Starting phenix.real_space_refine on Mon May 19 06:17:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gn7_34156/05_2025/8gn7_34156.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gn7_34156/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8gn7_34156/05_2025/8gn7_34156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gn7_34156/05_2025/8gn7_34156.map" model { file = "/net/cci-nas-00/data/ceres_data/8gn7_34156/05_2025/8gn7_34156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gn7_34156/05_2025/8gn7_34156.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 11.08, per 1000 atoms: 0.63 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: 4.74 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 1.72 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: 4.54 Time building geometry restraints manager: 5.44 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: 0.02 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: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 39.220 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.080 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:13.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.510 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (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 TRP 0.010 0.001 TRP P 25 HIS 0.004 0.001 HIS M 146 PHE 0.009 0.001 PHE P 200 TYR 0.010 0.001 TYR B 143 ARG 0.005 0.000 ARG P 76 Details of bonding type rmsd hydrogen bonds : bond 0.24064 ( 804) hydrogen bonds : angle 7.01881 ( 2382) SS BOND : bond 0.00113 ( 30) SS BOND : angle 0.47225 ( 60) covalent geometry : bond 0.00272 (18000) covalent geometry : angle 0.69943 (24480) *********************** 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 : 1.824 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: 0.9372 time to fit residues: 443.8030 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 : 1.862 ------------------------------------------------------------------------------- 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 168 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 60 optimal weight: 0.0370 chunk 95 optimal weight: 0.0770 chunk 116 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 overall best weight: 1.0220 ------------------------------------------------------------------------------- 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 = 0.3568 r_free = 0.3568 target = 0.141765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.113998 restraints weight = 17278.959| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.01 r_work: 0.2999 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1564 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= 0.140 Angle : 0.644 7.885 24540 Z= 0.308 Chirality : 0.043 0.158 2880 Planarity : 0.006 0.045 2770 Dihedral : 13.918 109.696 4994 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 5.69 % Allowed : 24.25 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.19), residues: 1990 helix: 0.27 (0.15), residues: 1360 sheet: 0.06 (0.52), residues: 110 loop : -1.53 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP b 202 HIS 0.008 0.003 HIS J 74 PHE 0.012 0.002 PHE S 9 TYR 0.007 0.001 TYR J 66 ARG 0.006 0.000 ARG P 76 Details of bonding type rmsd hydrogen bonds : bond 0.05892 ( 804) hydrogen bonds : angle 4.38961 ( 2382) SS BOND : bond 0.00279 ( 30) SS BOND : angle 0.77167 ( 60) covalent geometry : bond 0.00307 (18000) covalent geometry : angle 0.64401 (24480) *********************** 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 348 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 249 time to evaluate : 2.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 HIS cc_start: 0.6987 (OUTLIER) cc_final: 0.6335 (p90) REVERT: A 227 ARG cc_start: 0.4396 (OUTLIER) cc_final: 0.3823 (tpm-80) REVERT: B 47 ASP cc_start: 0.9002 (p0) cc_final: 0.8717 (p0) REVERT: B 76 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8719 (mpp-170) REVERT: B 80 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8884 (mm) REVERT: G 28 LEU cc_start: 0.8408 (mt) cc_final: 0.8179 (tp) REVERT: G 74 HIS cc_start: 0.7014 (OUTLIER) cc_final: 0.6246 (p90) REVERT: G 227 ARG cc_start: 0.4342 (OUTLIER) cc_final: 0.3832 (tpm-80) REVERT: J 28 LEU cc_start: 0.8330 (mt) cc_final: 0.8121 (tp) REVERT: J 74 HIS cc_start: 0.7186 (OUTLIER) cc_final: 0.6365 (p90) REVERT: M 74 HIS cc_start: 0.7023 (OUTLIER) cc_final: 0.6297 (p90) REVERT: P 47 ASP cc_start: 0.8979 (p0) cc_final: 0.8687 (p0) REVERT: P 80 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8865 (mm) REVERT: S 74 HIS cc_start: 0.7040 (OUTLIER) cc_final: 0.6347 (p90) REVERT: V 74 HIS cc_start: 0.7167 (OUTLIER) cc_final: 0.6417 (p90) REVERT: Y 74 HIS cc_start: 0.7121 (OUTLIER) cc_final: 0.6306 (p90) REVERT: b 34 MET cc_start: 0.9058 (mmm) cc_final: 0.8806 (mmm) REVERT: b 74 HIS cc_start: 0.6985 (OUTLIER) cc_final: 0.6307 (p90) REVERT: b 227 ARG cc_start: 0.4365 (OUTLIER) cc_final: 0.3837 (tpm-80) outliers start: 99 outliers final: 61 residues processed: 323 average time/residue: 0.9926 time to fit residues: 366.0314 Evaluate side-chains 309 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 234 time to evaluate : 1.709 ------------------------------------------------------------------------------- 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 80 ILE 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 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 181 THR 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 181 THR 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 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 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 94 VAL Chi-restraints excluded: chain S residue 146 HIS Chi-restraints excluded: chain S residue 181 THR Chi-restraints excluded: chain S residue 189 SER Chi-restraints excluded: chain V residue 74 HIS 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 146 HIS Chi-restraints excluded: chain V residue 148 LEU Chi-restraints excluded: chain V residue 181 THR Chi-restraints excluded: chain V residue 205 SER 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 83 VAL 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 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 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 93 optimal weight: 4.9990 chunk 195 optimal weight: 0.7980 chunk 194 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 136 optimal weight: 0.6980 chunk 61 optimal weight: 0.0020 chunk 83 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- 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 ** 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 = 0.3561 r_free = 0.3561 target = 0.141354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.113070 restraints weight = 17142.203| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.08 r_work: 0.3013 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18030 Z= 0.112 Angle : 0.545 7.118 24540 Z= 0.258 Chirality : 0.040 0.160 2880 Planarity : 0.005 0.038 2770 Dihedral : 13.306 103.343 4953 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 5.63 % Allowed : 23.51 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.19), residues: 1990 helix: 0.71 (0.15), residues: 1360 sheet: 0.12 (0.52), residues: 110 loop : -1.71 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP Y 202 HIS 0.006 0.002 HIS J 74 PHE 0.009 0.001 PHE S 9 TYR 0.006 0.001 TYR G 66 ARG 0.005 0.000 ARG Y 177 Details of bonding type rmsd hydrogen bonds : bond 0.04730 ( 804) hydrogen bonds : angle 3.87351 ( 2382) SS BOND : bond 0.00198 ( 30) SS BOND : angle 0.54826 ( 60) covalent geometry : bond 0.00241 (18000) covalent geometry : angle 0.54516 (24480) *********************** 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 357 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 259 time to evaluate : 1.891 Fit side-chains revert: symmetry clash REVERT: A 227 ARG cc_start: 0.4613 (OUTLIER) cc_final: 0.3981 (tpm-80) REVERT: B 47 ASP cc_start: 0.8957 (p0) cc_final: 0.8681 (p0) REVERT: B 80 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8868 (mm) REVERT: B 176 THR cc_start: 0.8674 (p) cc_final: 0.8444 (t) REVERT: B 227 ARG cc_start: 0.4768 (OUTLIER) cc_final: 0.4206 (tpm-80) REVERT: G 224 MET cc_start: 0.7245 (mtm) cc_final: 0.6783 (mpm) REVERT: G 227 ARG cc_start: 0.4605 (OUTLIER) cc_final: 0.4159 (tpm-80) REVERT: J 24 LEU cc_start: 0.8743 (tp) cc_final: 0.8378 (mt) REVERT: J 28 LEU cc_start: 0.8366 (mt) cc_final: 0.8155 (tp) REVERT: J 227 ARG cc_start: 0.4684 (OUTLIER) cc_final: 0.4126 (tpm-80) REVERT: M 24 LEU cc_start: 0.8868 (tp) cc_final: 0.8523 (mt) REVERT: M 213 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8989 (mt) REVERT: M 222 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.7003 (ttp80) REVERT: P 47 ASP cc_start: 0.8899 (p0) cc_final: 0.8657 (p0) REVERT: P 80 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8875 (mm) REVERT: P 176 THR cc_start: 0.8716 (p) cc_final: 0.8485 (t) REVERT: S 227 ARG cc_start: 0.4871 (OUTLIER) cc_final: 0.4188 (tpm-80) REVERT: V 24 LEU cc_start: 0.8725 (tp) cc_final: 0.8413 (mt) REVERT: V 176 THR cc_start: 0.8684 (p) cc_final: 0.8437 (t) REVERT: V 213 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8926 (mt) REVERT: V 221 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8160 (ttp80) REVERT: Y 24 LEU cc_start: 0.8883 (tp) cc_final: 0.8489 (mt) REVERT: Y 103 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8072 (tp) outliers start: 98 outliers final: 52 residues processed: 327 average time/residue: 1.1248 time to fit residues: 414.7739 Evaluate side-chains 299 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 235 time to evaluate : 2.032 ------------------------------------------------------------------------------- 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 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 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 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 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 M residue 213 LEU Chi-restraints excluded: chain M residue 222 ARG 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 80 ILE Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain S residue 146 HIS Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 227 ARG Chi-restraints excluded: chain V residue 28 LEU Chi-restraints excluded: chain V residue 74 HIS 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 213 LEU Chi-restraints excluded: chain V residue 221 ARG Chi-restraints excluded: chain Y residue 28 LEU Chi-restraints excluded: chain Y residue 74 HIS Chi-restraints excluded: chain Y residue 76 ARG Chi-restraints excluded: chain Y residue 94 VAL Chi-restraints excluded: chain Y residue 103 LEU Chi-restraints excluded: chain Y residue 146 HIS Chi-restraints excluded: chain 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 227 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 114 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 198 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 143 optimal weight: 0.4980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3525 r_free = 0.3525 target = 0.138612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.110110 restraints weight = 17307.276| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 0.94 r_work: 0.2880 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 18030 Z= 0.117 Angle : 0.562 8.222 24540 Z= 0.263 Chirality : 0.041 0.159 2880 Planarity : 0.005 0.051 2770 Dihedral : 12.861 101.998 4945 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 6.38 % Allowed : 21.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.19), residues: 1990 helix: 1.01 (0.14), residues: 1380 sheet: 0.09 (0.52), residues: 110 loop : -2.13 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Y 202 HIS 0.005 0.002 HIS J 74 PHE 0.009 0.001 PHE S 9 TYR 0.007 0.001 TYR V 66 ARG 0.004 0.000 ARG Y 227 Details of bonding type rmsd hydrogen bonds : bond 0.04733 ( 804) hydrogen bonds : angle 3.62767 ( 2382) SS BOND : bond 0.00246 ( 30) SS BOND : angle 0.61036 ( 60) covalent geometry : bond 0.00262 (18000) covalent geometry : angle 0.56180 (24480) *********************** 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 352 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 241 time to evaluate : 1.732 Fit side-chains revert: symmetry clash REVERT: A 227 ARG cc_start: 0.4746 (OUTLIER) cc_final: 0.3978 (tpm-80) REVERT: B 47 ASP cc_start: 0.9078 (p0) cc_final: 0.8808 (p0) REVERT: B 76 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8827 (mpp-170) REVERT: B 80 ILE cc_start: 0.9147 (OUTLIER) cc_final: 0.8932 (mm) REVERT: B 227 ARG cc_start: 0.4648 (OUTLIER) cc_final: 0.4233 (tpm170) REVERT: G 227 ARG cc_start: 0.4573 (OUTLIER) cc_final: 0.4045 (tpm-80) REVERT: J 24 LEU cc_start: 0.8902 (tp) cc_final: 0.8608 (mt) REVERT: J 227 ARG cc_start: 0.4676 (OUTLIER) cc_final: 0.3983 (tpm-80) REVERT: M 24 LEU cc_start: 0.8918 (tp) cc_final: 0.8652 (mt) REVERT: M 222 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7043 (ttp80) REVERT: P 24 LEU cc_start: 0.8997 (tp) cc_final: 0.8555 (mt) REVERT: P 47 ASP cc_start: 0.9016 (p0) cc_final: 0.8755 (p0) REVERT: S 227 ARG cc_start: 0.4787 (OUTLIER) cc_final: 0.4027 (tpm-80) REVERT: V 24 LEU cc_start: 0.8842 (tp) cc_final: 0.8592 (mt) REVERT: V 213 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.9000 (mt) REVERT: V 221 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8305 (ttp80) REVERT: Y 24 LEU cc_start: 0.8908 (tp) cc_final: 0.8643 (mt) REVERT: Y 103 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8127 (tp) REVERT: b 221 ARG cc_start: 0.8445 (ttm170) cc_final: 0.8213 (ttp-170) outliers start: 111 outliers final: 67 residues processed: 318 average time/residue: 0.9941 time to fit residues: 361.4525 Evaluate side-chains 308 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 230 time to evaluate : 1.863 ------------------------------------------------------------------------------- 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 208 SER Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 208 SER 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 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 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 224 MET Chi-restraints excluded: chain J residue 227 ARG Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 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 M residue 222 ARG Chi-restraints excluded: chain P residue 28 LEU 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 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 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 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 76 ARG 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.6251 > 50: distance: 9 - 117: 9.511 distance: 28 - 41: 17.196 distance: 37 - 41: 16.957 distance: 41 - 42: 15.474 distance: 42 - 43: 39.155 distance: 43 - 44: 30.177 distance: 43 - 45: 25.012 distance: 45 - 46: 8.298 distance: 46 - 47: 12.372 distance: 46 - 49: 10.805 distance: 47 - 48: 28.130 distance: 47 - 56: 19.972 distance: 49 - 50: 20.870 distance: 50 - 51: 5.143 distance: 50 - 52: 9.878 distance: 51 - 53: 17.489 distance: 52 - 54: 15.071 distance: 53 - 55: 4.975 distance: 54 - 55: 8.822 distance: 56 - 57: 36.923 distance: 57 - 58: 55.365 distance: 57 - 60: 33.495 distance: 58 - 59: 55.625 distance: 58 - 64: 13.302 distance: 60 - 61: 11.273 distance: 61 - 62: 38.754 distance: 61 - 63: 38.870 distance: 64 - 65: 21.881 distance: 65 - 66: 39.554 distance: 65 - 68: 43.702 distance: 66 - 67: 28.307 distance: 66 - 69: 44.996 distance: 69 - 70: 46.467 distance: 69 - 75: 33.760 distance: 70 - 71: 26.067 distance: 70 - 73: 23.085 distance: 71 - 72: 4.110 distance: 71 - 76: 31.273 distance: 73 - 74: 55.341 distance: 74 - 75: 32.171 distance: 76 - 77: 19.278 distance: 77 - 78: 15.369 distance: 77 - 80: 32.019 distance: 78 - 79: 17.525 distance: 78 - 85: 20.944 distance: 80 - 81: 15.654 distance: 81 - 82: 28.276 distance: 82 - 83: 22.395 distance: 83 - 84: 31.387 distance: 85 - 86: 22.563 distance: 86 - 87: 33.556 distance: 86 - 89: 42.391 distance: 87 - 88: 17.201 distance: 87 - 94: 17.499 distance: 89 - 90: 51.731 distance: 90 - 91: 29.025 distance: 91 - 92: 11.663 distance: 92 - 93: 16.817 distance: 94 - 95: 25.376 distance: 94 - 155: 27.773 distance: 95 - 96: 23.008 distance: 95 - 98: 19.320 distance: 96 - 97: 27.723 distance: 96 - 105: 20.707 distance: 97 - 152: 21.743 distance: 98 - 99: 14.435 distance: 99 - 100: 15.909 distance: 99 - 101: 19.384 distance: 100 - 102: 11.703 distance: 101 - 103: 14.659 distance: 102 - 104: 5.803 distance: 103 - 104: 5.205 distance: 105 - 106: 19.371 distance: 105 - 111: 28.531 distance: 106 - 107: 32.929 distance: 106 - 109: 33.342 distance: 107 - 108: 20.665 distance: 107 - 112: 36.492 distance: 109 - 110: 23.805 distance: 110 - 111: 19.090 distance: 112 - 113: 18.503 distance: 112 - 141: 24.900 distance: 113 - 114: 25.793 distance: 113 - 116: 11.731 distance: 114 - 115: 21.027 distance: 114 - 118: 13.261 distance: 115 - 138: 7.762 distance: 116 - 117: 14.613