Starting phenix.real_space_refine on Sun Aug 24 07:37:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gn7_34156/08_2025/8gn7_34156.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gn7_34156/08_2025/8gn7_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 { model { file = "/net/cci-nas-00/data/ceres_data/8gn7_34156/08_2025/8gn7_34156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gn7_34156/08_2025/8gn7_34156.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gn7_34156/08_2025/8gn7_34156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gn7_34156/08_2025/8gn7_34156.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 3.79, per 1000 atoms: 0.22 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: 1.22 Conformation dependent library (CDL) restraints added in 500.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.32 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: 2.19 Time building geometry restraints manager: 1.57 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 - 25.62: 10972 25.62 - 51.25: 1181 51.25 - 76.87: 145 76.87 - 102.49: 12 102.49 - 128.11: 10 Dihedral angle restraints: 12320 sinusoidal: 6490 harmonic: 5830 Sorted by residual: dihedral pdb=" O21 3PE J 301 " pdb=" C2 3PE J 301 " pdb=" C3 3PE J 301 " pdb=" O31 3PE J 301 " ideal model delta sinusoidal sigma weight residual 60.47 -171.42 -128.11 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" O21 3PE V 301 " pdb=" C2 3PE V 301 " pdb=" C3 3PE V 301 " pdb=" O31 3PE V 301 " ideal model delta sinusoidal sigma weight residual 60.47 -171.68 -127.85 1 3.00e+01 1.11e-03 1.72e+01 dihedral pdb=" O21 3PE Y 302 " pdb=" C2 3PE Y 302 " pdb=" C3 3PE Y 302 " pdb=" O31 3PE Y 302 " ideal model delta sinusoidal sigma weight residual 60.47 -172.47 -127.06 1 3.00e+01 1.11e-03 1.71e+01 ... (remaining 12317 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: 0.00 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: 3.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.770 Find NCS groups from input model: 0.310 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:5.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 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 : 18.236 128.114 8470 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 aren 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 covalent geometry : bond 0.00272 (18000) covalent geometry : angle 0.69943 (24480) SS BOND : bond 0.00113 ( 30) SS BOND : angle 0.47225 ( 60) hydrogen bonds : bond 0.24064 ( 804) hydrogen bonds : angle 7.01881 ( 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 : 0.504 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: 0.4206 time to fit residues: 198.3674 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 : 0.686 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3603 r_free = 0.3603 target = 0.144819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.117156 restraints weight = 17224.052| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.12 r_work: 0.3064 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18030 Z= 0.120 Angle : 0.589 8.534 24540 Z= 0.281 Chirality : 0.040 0.163 2880 Planarity : 0.005 0.039 2770 Dihedral : 13.862 111.368 4994 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 5.46 % Allowed : 25.23 % Favored : 69.31 % 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 aren not related in a simple way. whole: -0.24 (0.20), residues: 1990 helix: 0.35 (0.15), residues: 1360 sheet: 0.05 (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 Y 177 TYR 0.005 0.001 TYR V 143 PHE 0.009 0.001 PHE B 139 TRP 0.005 0.001 TRP P 25 HIS 0.008 0.002 HIS P 74 Details of bonding type rmsd covalent geometry : bond 0.00242 (18000) covalent geometry : angle 0.58935 (24480) SS BOND : bond 0.00161 ( 30) SS BOND : angle 0.51798 ( 60) hydrogen bonds : bond 0.05243 ( 804) hydrogen bonds : angle 4.46784 ( 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 344 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 249 time to evaluate : 0.619 Fit side-chains REVERT: A 74 HIS cc_start: 0.6742 (OUTLIER) cc_final: 0.6206 (p90) REVERT: A 227 ARG cc_start: 0.4349 (OUTLIER) cc_final: 0.3814 (tpm-80) REVERT: B 47 ASP cc_start: 0.8976 (p0) cc_final: 0.8698 (p0) REVERT: B 74 HIS cc_start: 0.6741 (OUTLIER) cc_final: 0.6231 (p90) REVERT: B 80 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8837 (mm) REVERT: B 176 THR cc_start: 0.8720 (p) cc_final: 0.8448 (t) REVERT: B 227 ARG cc_start: 0.4733 (OUTLIER) cc_final: 0.4143 (tpm-80) REVERT: G 74 HIS cc_start: 0.6812 (OUTLIER) cc_final: 0.6328 (p90) REVERT: G 227 ARG cc_start: 0.4314 (OUTLIER) cc_final: 0.3799 (tpm-80) REVERT: J 74 HIS cc_start: 0.6981 (OUTLIER) cc_final: 0.6334 (p90) REVERT: M 74 HIS cc_start: 0.6706 (OUTLIER) cc_final: 0.6196 (p90) REVERT: P 47 ASP cc_start: 0.8920 (p0) cc_final: 0.8654 (p0) REVERT: P 74 HIS cc_start: 0.6769 (OUTLIER) cc_final: 0.6275 (p90) REVERT: P 80 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8851 (mm) REVERT: P 176 THR cc_start: 0.8704 (p) cc_final: 0.8446 (t) REVERT: S 74 HIS cc_start: 0.6878 (OUTLIER) cc_final: 0.6458 (p90) REVERT: S 80 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8771 (mm) REVERT: S 227 ARG cc_start: 0.4709 (OUTLIER) cc_final: 0.3997 (tpm-80) REVERT: V 74 HIS cc_start: 0.6928 (OUTLIER) cc_final: 0.6366 (p90) REVERT: V 227 ARG cc_start: 0.4169 (OUTLIER) cc_final: 0.3914 (tpm-80) REVERT: Y 74 HIS cc_start: 0.6857 (OUTLIER) cc_final: 0.6262 (p90) REVERT: b 74 HIS cc_start: 0.6731 (OUTLIER) cc_final: 0.6176 (p90) REVERT: b 227 ARG cc_start: 0.4350 (OUTLIER) cc_final: 0.3851 (tpm-80) outliers start: 95 outliers final: 49 residues processed: 321 average time/residue: 0.4590 time to fit residues: 167.5915 Evaluate side-chains 298 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 230 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 103 LEU 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 7 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 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: 4.9990 chunk 4 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 176 optimal weight: 0.8980 chunk 120 optimal weight: 0.0670 chunk 12 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 62 optimal weight: 0.4980 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 15 ASN ** 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 = 0.3561 r_free = 0.3561 target = 0.141709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.112979 restraints weight = 17409.364| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.00 r_work: 0.2984 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 18030 Z= 0.113 Angle : 0.550 7.323 24540 Z= 0.261 Chirality : 0.041 0.160 2880 Planarity : 0.005 0.039 2770 Dihedral : 13.379 104.734 4953 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.00 % Allowed : 23.33 % Favored : 71.67 % 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 aren not related in a simple way. whole: 0.09 (0.19), residues: 1990 helix: 0.72 (0.15), residues: 1360 sheet: -0.08 (0.50), residues: 110 loop : -1.53 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 177 TYR 0.005 0.001 TYR G 66 PHE 0.009 0.001 PHE S 139 TRP 0.005 0.001 TRP M 202 HIS 0.006 0.002 HIS J 74 Details of bonding type rmsd covalent geometry : bond 0.00249 (18000) covalent geometry : angle 0.55011 (24480) SS BOND : bond 0.00206 ( 30) SS BOND : angle 0.53861 ( 60) hydrogen bonds : bond 0.04887 ( 804) hydrogen bonds : angle 3.94267 ( 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 341 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 254 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: A 74 HIS cc_start: 0.6981 (OUTLIER) cc_final: 0.6272 (p90) REVERT: A 227 ARG cc_start: 0.4590 (OUTLIER) cc_final: 0.4002 (tpm-80) REVERT: B 47 ASP cc_start: 0.8974 (p0) cc_final: 0.8716 (p0) REVERT: B 74 HIS cc_start: 0.7017 (OUTLIER) cc_final: 0.6045 (p90) REVERT: B 80 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8892 (mm) REVERT: B 176 THR cc_start: 0.8784 (p) cc_final: 0.8505 (t) REVERT: B 227 ARG cc_start: 0.4897 (OUTLIER) cc_final: 0.4284 (tpm-80) REVERT: G 74 HIS cc_start: 0.7033 (OUTLIER) cc_final: 0.6049 (p90) REVERT: G 227 ARG cc_start: 0.4464 (OUTLIER) cc_final: 0.3959 (tpm-80) REVERT: J 24 LEU cc_start: 0.8740 (tp) cc_final: 0.8392 (mt) REVERT: J 74 HIS cc_start: 0.7150 (OUTLIER) cc_final: 0.6175 (p90) REVERT: J 227 ARG cc_start: 0.4640 (OUTLIER) cc_final: 0.4140 (tpm-80) REVERT: M 74 HIS cc_start: 0.6952 (OUTLIER) cc_final: 0.6148 (p90) REVERT: P 47 ASP cc_start: 0.8922 (p0) cc_final: 0.8676 (p0) REVERT: P 74 HIS cc_start: 0.6891 (OUTLIER) cc_final: 0.6012 (p90) REVERT: P 80 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8893 (mm) REVERT: P 176 THR cc_start: 0.8785 (p) cc_final: 0.8515 (t) REVERT: S 74 HIS cc_start: 0.7122 (OUTLIER) cc_final: 0.6214 (p90) REVERT: S 213 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8929 (mt) REVERT: S 227 ARG cc_start: 0.4866 (OUTLIER) cc_final: 0.4161 (tpm-80) REVERT: V 74 HIS cc_start: 0.7177 (OUTLIER) cc_final: 0.6324 (p90) REVERT: V 213 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8888 (mt) REVERT: Y 74 HIS cc_start: 0.7143 (OUTLIER) cc_final: 0.6292 (p90) REVERT: Y 103 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8092 (tp) REVERT: b 74 HIS cc_start: 0.6957 (OUTLIER) cc_final: 0.6225 (p90) outliers start: 87 outliers final: 43 residues processed: 314 average time/residue: 0.4771 time to fit residues: 169.5109 Evaluate side-chains 293 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 230 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 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 227 ARG 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 103 LEU Chi-restraints excluded: chain M residue 146 HIS 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 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 213 LEU 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 213 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 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: 0.6980 chunk 21 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 184 optimal weight: 0.5980 chunk 30 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 110 optimal weight: 0.2980 chunk 72 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 ASN P 15 ASN Y 15 ASN ** b 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.136521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.107743 restraints weight = 17336.655| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.08 r_work: 0.2886 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18030 Z= 0.132 Angle : 0.595 8.471 24540 Z= 0.282 Chirality : 0.042 0.156 2880 Planarity : 0.005 0.042 2770 Dihedral : 12.925 101.519 4945 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 6.44 % Allowed : 21.95 % Favored : 71.61 % 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 aren not related in a simple way. whole: 0.12 (0.19), residues: 1990 helix: 0.91 (0.14), residues: 1380 sheet: -0.08 (0.51), residues: 110 loop : -2.14 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 177 TYR 0.008 0.001 TYR J 66 PHE 0.010 0.001 PHE b 52 TRP 0.006 0.001 TRP b 202 HIS 0.006 0.002 HIS J 74 Details of bonding type rmsd covalent geometry : bond 0.00304 (18000) covalent geometry : angle 0.59505 (24480) SS BOND : bond 0.00319 ( 30) SS BOND : angle 0.74596 ( 60) hydrogen bonds : bond 0.05373 ( 804) hydrogen bonds : angle 3.71529 ( 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 353 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 241 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 227 ARG cc_start: 0.4768 (OUTLIER) cc_final: 0.4013 (tpm-80) REVERT: B 47 ASP cc_start: 0.9064 (p0) cc_final: 0.8761 (p0) REVERT: B 76 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8806 (mpp-170) REVERT: B 227 ARG cc_start: 0.4695 (OUTLIER) cc_final: 0.4128 (tpm-80) REVERT: G 227 ARG cc_start: 0.4496 (OUTLIER) cc_final: 0.4043 (tpm-80) REVERT: J 24 LEU cc_start: 0.8877 (tp) cc_final: 0.8573 (mt) REVERT: J 213 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.9007 (mt) REVERT: J 221 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.8197 (ttp80) REVERT: J 227 ARG cc_start: 0.4768 (OUTLIER) cc_final: 0.4086 (tpm-80) REVERT: M 24 LEU cc_start: 0.8927 (tp) cc_final: 0.8625 (mt) REVERT: P 24 LEU cc_start: 0.8896 (tp) cc_final: 0.8514 (mt) REVERT: P 47 ASP cc_start: 0.9027 (p0) cc_final: 0.8752 (p0) REVERT: S 227 ARG cc_start: 0.4764 (OUTLIER) cc_final: 0.4044 (tpm-80) REVERT: V 24 LEU cc_start: 0.8783 (tp) cc_final: 0.8566 (mt) REVERT: V 221 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.8316 (ttp80) REVERT: Y 24 LEU cc_start: 0.8940 (tp) cc_final: 0.8613 (mt) REVERT: Y 103 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8118 (tp) outliers start: 112 outliers final: 65 residues processed: 320 average time/residue: 0.4530 time to fit residues: 164.8344 Evaluate side-chains 299 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 224 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 76 ARG 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 29 THR 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 70 SER 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 181 THR Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain J residue 221 ARG 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 83 VAL 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 205 SER Chi-restraints excluded: chain P residue 70 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 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 70 SER Chi-restraints excluded: chain V residue 79 LEU Chi-restraints excluded: chain V residue 83 VAL 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 181 THR Chi-restraints excluded: chain V residue 221 ARG 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 181 THR 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 208 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: 1.9990 chunk 156 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 171 optimal weight: 0.0970 chunk 192 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 HIS G 74 HIS ** b 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.136853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.107397 restraints weight = 17260.119| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 0.96 r_work: 0.2842 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2472 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= 0.116 Angle : 0.553 8.352 24540 Z= 0.260 Chirality : 0.041 0.159 2880 Planarity : 0.005 0.037 2770 Dihedral : 12.666 100.993 4920 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 5.46 % Allowed : 22.70 % Favored : 71.84 % 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 aren not related in a simple way. whole: 0.39 (0.19), residues: 1990 helix: 1.09 (0.14), residues: 1400 sheet: -0.04 (0.51), residues: 110 loop : -2.12 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 177 TYR 0.008 0.001 TYR G 66 PHE 0.008 0.001 PHE S 9 TRP 0.007 0.001 TRP M 202 HIS 0.006 0.002 HIS G 74 Details of bonding type rmsd covalent geometry : bond 0.00266 (18000) covalent geometry : angle 0.55273 (24480) SS BOND : bond 0.00243 ( 30) SS BOND : angle 0.62335 ( 60) hydrogen bonds : bond 0.04797 ( 804) hydrogen bonds : angle 3.62300 ( 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 326 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 231 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: A 227 ARG cc_start: 0.4636 (OUTLIER) cc_final: 0.3881 (tpm-80) REVERT: B 47 ASP cc_start: 0.8946 (p0) cc_final: 0.8641 (p0) REVERT: B 227 ARG cc_start: 0.4589 (OUTLIER) cc_final: 0.4235 (tpm170) REVERT: G 227 ARG cc_start: 0.4402 (OUTLIER) cc_final: 0.3969 (tpm-80) REVERT: J 213 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8998 (mt) REVERT: J 221 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7957 (ttp80) REVERT: P 24 LEU cc_start: 0.8886 (tp) cc_final: 0.8525 (mt) REVERT: P 47 ASP cc_start: 0.8910 (p0) cc_final: 0.8632 (p0) REVERT: P 176 THR cc_start: 0.8820 (p) cc_final: 0.8545 (t) REVERT: S 227 ARG cc_start: 0.4707 (OUTLIER) cc_final: 0.4036 (tpm-80) REVERT: V 213 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.9014 (mt) REVERT: V 221 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8001 (ttp80) REVERT: Y 103 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8145 (tp) REVERT: Y 213 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9091 (mt) outliers start: 95 outliers final: 69 residues processed: 304 average time/residue: 0.5100 time to fit residues: 176.5719 Evaluate side-chains 302 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 223 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 70 SER 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 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 208 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 28 LEU Chi-restraints excluded: chain J residue 70 SER 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 181 THR Chi-restraints excluded: chain J residue 213 LEU 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 94 VAL 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 70 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 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 181 THR 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 70 SER 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 208 SER Chi-restraints excluded: chain V residue 213 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 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 Y residue 205 SER Chi-restraints excluded: chain Y residue 213 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 64 optimal weight: 0.0270 chunk 116 optimal weight: 0.0770 chunk 15 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 171 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS B 74 HIS G 74 HIS J 74 HIS M 46 GLN M 74 HIS P 74 HIS V 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 = 0.3526 r_free = 0.3526 target = 0.139127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.110830 restraints weight = 17328.366| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.03 r_work: 0.2914 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2627 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= 0.091 Angle : 0.497 7.608 24540 Z= 0.232 Chirality : 0.040 0.164 2880 Planarity : 0.005 0.034 2770 Dihedral : 12.334 100.697 4912 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 5.06 % Allowed : 22.76 % Favored : 72.18 % 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 aren not related in a simple way. whole: 0.92 (0.19), residues: 1990 helix: 1.53 (0.14), residues: 1400 sheet: -0.04 (0.50), residues: 110 loop : -2.02 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y 227 TYR 0.006 0.001 TYR G 66 PHE 0.007 0.001 PHE S 9 TRP 0.007 0.001 TRP Y 202 HIS 0.005 0.001 HIS b 74 Details of bonding type rmsd covalent geometry : bond 0.00197 (18000) covalent geometry : angle 0.49665 (24480) SS BOND : bond 0.00150 ( 30) SS BOND : angle 0.47434 ( 60) hydrogen bonds : bond 0.03733 ( 804) hydrogen bonds : angle 3.49404 ( 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 323 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 235 time to evaluate : 0.435 Fit side-chains REVERT: A 227 ARG cc_start: 0.4684 (OUTLIER) cc_final: 0.3878 (tpm-80) REVERT: B 47 ASP cc_start: 0.8952 (p0) cc_final: 0.8741 (p0) REVERT: B 74 HIS cc_start: 0.8253 (m90) cc_final: 0.7966 (m-70) REVERT: B 176 THR cc_start: 0.8701 (p) cc_final: 0.8441 (t) REVERT: B 227 ARG cc_start: 0.4609 (OUTLIER) cc_final: 0.4224 (tpm170) REVERT: G 74 HIS cc_start: 0.8221 (m90) cc_final: 0.7915 (m-70) REVERT: G 227 ARG cc_start: 0.4590 (OUTLIER) cc_final: 0.4036 (tpm-80) REVERT: J 221 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.8057 (ttp80) REVERT: J 227 ARG cc_start: 0.4488 (OUTLIER) cc_final: 0.3866 (tpm-80) REVERT: M 80 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8786 (mm) REVERT: M 176 THR cc_start: 0.8712 (p) cc_final: 0.8431 (t) REVERT: P 24 LEU cc_start: 0.8948 (tp) cc_final: 0.8657 (mt) REVERT: P 47 ASP cc_start: 0.8961 (p0) cc_final: 0.8735 (p0) REVERT: P 74 HIS cc_start: 0.8236 (m90) cc_final: 0.8005 (m-70) REVERT: P 176 THR cc_start: 0.8743 (p) cc_final: 0.8494 (t) REVERT: S 227 ARG cc_start: 0.4689 (OUTLIER) cc_final: 0.3948 (tpm-80) REVERT: V 176 THR cc_start: 0.8677 (p) cc_final: 0.8412 (t) REVERT: V 221 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8103 (ttp80) REVERT: Y 102 THR cc_start: 0.8147 (t) cc_final: 0.7580 (p) REVERT: Y 176 THR cc_start: 0.8691 (p) cc_final: 0.8414 (t) REVERT: b 227 ARG cc_start: 0.4557 (OUTLIER) cc_final: 0.3877 (tpm-80) outliers start: 88 outliers final: 44 residues processed: 301 average time/residue: 0.4901 time to fit residues: 167.7894 Evaluate side-chains 275 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 222 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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 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 146 HIS 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 70 SER Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 146 HIS 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 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 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 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 70 SER Chi-restraints excluded: chain V residue 94 VAL Chi-restraints excluded: chain V residue 146 HIS 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 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: 1.9990 chunk 120 optimal weight: 2.9990 chunk 116 optimal weight: 0.0370 chunk 152 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 4 optimal weight: 0.0670 chunk 166 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 157 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS b 15 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.137865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.109379 restraints weight = 17373.016| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 0.95 r_work: 0.2865 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2732 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= 0.106 Angle : 0.527 8.499 24540 Z= 0.246 Chirality : 0.041 0.159 2880 Planarity : 0.005 0.038 2770 Dihedral : 12.156 100.568 4904 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.25 % Allowed : 22.70 % Favored : 73.05 % 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 aren not related in a simple way. whole: 1.07 (0.19), residues: 1990 helix: 1.67 (0.14), residues: 1400 sheet: -0.01 (0.50), residues: 110 loop : -2.05 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 177 TYR 0.008 0.001 TYR G 66 PHE 0.008 0.001 PHE S 9 TRP 0.006 0.001 TRP Y 202 HIS 0.005 0.002 HIS b 146 Details of bonding type rmsd covalent geometry : bond 0.00240 (18000) covalent geometry : angle 0.52643 (24480) SS BOND : bond 0.00222 ( 30) SS BOND : angle 0.59197 ( 60) hydrogen bonds : bond 0.04425 ( 804) hydrogen bonds : angle 3.47436 ( 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 299 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 225 time to evaluate : 0.657 Fit side-chains REVERT: A 227 ARG cc_start: 0.4647 (OUTLIER) cc_final: 0.3903 (tpm-80) REVERT: B 47 ASP cc_start: 0.8911 (p0) cc_final: 0.8655 (p0) REVERT: B 227 ARG cc_start: 0.4559 (OUTLIER) cc_final: 0.4236 (tpm170) REVERT: G 74 HIS cc_start: 0.8085 (m90) cc_final: 0.7856 (m-70) REVERT: G 227 ARG cc_start: 0.4561 (OUTLIER) cc_final: 0.4015 (tpm-80) REVERT: J 221 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7847 (ttp80) REVERT: J 222 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7108 (ttp80) REVERT: P 47 ASP cc_start: 0.8878 (p0) cc_final: 0.8641 (p0) REVERT: S 74 HIS cc_start: 0.8260 (m-70) cc_final: 0.8033 (m-70) REVERT: V 221 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7895 (ttp80) REVERT: Y 102 THR cc_start: 0.8144 (t) cc_final: 0.7598 (p) REVERT: b 74 HIS cc_start: 0.8324 (m-70) cc_final: 0.7972 (m-70) REVERT: b 227 ARG cc_start: 0.4580 (OUTLIER) cc_final: 0.3933 (tpm-80) outliers start: 74 outliers final: 56 residues processed: 278 average time/residue: 0.4808 time to fit residues: 151.9354 Evaluate side-chains 283 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 220 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 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 29 THR 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 6 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 70 SER 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 221 ARG Chi-restraints excluded: chain J residue 222 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 94 VAL 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 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 208 SER Chi-restraints excluded: chain V residue 6 LEU Chi-restraints excluded: chain V residue 70 SER 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 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 181 THR Chi-restraints excluded: chain Y residue 205 SER 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 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: 0.6980 chunk 49 optimal weight: 3.9990 chunk 186 optimal weight: 0.7980 chunk 192 optimal weight: 3.9990 chunk 162 optimal weight: 0.6980 chunk 59 optimal weight: 6.9990 chunk 178 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 166 optimal weight: 0.8980 chunk 141 optimal weight: 0.4980 chunk 27 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 74 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.138024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.109609 restraints weight = 17299.257| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 0.94 r_work: 0.2867 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 18030 Z= 0.100 Angle : 0.510 8.315 24540 Z= 0.238 Chirality : 0.040 0.161 2880 Planarity : 0.005 0.035 2770 Dihedral : 12.085 100.153 4902 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.08 % Allowed : 22.76 % Favored : 73.16 % 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 aren not related in a simple way. whole: 1.24 (0.19), residues: 1990 helix: 1.82 (0.14), residues: 1400 sheet: -0.02 (0.50), residues: 110 loop : -2.06 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 177 TYR 0.008 0.001 TYR G 66 PHE 0.007 0.001 PHE S 9 TRP 0.007 0.001 TRP Y 202 HIS 0.005 0.001 HIS Y 74 Details of bonding type rmsd covalent geometry : bond 0.00225 (18000) covalent geometry : angle 0.51000 (24480) SS BOND : bond 0.00194 ( 30) SS BOND : angle 0.53694 ( 60) hydrogen bonds : bond 0.04131 ( 804) hydrogen bonds : angle 3.43780 ( 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 298 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 227 time to evaluate : 0.454 Fit side-chains REVERT: A 102 THR cc_start: 0.8346 (t) cc_final: 0.7788 (p) REVERT: A 227 ARG cc_start: 0.4667 (OUTLIER) cc_final: 0.3904 (tpm-80) REVERT: B 47 ASP cc_start: 0.8864 (p0) cc_final: 0.8645 (p0) REVERT: G 74 HIS cc_start: 0.8061 (m90) cc_final: 0.7829 (m-70) REVERT: G 227 ARG cc_start: 0.4668 (OUTLIER) cc_final: 0.4017 (tpm-80) REVERT: J 221 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7584 (ttp80) REVERT: M 74 HIS cc_start: 0.8176 (m-70) cc_final: 0.7889 (m-70) REVERT: P 24 LEU cc_start: 0.8900 (tp) cc_final: 0.8643 (mt) REVERT: P 47 ASP cc_start: 0.8876 (p0) cc_final: 0.8640 (p0) REVERT: P 74 HIS cc_start: 0.8220 (m-70) cc_final: 0.7953 (m-70) REVERT: S 74 HIS cc_start: 0.8230 (m-70) cc_final: 0.8017 (m-70) REVERT: V 221 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7858 (ttp80) REVERT: Y 102 THR cc_start: 0.8163 (t) cc_final: 0.7622 (p) REVERT: b 74 HIS cc_start: 0.8281 (m-70) cc_final: 0.7965 (m-70) outliers start: 71 outliers final: 57 residues processed: 279 average time/residue: 0.4445 time to fit residues: 141.7011 Evaluate side-chains 283 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 222 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 146 HIS Chi-restraints excluded: chain B residue 148 LEU 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 181 THR Chi-restraints excluded: chain G residue 208 SER Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 70 SER 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 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 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 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 V residue 28 LEU Chi-restraints excluded: chain V residue 70 SER 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 76 ARG 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 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: 0.6980 chunk 48 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 0.0370 chunk 193 optimal weight: 0.8980 chunk 153 optimal weight: 4.9990 chunk 90 optimal weight: 20.0000 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.138613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.110232 restraints weight = 17500.823| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 0.95 r_work: 0.2894 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 18030 Z= 0.095 Angle : 0.502 8.236 24540 Z= 0.233 Chirality : 0.040 0.162 2880 Planarity : 0.005 0.035 2770 Dihedral : 11.990 99.959 4899 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.39 % Allowed : 23.39 % Favored : 73.22 % 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 aren not related in a simple way. whole: 1.47 (0.19), residues: 1990 helix: 2.01 (0.14), residues: 1400 sheet: -0.01 (0.49), residues: 110 loop : -2.02 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 177 TYR 0.007 0.001 TYR G 66 PHE 0.007 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 covalent geometry : bond 0.00211 (18000) covalent geometry : angle 0.50178 (24480) SS BOND : bond 0.00164 ( 30) SS BOND : angle 0.50147 ( 60) hydrogen bonds : bond 0.03897 ( 804) hydrogen bonds : angle 3.40791 ( 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: 59 poor density : 228 time to evaluate : 0.544 Fit side-chains REVERT: A 102 THR cc_start: 0.8373 (t) cc_final: 0.7819 (p) REVERT: B 47 ASP cc_start: 0.8985 (p0) cc_final: 0.8778 (p0) REVERT: B 176 THR cc_start: 0.8750 (p) cc_final: 0.8472 (t) REVERT: B 227 ARG cc_start: 0.4629 (OUTLIER) cc_final: 0.4088 (tpm-80) REVERT: G 74 HIS cc_start: 0.8240 (m90) cc_final: 0.7952 (m-70) REVERT: J 221 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7737 (ttp80) REVERT: M 74 HIS cc_start: 0.8329 (m-70) cc_final: 0.8048 (m-70) REVERT: M 102 THR cc_start: 0.8158 (t) cc_final: 0.7610 (p) REVERT: P 24 LEU cc_start: 0.8951 (tp) cc_final: 0.8693 (mt) REVERT: P 47 ASP cc_start: 0.8983 (p0) cc_final: 0.8755 (p0) REVERT: P 74 HIS cc_start: 0.8302 (m-70) cc_final: 0.8037 (m-70) REVERT: S 74 HIS cc_start: 0.8345 (m-70) cc_final: 0.8135 (m-70) REVERT: V 221 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8075 (ttp80) REVERT: Y 74 HIS cc_start: 0.8370 (m-70) cc_final: 0.8037 (m-70) REVERT: Y 102 THR cc_start: 0.8245 (t) cc_final: 0.7705 (p) REVERT: b 74 HIS cc_start: 0.8391 (m-70) cc_final: 0.8062 (m-70) REVERT: b 102 THR cc_start: 0.8433 (t) cc_final: 0.7841 (p) REVERT: b 227 ARG cc_start: 0.4657 (OUTLIER) cc_final: 0.3969 (tpm-80) outliers start: 59 outliers final: 48 residues processed: 273 average time/residue: 0.4623 time to fit residues: 144.0315 Evaluate side-chains 273 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 221 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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 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 227 ARG 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 208 SER Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 70 SER 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 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 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 V residue 28 LEU Chi-restraints excluded: chain V residue 70 SER 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 80 ILE Chi-restraints excluded: chain Y residue 146 HIS Chi-restraints excluded: chain Y residue 205 SER Chi-restraints excluded: chain b residue 24 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 Chi-restraints excluded: chain b residue 227 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 28 optimal weight: 0.6980 chunk 160 optimal weight: 0.9990 chunk 168 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 177 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3512 r_free = 0.3512 target = 0.137845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.109790 restraints weight = 17222.340| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 0.99 r_work: 0.2886 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 18030 Z= 0.105 Angle : 0.517 8.495 24540 Z= 0.241 Chirality : 0.041 0.160 2880 Planarity : 0.005 0.036 2770 Dihedral : 11.886 100.080 4895 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.45 % Allowed : 23.16 % Favored : 73.39 % 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 aren not related in a simple way. whole: 1.50 (0.19), residues: 1990 helix: 2.04 (0.14), residues: 1400 sheet: 0.01 (0.50), residues: 110 loop : -2.05 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 177 TYR 0.008 0.001 TYR G 66 PHE 0.008 0.001 PHE S 9 TRP 0.006 0.001 TRP A 202 HIS 0.005 0.002 HIS M 74 Details of bonding type rmsd covalent geometry : bond 0.00238 (18000) covalent geometry : angle 0.51641 (24480) SS BOND : bond 0.00208 ( 30) SS BOND : angle 0.56892 ( 60) hydrogen bonds : bond 0.04244 ( 804) hydrogen bonds : angle 3.41594 ( 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 282 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 222 time to evaluate : 0.512 Fit side-chains REVERT: A 102 THR cc_start: 0.8394 (t) cc_final: 0.7827 (p) REVERT: B 47 ASP cc_start: 0.8984 (p0) cc_final: 0.8761 (p0) REVERT: G 74 HIS cc_start: 0.8260 (m90) cc_final: 0.7954 (m-70) REVERT: J 221 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7675 (ttp80) REVERT: M 74 HIS cc_start: 0.8354 (m-70) cc_final: 0.8068 (m-70) REVERT: M 102 THR cc_start: 0.8139 (t) cc_final: 0.7586 (p) REVERT: P 24 LEU cc_start: 0.8965 (tp) cc_final: 0.8692 (mt) REVERT: P 47 ASP cc_start: 0.8991 (p0) cc_final: 0.8755 (p0) REVERT: P 74 HIS cc_start: 0.8330 (m-70) cc_final: 0.8062 (m-70) REVERT: S 74 HIS cc_start: 0.8382 (m-70) cc_final: 0.8164 (m-70) REVERT: V 221 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.8120 (ttp-170) REVERT: Y 74 HIS cc_start: 0.8380 (m-70) cc_final: 0.8075 (m-70) REVERT: Y 102 THR cc_start: 0.8201 (t) cc_final: 0.7645 (p) REVERT: b 74 HIS cc_start: 0.8409 (m-70) cc_final: 0.8083 (m-70) REVERT: b 102 THR cc_start: 0.8425 (t) cc_final: 0.7818 (p) outliers start: 60 outliers final: 53 residues processed: 268 average time/residue: 0.4402 time to fit residues: 134.7971 Evaluate side-chains 276 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 221 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 70 SER 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 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 181 THR 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 70 SER 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 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 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 181 THR Chi-restraints excluded: chain V residue 28 LEU Chi-restraints excluded: chain V residue 70 SER 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 80 ILE 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 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: 3.9990 chunk 49 optimal weight: 3.9990 chunk 90 optimal weight: 0.0010 chunk 146 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 188 optimal weight: 0.0170 chunk 88 optimal weight: 0.9990 chunk 190 optimal weight: 0.0980 overall best weight: 0.3426 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.142451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.114980 restraints weight = 17365.764| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.07 r_work: 0.2997 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2963 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= 0.085 Angle : 0.476 8.241 24540 Z= 0.219 Chirality : 0.040 0.168 2880 Planarity : 0.004 0.037 2770 Dihedral : 11.746 99.659 4895 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.47 % Allowed : 24.08 % 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 aren not related in a simple way. whole: 1.80 (0.19), residues: 1990 helix: 2.28 (0.14), residues: 1400 sheet: -0.02 (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 S 177 TYR 0.005 0.001 TYR J 162 PHE 0.006 0.001 PHE G 9 TRP 0.007 0.001 TRP M 202 HIS 0.004 0.001 HIS M 74 Details of bonding type rmsd covalent geometry : bond 0.00180 (18000) covalent geometry : angle 0.47582 (24480) SS BOND : bond 0.00095 ( 30) SS BOND : angle 0.44718 ( 60) hydrogen bonds : bond 0.03287 ( 804) hydrogen bonds : angle 3.36357 ( 2382) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4731.37 seconds wall clock time: 81 minutes 20.65 seconds (4880.65 seconds total)