) cc_final: 0.8558 (mt) REVERT: V 103 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8085 (tp) REVERT: V 221 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8240 (ttp80) REVERT: Y 24 LEU cc_start: 0.8907 (tp) cc_final: 0.8624 (mt) REVERT: Y 103 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8104 (tp) REVERT: b 221 ARG cc_start: 0.8398 (ttm170) cc_final: 0.8196 (ttp-170) REVERT: b 227 ARG cc_start: 0.4565 (OUTLIER) cc_final: 0.3890 (tpm-80) outliers start: 92 outliers final: 51 residues processed: 302 average time/residue: 0.5262 time to fit residues: 180.8523 Evaluate side-chains 292 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 228 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 146 HIS Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 146 HIS Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 221 ARG Chi-restraints excluded: chain J residue 224 MET Chi-restraints excluded: chain J residue 227 ARG Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 146 HIS Chi-restraints excluded: chain P residue 70 SER Chi-restraints excluded: chain P residue 80 ILE Chi-restraints excluded: chain P residue 146 HIS Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 80 ILE Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain S residue 146 HIS Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 227 ARG Chi-restraints excluded: chain V residue 94 VAL Chi-restraints excluded: chain V residue 103 LEU Chi-restraints excluded: chain V residue 146 HIS Chi-restraints excluded: chain V residue 148 LEU Chi-restraints excluded: chain V residue 221 ARG Chi-restraints excluded: chain Y residue 28 LEU Chi-restraints excluded: chain Y residue 70 SER Chi-restraints excluded: chain Y residue 76 ARG Chi-restraints excluded: chain Y residue 80 ILE Chi-restraints excluded: chain Y residue 94 VAL Chi-restraints excluded: chain Y residue 103 LEU Chi-restraints excluded: chain Y residue 146 HIS Chi-restraints excluded: chain Y residue 205 SER Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 76 ARG Chi-restraints excluded: chain b residue 83 VAL Chi-restraints excluded: chain b residue 94 VAL Chi-restraints excluded: chain b residue 146 HIS Chi-restraints excluded: chain b residue 205 SER Chi-restraints excluded: chain b residue 227 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 0.9990 chunk 156 optimal weight: 0.0020 chunk 46 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 43 optimal weight: 0.0670 chunk 29 optimal weight: 0.8980 chunk 144 optimal weight: 0.6980 chunk 171 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 overall best weight: 0.5126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 74 HIS G 74 HIS S 74 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.140329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.111938 restraints weight = 17299.498| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 0.94 r_work: 0.2908 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 18030 Z= 0.093 Angle : 0.503 7.559 24540 Z= 0.235 Chirality : 0.039 0.164 2880 Planarity : 0.004 0.035 2770 Dihedral : 10.848 63.636 3060 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.83 % Allowed : 22.82 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.74 (0.19), residues: 1990 helix: 1.35 (0.14), residues: 1400 sheet: -0.01 (0.50), residues: 110 loop : -1.94 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 227 TYR 0.006 0.001 TYR J 66 PHE 0.007 0.001 PHE S 139 TRP 0.006 0.001 TRP M 202 HIS 0.006 0.001 HIS G 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.09 (18000) covalent geometry : angle 0.50295 / 0.24 (24480) SS BOND : bond 0.00151 / 0.10 ( 30) SS BOND : angle 0.45508 / 0.31 ( 60) hydrogen bonds : bond 0.03888 / 2.63 ( 804) hydrogen bonds : angle 3.53206 / 2.49 ( 2382) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 238 time to evaluate : 0.723 Fit side-chains REVERT: A 227 ARG cc_start: 0.4597 (OUTLIER) cc_final: 0.3880 (tpm-80) REVERT: B 47 ASP cc_start: 0.8899 (p0) cc_final: 0.8632 (p0) REVERT: B 80 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8916 (mm) REVERT: B 176 THR cc_start: 0.8762 (p) cc_final: 0.8519 (t) REVERT: B 227 ARG cc_start: 0.4550 (OUTLIER) cc_final: 0.4072 (tpm-80) REVERT: G 227 ARG cc_start: 0.4496 (OUTLIER) cc_final: 0.3992 (tpm-80) REVERT: J 221 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7943 (ttp80) REVERT: J 227 ARG cc_start: 0.4452 (OUTLIER) cc_final: 0.3927 (tpm-80) REVERT: P 24 LEU cc_start: 0.8862 (tp) cc_final: 0.8557 (mt) REVERT: P 47 ASP cc_start: 0.8860 (p0) cc_final: 0.8629 (p0) REVERT: P 80 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8879 (mm) REVERT: P 176 THR cc_start: 0.8813 (p) cc_final: 0.8570 (t) REVERT: S 227 ARG cc_start: 0.4722 (OUTLIER) cc_final: 0.4048 (tpm-80) REVERT: V 221 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7968 (ttp80) REVERT: b 221 ARG cc_start: 0.8183 (ttm170) cc_final: 0.7942 (ttp-170) REVERT: b 227 ARG cc_start: 0.4454 (OUTLIER) cc_final: 0.3876 (tpm-80) outliers start: 84 outliers final: 48 residues processed: 300 average time/residue: 0.4942 time to fit residues: 169.0570 Evaluate side-chains 282 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 224 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 146 HIS Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 146 HIS Chi-restraints excluded: chain J residue 205 SER Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 221 ARG Chi-restraints excluded: chain J residue 227 ARG Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 146 HIS Chi-restraints excluded: chain M residue 205 SER Chi-restraints excluded: chain M residue 208 SER Chi-restraints excluded: chain P residue 80 ILE Chi-restraints excluded: chain P residue 146 HIS Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain S residue 146 HIS Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 208 SER Chi-restraints excluded: chain S residue 227 ARG Chi-restraints excluded: chain V residue 6 LEU Chi-restraints excluded: chain V residue 28 LEU Chi-restraints excluded: chain V residue 94 VAL Chi-restraints excluded: chain V residue 146 HIS Chi-restraints excluded: chain V residue 205 SER Chi-restraints excluded: chain V residue 208 SER Chi-restraints excluded: chain V residue 221 ARG Chi-restraints excluded: chain Y residue 28 LEU Chi-restraints excluded: chain Y residue 76 ARG Chi-restraints excluded: chain Y residue 94 VAL Chi-restraints excluded: chain Y residue 146 HIS Chi-restraints excluded: chain Y residue 205 SER Chi-restraints excluded: chain b residue 94 VAL Chi-restraints excluded: chain b residue 146 HIS Chi-restraints excluded: chain b residue 205 SER Chi-restraints excluded: chain b residue 208 SER Chi-restraints excluded: chain b residue 227 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 64 optimal weight: 3.9990 chunk 116 optimal weight: 0.0040 chunk 15 optimal weight: 0.0030 chunk 144 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 overall best weight: 0.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 HIS B 74 HIS G 74 HIS J 74 HIS M 46 GLN M 74 HIS P 74 HIS S 74 HIS Y 74 HIS b 74 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.139929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.111439 restraints weight = 17231.582| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 0.96 r_work: 0.2921 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 18030 Z= 0.094 Angle : 0.501 8.269 24540 Z= 0.234 Chirality : 0.039 0.163 2880 Planarity : 0.004 0.035 2770 Dihedral : 10.407 62.746 3048 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.89 % Allowed : 22.01 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.15 (0.19), residues: 1990 helix: 1.71 (0.14), residues: 1400 sheet: -0.03 (0.50), residues: 110 loop : -1.92 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y 227 TYR 0.007 0.001 TYR V 66 PHE 0.007 0.001 PHE S 9 TRP 0.006 0.001 TRP G 202 HIS 0.005 0.001 HIS b 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 (18000) covalent geometry : angle 0.50114 / 0.23 (24480) SS BOND : bond 0.00162 / 0.10 ( 30) SS BOND : angle 0.47730 / 0.32 ( 60) hydrogen bonds : bond 0.03891 / 2.64 ( 804) hydrogen bonds : angle 3.46752 / 2.44 ( 2382) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 239 time to evaluate : 0.641 Fit side-chains REVERT: A 102 THR cc_start: 0.8342 (t) cc_final: 0.7755 (p) REVERT: A 227 ARG cc_start: 0.4689 (OUTLIER) cc_final: 0.3825 (tpm-80) REVERT: B 47 ASP cc_start: 0.9016 (p0) cc_final: 0.8754 (p0) REVERT: B 80 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8938 (mm) REVERT: B 176 THR cc_start: 0.8768 (p) cc_final: 0.8482 (t) REVERT: B 227 ARG cc_start: 0.4624 (OUTLIER) cc_final: 0.4078 (tpm-80) REVERT: G 227 ARG cc_start: 0.4570 (OUTLIER) cc_final: 0.3946 (tpm-80) REVERT: J 221 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8021 (ttp80) REVERT: J 222 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7171 (ttp80) REVERT: J 227 ARG cc_start: 0.4470 (OUTLIER) cc_final: 0.3842 (tpm-80) REVERT: M 80 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8791 (mm) REVERT: P 24 LEU cc_start: 0.9013 (tp) cc_final: 0.8684 (mt) REVERT: P 47 ASP cc_start: 0.8978 (p0) cc_final: 0.8744 (p0) REVERT: P 176 THR cc_start: 0.8824 (p) cc_final: 0.8547 (t) REVERT: S 227 ARG cc_start: 0.4703 (OUTLIER) cc_final: 0.3926 (tpm-80) REVERT: V 221 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.8087 (ttp80) REVERT: Y 102 THR cc_start: 0.8145 (t) cc_final: 0.7572 (p) REVERT: b 221 ARG cc_start: 0.8360 (ttm170) cc_final: 0.8137 (ttp-170) REVERT: b 227 ARG cc_start: 0.4575 (OUTLIER) cc_final: 0.3853 (tpm-80) outliers start: 85 outliers final: 52 residues processed: 302 average time/residue: 0.4465 time to fit residues: 154.5629 Evaluate side-chains 289 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 226 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 146 HIS Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 208 SER Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 146 HIS Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 205 SER Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 221 ARG Chi-restraints excluded: chain J residue 222 ARG Chi-restraints excluded: chain J residue 224 MET Chi-restraints excluded: chain J residue 227 ARG Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 146 HIS Chi-restraints excluded: chain M residue 205 SER Chi-restraints excluded: chain M residue 208 SER Chi-restraints excluded: chain P residue 146 HIS Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 146 HIS Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 208 SER Chi-restraints excluded: chain S residue 227 ARG Chi-restraints excluded: chain V residue 28 LEU Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 94 VAL Chi-restraints excluded: chain V residue 146 HIS Chi-restraints excluded: chain V residue 148 LEU Chi-restraints excluded: chain V residue 205 SER Chi-restraints excluded: chain V residue 208 SER Chi-restraints excluded: chain V residue 221 ARG Chi-restraints excluded: chain Y residue 28 LEU Chi-restraints excluded: chain Y residue 80 ILE Chi-restraints excluded: chain Y residue 94 VAL Chi-restraints excluded: chain Y residue 146 HIS Chi-restraints excluded: chain Y residue 205 SER Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 94 VAL Chi-restraints excluded: chain b residue 146 HIS Chi-restraints excluded: chain b residue 205 SER Chi-restraints excluded: chain b residue 208 SER Chi-restraints excluded: chain b residue 227 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 45 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 152 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 4 optimal weight: 0.0370 chunk 166 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 HIS V 74 HIS b 74 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.138639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.109933 restraints weight = 17286.926| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 0.99 r_work: 0.2885 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 18030 Z= 0.102 Angle : 0.513 8.113 24540 Z= 0.240 Chirality : 0.040 0.161 2880 Planarity : 0.004 0.036 2770 Dihedral : 10.262 62.407 3042 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.43 % Allowed : 22.13 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.28 (0.19), residues: 1990 helix: 1.83 (0.14), residues: 1400 sheet: -0.06 (0.50), residues: 110 loop : -1.96 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Y 227 TYR 0.008 0.001 TYR G 66 PHE 0.007 0.001 PHE S 9 TRP 0.006 0.001 TRP b 202 HIS 0.005 0.002 HIS Y 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (18000) covalent geometry : angle 0.51297 / 0.24 (24480) SS BOND : bond 0.00204 / 0.13 ( 30) SS BOND : angle 0.53291 / 0.36 ( 60) hydrogen bonds : bond 0.04237 / 2.87 ( 804) hydrogen bonds : angle 3.44832 / 2.43 ( 2382) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 226 time to evaluate : 0.715 Fit side-chains REVERT: A 102 THR cc_start: 0.8401 (t) cc_final: 0.7849 (p) REVERT: A 227 ARG cc_start: 0.4626 (OUTLIER) cc_final: 0.3925 (tpm-80) REVERT: B 47 ASP cc_start: 0.8909 (p0) cc_final: 0.8632 (p0) REVERT: B 74 HIS cc_start: 0.8192 (m-70) cc_final: 0.7930 (m-70) REVERT: B 80 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8919 (mm) REVERT: B 227 ARG cc_start: 0.4525 (OUTLIER) cc_final: 0.4125 (tpm-80) REVERT: G 74 HIS cc_start: 0.8201 (m-70) cc_final: 0.7894 (m-70) REVERT: G 227 ARG cc_start: 0.4546 (OUTLIER) cc_final: 0.4057 (tpm-80) REVERT: J 221 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7860 (ttp80) REVERT: J 222 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7093 (ttp80) REVERT: P 24 LEU cc_start: 0.8874 (tp) cc_final: 0.8616 (mt) REVERT: P 47 ASP cc_start: 0.8885 (p0) cc_final: 0.8626 (p0) REVERT: P 74 HIS cc_start: 0.8271 (m-70) cc_final: 0.7978 (m-70) REVERT: P 176 THR cc_start: 0.8867 (p) cc_final: 0.8573 (t) REVERT: S 74 HIS cc_start: 0.8280 (m-70) cc_final: 0.8047 (m-70) REVERT: V 221 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7877 (ttp80) REVERT: Y 102 THR cc_start: 0.8180 (t) cc_final: 0.7657 (p) REVERT: b 221 ARG cc_start: 0.8194 (ttm170) cc_final: 0.7951 (ttp-170) REVERT: b 227 ARG cc_start: 0.4568 (OUTLIER) cc_final: 0.3947 (tpm-80) outliers start: 77 outliers final: 56 residues processed: 284 average time/residue: 0.4258 time to fit residues: 139.1638 Evaluate side-chains 288 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 224 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 146 HIS Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 208 SER Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 146 HIS Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 221 ARG Chi-restraints excluded: chain J residue 222 ARG Chi-restraints excluded: chain J residue 224 MET Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 146 HIS Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain M residue 205 SER Chi-restraints excluded: chain M residue 208 SER Chi-restraints excluded: chain P residue 146 HIS Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 208 SER Chi-restraints excluded: chain S residue 24 LEU Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 146 HIS Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 181 THR Chi-restraints excluded: chain S residue 208 SER Chi-restraints excluded: chain V residue 28 LEU Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 146 HIS Chi-restraints excluded: chain V residue 148 LEU Chi-restraints excluded: chain V residue 205 SER Chi-restraints excluded: chain V residue 208 SER Chi-restraints excluded: chain V residue 221 ARG Chi-restraints excluded: chain Y residue 28 LEU Chi-restraints excluded: chain Y residue 70 SER Chi-restraints excluded: chain Y residue 80 ILE Chi-restraints excluded: chain Y residue 94 VAL Chi-restraints excluded: chain Y residue 146 HIS Chi-restraints excluded: chain Y residue 181 THR Chi-restraints excluded: chain Y residue 205 SER Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 80 ILE Chi-restraints excluded: chain b residue 146 HIS Chi-restraints excluded: chain b residue 205 SER Chi-restraints excluded: chain b residue 208 SER Chi-restraints excluded: chain b residue 227 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 1 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 186 optimal weight: 0.9980 chunk 192 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 178 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 166 optimal weight: 0.9980 chunk 141 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 HIS V 74 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.137596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.108987 restraints weight = 17219.693| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.07 r_work: 0.2871 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 18030 Z= 0.110 Angle : 0.525 8.479 24540 Z= 0.245 Chirality : 0.041 0.159 2880 Planarity : 0.005 0.037 2770 Dihedral : 10.266 62.368 3036 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.08 % Allowed : 22.24 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.32 (0.19), residues: 1990 helix: 1.87 (0.14), residues: 1400 sheet: -0.04 (0.50), residues: 110 loop : -2.00 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Y 227 TYR 0.009 0.001 TYR V 66 PHE 0.007 0.001 PHE S 9 TRP 0.006 0.001 TRP M 202 HIS 0.005 0.002 HIS Y 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (18000) covalent geometry : angle 0.52492 / 0.25 (24480) SS BOND : bond 0.00237 / 0.15 ( 30) SS BOND : angle 0.58687 / 0.39 ( 60) hydrogen bonds : bond 0.04486 / 3.03 ( 804) hydrogen bonds : angle 3.43982 / 2.42 ( 2382) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 228 time to evaluate : 0.671 Fit side-chains REVERT: A 102 THR cc_start: 0.8392 (t) cc_final: 0.7810 (p) REVERT: A 227 ARG cc_start: 0.4637 (OUTLIER) cc_final: 0.3813 (tpm-80) REVERT: B 47 ASP cc_start: 0.9036 (p0) cc_final: 0.8777 (p0) REVERT: B 74 HIS cc_start: 0.8306 (m-70) cc_final: 0.8028 (m-70) REVERT: B 80 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8939 (mm) REVERT: G 74 HIS cc_start: 0.8348 (m-70) cc_final: 0.8030 (m-70) REVERT: J 221 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7996 (ttp80) REVERT: M 74 HIS cc_start: 0.8375 (m-70) cc_final: 0.8057 (m-70) REVERT: P 24 LEU cc_start: 0.8957 (tp) cc_final: 0.8666 (mt) REVERT: P 47 ASP cc_start: 0.9012 (p0) cc_final: 0.8771 (p0) REVERT: P 74 HIS cc_start: 0.8362 (m-70) cc_final: 0.8027 (m-70) REVERT: S 74 HIS cc_start: 0.8436 (m-70) cc_final: 0.8172 (m-70) REVERT: V 74 HIS cc_start: 0.8482 (m90) cc_final: 0.8242 (m-70) REVERT: V 221 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8046 (ttp80) REVERT: Y 74 HIS cc_start: 0.8355 (m-70) cc_final: 0.8032 (m-70) REVERT: Y 102 THR cc_start: 0.8219 (t) cc_final: 0.7660 (p) REVERT: b 102 THR cc_start: 0.8425 (t) cc_final: 0.7809 (p) REVERT: b 221 ARG cc_start: 0.8324 (ttm170) cc_final: 0.8100 (ttp-170) outliers start: 71 outliers final: 55 residues processed: 277 average time/residue: 0.4290 time to fit residues: 136.9188 Evaluate side-chains 282 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 223 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 146 HIS Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 208 SER Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 146 HIS Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 221 ARG Chi-restraints excluded: chain J residue 224 MET Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 146 HIS Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain M residue 205 SER Chi-restraints excluded: chain M residue 208 SER Chi-restraints excluded: chain P residue 146 HIS Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain S residue 24 LEU Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 146 HIS Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 181 THR Chi-restraints excluded: chain V residue 28 LEU Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 146 HIS Chi-restraints excluded: chain V residue 148 LEU Chi-restraints excluded: chain V residue 181 THR Chi-restraints excluded: chain V residue 208 SER Chi-restraints excluded: chain V residue 221 ARG Chi-restraints excluded: chain Y residue 28 LEU Chi-restraints excluded: chain Y residue 70 SER Chi-restraints excluded: chain Y residue 80 ILE Chi-restraints excluded: chain Y residue 146 HIS Chi-restraints excluded: chain Y residue 181 THR Chi-restraints excluded: chain Y residue 205 SER Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 83 VAL Chi-restraints excluded: chain b residue 146 HIS Chi-restraints excluded: chain b residue 205 SER Chi-restraints excluded: chain b residue 208 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 175 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 99 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 124 optimal weight: 0.4980 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.0770 chunk 193 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 74 HIS ** 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 = 0.3528 r_free = 0.3528 target = 0.139319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.110962 restraints weight = 17396.948| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 0.93 r_work: 0.2887 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 18030 Z= 0.090 Angle : 0.486 8.174 24540 Z= 0.226 Chirality : 0.039 0.164 2880 Planarity : 0.004 0.033 2770 Dihedral : 10.096 62.272 3035 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.28 % Allowed : 23.10 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.62 (0.19), residues: 1990 helix: 2.12 (0.14), residues: 1400 sheet: -0.05 (0.49), residues: 110 loop : -1.96 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 227 TYR 0.007 0.001 TYR J 66 PHE 0.006 0.001 PHE S 9 TRP 0.007 0.001 TRP M 202 HIS 0.004 0.001 HIS Y 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 (18000) covalent geometry : angle 0.48646 / 0.23 (24480) SS BOND : bond 0.00143 / 0.09 ( 30) SS BOND : angle 0.47020 / 0.32 ( 60) hydrogen bonds : bond 0.03691 / 2.50 ( 804) hydrogen bonds : angle 3.39919 / 2.39 ( 2382) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 230 time to evaluate : 0.702 Fit side-chains REVERT: A 102 THR cc_start: 0.8332 (t) cc_final: 0.7800 (p) REVERT: B 47 ASP cc_start: 0.8860 (p0) cc_final: 0.8653 (p0) REVERT: B 74 HIS cc_start: 0.8165 (m-70) cc_final: 0.7924 (m-70) REVERT: B 176 THR cc_start: 0.8750 (p) cc_final: 0.8491 (t) REVERT: G 34 MET cc_start: 0.9239 (mmm) cc_final: 0.9011 (mmp) REVERT: G 74 HIS cc_start: 0.8145 (m-70) cc_final: 0.7875 (m-70) REVERT: J 221 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7820 (ttp80) REVERT: M 74 HIS cc_start: 0.8171 (m-70) cc_final: 0.7892 (m-70) REVERT: M 102 THR cc_start: 0.8108 (t) cc_final: 0.7578 (p) REVERT: P 24 LEU cc_start: 0.8859 (tp) cc_final: 0.8641 (mt) REVERT: P 74 HIS cc_start: 0.8214 (m-70) cc_final: 0.7951 (m-70) REVERT: P 176 THR cc_start: 0.8772 (p) cc_final: 0.8528 (t) REVERT: V 74 HIS cc_start: 0.8242 (m90) cc_final: 0.8010 (m-70) REVERT: V 221 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7812 (ttp80) REVERT: Y 74 HIS cc_start: 0.8188 (m-70) cc_final: 0.7920 (m-70) REVERT: Y 102 THR cc_start: 0.8169 (t) cc_final: 0.7664 (p) REVERT: b 102 THR cc_start: 0.8358 (t) cc_final: 0.7776 (p) REVERT: b 221 ARG cc_start: 0.8187 (ttm170) cc_final: 0.7952 (ttp-170) outliers start: 57 outliers final: 43 residues processed: 271 average time/residue: 0.4450 time to fit residues: 138.7059 Evaluate side-chains 269 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 224 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 146 HIS Chi-restraints excluded: chain G residue 208 SER Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 146 HIS Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 221 ARG Chi-restraints excluded: chain J residue 224 MET Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 146 HIS Chi-restraints excluded: chain M residue 205 SER Chi-restraints excluded: chain M residue 208 SER Chi-restraints excluded: chain P residue 146 HIS Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 146 HIS Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 208 SER Chi-restraints excluded: chain V residue 28 LEU Chi-restraints excluded: chain V residue 146 HIS Chi-restraints excluded: chain V residue 148 LEU Chi-restraints excluded: chain V residue 208 SER Chi-restraints excluded: chain V residue 221 ARG Chi-restraints excluded: chain Y residue 28 LEU Chi-restraints excluded: chain Y residue 70 SER Chi-restraints excluded: chain Y residue 80 ILE Chi-restraints excluded: chain Y residue 146 HIS Chi-restraints excluded: chain Y residue 205 SER Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 146 HIS Chi-restraints excluded: chain b residue 205 SER Chi-restraints excluded: chain b residue 208 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 28 optimal weight: 0.5980 chunk 160 optimal weight: 0.5980 chunk 168 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 177 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 14 optimal weight: 0.3980 chunk 149 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** S 161 HIS ** 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 = 0.3521 r_free = 0.3521 target = 0.138611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.110375 restraints weight = 17166.158| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 0.90 r_work: 0.2910 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 18030 Z= 0.098 Angle : 0.501 8.418 24540 Z= 0.233 Chirality : 0.040 0.161 2880 Planarity : 0.004 0.036 2770 Dihedral : 9.992 62.279 3031 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.93 % Allowed : 23.39 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.67 (0.19), residues: 1990 helix: 2.17 (0.14), residues: 1400 sheet: -0.02 (0.50), residues: 110 loop : -1.94 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Y 227 TYR 0.008 0.001 TYR J 66 PHE 0.007 0.001 PHE S 9 TRP 0.006 0.001 TRP M 202 HIS 0.004 0.002 HIS M 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (18000) covalent geometry : angle 0.50137 / 0.23 (24480) SS BOND : bond 0.00183 / 0.12 ( 30) SS BOND : angle 0.51112 / 0.34 ( 60) hydrogen bonds : bond 0.03994 / 2.70 ( 804) hydrogen bonds : angle 3.39615 / 2.39 ( 2382) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 226 time to evaluate : 0.652 Fit side-chains REVERT: A 102 THR cc_start: 0.8443 (t) cc_final: 0.7906 (p) REVERT: B 47 ASP cc_start: 0.8962 (p0) cc_final: 0.8759 (p0) REVERT: B 74 HIS cc_start: 0.8263 (m-70) cc_final: 0.8005 (m-70) REVERT: G 74 HIS cc_start: 0.8256 (m-70) cc_final: 0.7972 (m-70) REVERT: J 221 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7921 (ttp80) REVERT: M 74 HIS cc_start: 0.8283 (m-70) cc_final: 0.7992 (m-70) REVERT: M 102 THR cc_start: 0.8112 (t) cc_final: 0.7562 (p) REVERT: P 24 LEU cc_start: 0.8946 (tp) cc_final: 0.8693 (mt) REVERT: P 74 HIS cc_start: 0.8316 (m-70) cc_final: 0.8030 (m-70) REVERT: P 176 THR cc_start: 0.8812 (p) cc_final: 0.8534 (t) REVERT: V 74 HIS cc_start: 0.8416 (m90) cc_final: 0.8126 (m-70) REVERT: Y 74 HIS cc_start: 0.8312 (m-70) cc_final: 0.8025 (m-70) REVERT: Y 102 THR cc_start: 0.8208 (t) cc_final: 0.7682 (p) REVERT: b 102 THR cc_start: 0.8431 (t) cc_final: 0.7811 (p) REVERT: b 221 ARG cc_start: 0.8289 (ttm170) cc_final: 0.8064 (ttp-170) outliers start: 51 outliers final: 48 residues processed: 263 average time/residue: 0.4571 time to fit residues: 138.0864 Evaluate side-chains 274 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 225 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain G residue 146 HIS Chi-restraints excluded: chain G residue 208 SER Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 146 HIS Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 221 ARG Chi-restraints excluded: chain J residue 224 MET Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 146 HIS Chi-restraints excluded: chain M residue 205 SER Chi-restraints excluded: chain M residue 208 SER Chi-restraints excluded: chain P residue 146 HIS Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 146 HIS Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 181 THR Chi-restraints excluded: chain S residue 208 SER Chi-restraints excluded: chain V residue 28 LEU Chi-restraints excluded: chain V residue 146 HIS Chi-restraints excluded: chain V residue 148 LEU Chi-restraints excluded: chain V residue 208 SER Chi-restraints excluded: chain Y residue 28 LEU Chi-restraints excluded: chain Y residue 70 SER Chi-restraints excluded: chain Y residue 80 ILE Chi-restraints excluded: chain Y residue 146 HIS Chi-restraints excluded: chain Y residue 181 THR Chi-restraints excluded: chain Y residue 205 SER Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 83 VAL Chi-restraints excluded: chain b residue 146 HIS Chi-restraints excluded: chain b residue 205 SER Chi-restraints excluded: chain b residue 208 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 153 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 90 optimal weight: 0.0370 chunk 146 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 188 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 190 optimal weight: 10.0000 overall best weight: 0.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** S 74 HIS ** 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 = 0.3535 r_free = 0.3535 target = 0.139076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.111076 restraints weight = 17272.419| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.00 r_work: 0.2880 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 18030 Z= 0.115 Angle : 0.535 9.049 24540 Z= 0.250 Chirality : 0.041 0.157 2880 Planarity : 0.005 0.037 2770 Dihedral : 10.136 62.739 3031 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.28 % Allowed : 23.22 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.56 (0.19), residues: 1990 helix: 2.08 (0.14), residues: 1400 sheet: -0.01 (0.50), residues: 110 loop : -2.00 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 227 TYR 0.010 0.001 TYR G 66 PHE 0.008 0.001 PHE S 9 TRP 0.006 0.001 TRP P 202 HIS 0.005 0.002 HIS Y 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (18000) covalent geometry : angle 0.53497 / 0.25 (24480) SS BOND : bond 0.00262 / 0.17 ( 30) SS BOND : angle 0.62995 / 0.42 ( 60) hydrogen bonds : bond 0.04637 / 3.14 ( 804) hydrogen bonds : angle 3.43922 / 2.42 ( 2382) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5024.12 seconds wall clock time: 86 minutes 28.34 seconds (5188.34 seconds total)