Starting phenix.real_space_refine on Wed Mar 4 20:02:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bjm_16089/03_2026/8bjm_16089.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bjm_16089/03_2026/8bjm_16089.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8bjm_16089/03_2026/8bjm_16089.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bjm_16089/03_2026/8bjm_16089.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bjm_16089/03_2026/8bjm_16089.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bjm_16089/03_2026/8bjm_16089.map" } resolution = 2.2 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= -0.011 sd= 0.919 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: 4 Type Number sf(0) Gaussians S 88 5.16 5 C 10122 2.51 5 N 2909 2.21 5 O 3536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16655 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1465 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 4, 'TRANS': 181} Chain: "B" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1476 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 4, 'TRANS': 182} Chain: "C" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1465 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 4, 'TRANS': 181} Chain: "D" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1464 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 4, 'TRANS': 181} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1465 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 4, 'TRANS': 181} Chain: "F" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1476 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 4, 'TRANS': 182} Chain: "G" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1465 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 4, 'TRANS': 181} Chain: "H" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1465 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 4, 'TRANS': 181} Chain: "I" Number of atoms: 1475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1475 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 4, 'TRANS': 182} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "J" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1465 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 4, 'TRANS': 181} Chain: "K" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1476 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 4, 'TRANS': 182} Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "F" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "G" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "H" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "I" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "J" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "K" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Time building chain proxies: 3.98, per 1000 atoms: 0.24 Number of scatterers: 16655 At special positions: 0 Unit cell: (133.042, 133.042, 77.486, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 88 16.00 O 3536 8.00 N 2909 7.00 C 10122 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 809.0 milliseconds 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3726 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 22 sheets defined 47.5% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 32 through 44 removed outlier: 3.778A pdb=" N ARG A 44 " --> pdb=" O GLN A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 52 Processing helix chain 'A' and resid 67 through 80 Processing helix chain 'A' and resid 134 through 157 removed outlier: 3.876A pdb=" N SER A 157 " --> pdb=" O ARG A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 167 removed outlier: 6.563A pdb=" N ALA A 161 " --> pdb=" O PHE A 158 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ASN A 164 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N CYS A 165 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 167 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 178 removed outlier: 3.572A pdb=" N LEU A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 208 Processing helix chain 'B' and resid 32 through 44 removed outlier: 3.699A pdb=" N ARG B 44 " --> pdb=" O GLN B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 52 Processing helix chain 'B' and resid 67 through 80 Processing helix chain 'B' and resid 134 through 157 removed outlier: 3.829A pdb=" N SER B 157 " --> pdb=" O ARG B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 163 removed outlier: 6.551A pdb=" N ALA B 161 " --> pdb=" O PHE B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 167 Processing helix chain 'B' and resid 168 through 177 Processing helix chain 'B' and resid 197 through 209 removed outlier: 4.222A pdb=" N ARG B 209 " --> pdb=" O TYR B 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 44 removed outlier: 3.732A pdb=" N ARG C 44 " --> pdb=" O GLN C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 52 Processing helix chain 'C' and resid 67 through 80 Processing helix chain 'C' and resid 134 through 157 removed outlier: 3.846A pdb=" N SER C 157 " --> pdb=" O ARG C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 167 removed outlier: 6.573A pdb=" N ALA C 161 " --> pdb=" O PHE C 158 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ASN C 164 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N CYS C 165 " --> pdb=" O LEU C 162 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 167 " --> pdb=" O ASN C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 178 Processing helix chain 'C' and resid 197 through 208 Processing helix chain 'D' and resid 32 through 45 removed outlier: 3.736A pdb=" N ARG D 44 " --> pdb=" O GLN D 40 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLN D 45 " --> pdb=" O LYS D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 52 Processing helix chain 'D' and resid 67 through 80 Processing helix chain 'D' and resid 134 through 157 removed outlier: 3.882A pdb=" N SER D 157 " --> pdb=" O ARG D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 167 removed outlier: 6.594A pdb=" N ALA D 161 " --> pdb=" O PHE D 158 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ASN D 164 " --> pdb=" O ALA D 161 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N CYS D 165 " --> pdb=" O LEU D 162 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 167 " --> pdb=" O ASN D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 177 Processing helix chain 'D' and resid 197 through 208 Processing helix chain 'E' and resid 32 through 44 removed outlier: 3.731A pdb=" N ARG E 44 " --> pdb=" O GLN E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 52 Processing helix chain 'E' and resid 67 through 80 Processing helix chain 'E' and resid 134 through 157 removed outlier: 3.863A pdb=" N SER E 157 " --> pdb=" O ARG E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 167 removed outlier: 6.535A pdb=" N ALA E 161 " --> pdb=" O PHE E 158 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ASN E 164 " --> pdb=" O ALA E 161 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N CYS E 165 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU E 167 " --> pdb=" O ASN E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 178 Processing helix chain 'E' and resid 197 through 208 Processing helix chain 'F' and resid 32 through 44 removed outlier: 3.771A pdb=" N ARG F 44 " --> pdb=" O GLN F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 52 Processing helix chain 'F' and resid 67 through 80 Processing helix chain 'F' and resid 134 through 157 removed outlier: 3.884A pdb=" N SER F 157 " --> pdb=" O ARG F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 167 removed outlier: 6.530A pdb=" N ALA F 161 " --> pdb=" O PHE F 158 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASN F 164 " --> pdb=" O ALA F 161 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N CYS F 165 " --> pdb=" O LEU F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 177 Processing helix chain 'F' and resid 197 through 209 removed outlier: 3.827A pdb=" N ARG F 209 " --> pdb=" O TYR F 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 45 removed outlier: 3.695A pdb=" N ARG G 44 " --> pdb=" O GLN G 40 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN G 45 " --> pdb=" O LYS G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 52 Processing helix chain 'G' and resid 67 through 80 Processing helix chain 'G' and resid 134 through 157 removed outlier: 3.843A pdb=" N SER G 157 " --> pdb=" O ARG G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 167 removed outlier: 6.547A pdb=" N ALA G 161 " --> pdb=" O PHE G 158 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ASN G 164 " --> pdb=" O ALA G 161 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N CYS G 165 " --> pdb=" O LEU G 162 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU G 167 " --> pdb=" O ASN G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 177 Processing helix chain 'G' and resid 197 through 208 Processing helix chain 'H' and resid 32 through 44 removed outlier: 3.794A pdb=" N ARG H 44 " --> pdb=" O GLN H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 80 Processing helix chain 'H' and resid 134 through 157 removed outlier: 3.882A pdb=" N SER H 157 " --> pdb=" O ARG H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 158 through 167 removed outlier: 6.564A pdb=" N ALA H 161 " --> pdb=" O PHE H 158 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ASN H 164 " --> pdb=" O ALA H 161 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N CYS H 165 " --> pdb=" O LEU H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 178 removed outlier: 3.604A pdb=" N LEU H 178 " --> pdb=" O SER H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 208 Processing helix chain 'I' and resid 32 through 45 WARNING: missing atoms! removed outlier: 3.680A pdb=" N ARG I 44 " --> pdb=" O GLN I 40 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN I 45 " --> pdb=" O LYS I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 52 Processing helix chain 'I' and resid 67 through 80 Processing helix chain 'I' and resid 134 through 157 removed outlier: 3.866A pdb=" N SER I 157 " --> pdb=" O ARG I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 158 through 167 removed outlier: 6.563A pdb=" N ALA I 161 " --> pdb=" O PHE I 158 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASN I 164 " --> pdb=" O ALA I 161 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N CYS I 165 " --> pdb=" O LEU I 162 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU I 167 " --> pdb=" O ASN I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 177 removed outlier: 3.565A pdb=" N LYS I 177 " --> pdb=" O ARG I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 208 Processing helix chain 'J' and resid 32 through 43 Processing helix chain 'J' and resid 48 through 52 Processing helix chain 'J' and resid 67 through 80 Processing helix chain 'J' and resid 134 through 157 removed outlier: 3.848A pdb=" N SER J 157 " --> pdb=" O ARG J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 167 removed outlier: 6.581A pdb=" N ALA J 161 " --> pdb=" O PHE J 158 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ASN J 164 " --> pdb=" O ALA J 161 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N CYS J 165 " --> pdb=" O LEU J 162 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU J 167 " --> pdb=" O ASN J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 177 removed outlier: 3.518A pdb=" N LYS J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 208 Processing helix chain 'K' and resid 32 through 44 removed outlier: 3.738A pdb=" N ARG K 44 " --> pdb=" O GLN K 40 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 52 Processing helix chain 'K' and resid 67 through 80 Processing helix chain 'K' and resid 134 through 157 removed outlier: 3.859A pdb=" N SER K 157 " --> pdb=" O ARG K 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 158 through 167 removed outlier: 6.549A pdb=" N ALA K 161 " --> pdb=" O PHE K 158 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ASN K 164 " --> pdb=" O ALA K 161 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N CYS K 165 " --> pdb=" O LEU K 162 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU K 167 " --> pdb=" O ASN K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 168 through 178 removed outlier: 3.526A pdb=" N LEU K 178 " --> pdb=" O SER K 174 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 209 removed outlier: 4.133A pdb=" N ARG K 209 " --> pdb=" O TYR K 205 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 99 removed outlier: 5.350A pdb=" N HIS A 86 " --> pdb=" O GLN A 114 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N GLN A 114 " --> pdb=" O HIS A 86 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ILE A 88 " --> pdb=" O ARG A 112 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ARG A 112 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN A 90 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLY A 106 " --> pdb=" O ASP A 94 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL A 96 " --> pdb=" O TYR A 104 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TYR A 104 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU A 98 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LYS A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N PHE A 103 " --> pdb=" O GLY A 131 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 99 removed outlier: 5.359A pdb=" N HIS B 86 " --> pdb=" O GLN B 114 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLN B 114 " --> pdb=" O HIS B 86 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ILE B 88 " --> pdb=" O ARG B 112 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG B 112 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN B 90 " --> pdb=" O PHE B 110 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLY B 106 " --> pdb=" O ASP B 94 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL B 96 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TYR B 104 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU B 98 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LYS B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N PHE B 103 " --> pdb=" O GLY B 131 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AA6, first strand: chain 'C' and resid 84 through 99 removed outlier: 5.363A pdb=" N HIS C 86 " --> pdb=" O GLN C 114 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLN C 114 " --> pdb=" O HIS C 86 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ILE C 88 " --> pdb=" O ARG C 112 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ARG C 112 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN C 90 " --> pdb=" O PHE C 110 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLY C 106 " --> pdb=" O ASP C 94 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL C 96 " --> pdb=" O TYR C 104 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TYR C 104 " --> pdb=" O VAL C 96 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU C 98 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LYS C 102 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N PHE C 103 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 54 through 56 Processing sheet with id=AA8, first strand: chain 'D' and resid 84 through 99 removed outlier: 5.352A pdb=" N HIS D 86 " --> pdb=" O GLN D 114 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N GLN D 114 " --> pdb=" O HIS D 86 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ILE D 88 " --> pdb=" O ARG D 112 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG D 112 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN D 90 " --> pdb=" O PHE D 110 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLY D 106 " --> pdb=" O ASP D 94 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL D 96 " --> pdb=" O TYR D 104 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TYR D 104 " --> pdb=" O VAL D 96 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU D 98 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LYS D 102 " --> pdb=" O LEU D 98 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N PHE D 103 " --> pdb=" O GLY D 131 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 53 through 57 removed outlier: 3.654A pdb=" N ALA E 57 " --> pdb=" O GLN E 61 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 84 through 99 removed outlier: 5.357A pdb=" N HIS E 86 " --> pdb=" O GLN E 114 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLN E 114 " --> pdb=" O HIS E 86 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ILE E 88 " --> pdb=" O ARG E 112 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ARG E 112 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN E 90 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLY E 106 " --> pdb=" O ASP E 94 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL E 96 " --> pdb=" O TYR E 104 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TYR E 104 " --> pdb=" O VAL E 96 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU E 98 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LYS E 102 " --> pdb=" O LEU E 98 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N PHE E 103 " --> pdb=" O GLY E 131 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 53 through 56 Processing sheet with id=AB3, first strand: chain 'F' and resid 84 through 99 removed outlier: 5.368A pdb=" N HIS F 86 " --> pdb=" O GLN F 114 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLN F 114 " --> pdb=" O HIS F 86 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ILE F 88 " --> pdb=" O ARG F 112 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG F 112 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN F 90 " --> pdb=" O PHE F 110 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY F 106 " --> pdb=" O ASP F 94 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL F 96 " --> pdb=" O TYR F 104 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N TYR F 104 " --> pdb=" O VAL F 96 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU F 98 " --> pdb=" O LYS F 102 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LYS F 102 " --> pdb=" O LEU F 98 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N PHE F 103 " --> pdb=" O GLY F 131 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 53 through 56 Processing sheet with id=AB5, first strand: chain 'G' and resid 84 through 99 removed outlier: 5.356A pdb=" N HIS G 86 " --> pdb=" O GLN G 114 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLN G 114 " --> pdb=" O HIS G 86 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ILE G 88 " --> pdb=" O ARG G 112 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG G 112 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN G 90 " --> pdb=" O PHE G 110 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLY G 106 " --> pdb=" O ASP G 94 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL G 96 " --> pdb=" O TYR G 104 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TYR G 104 " --> pdb=" O VAL G 96 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU G 98 " --> pdb=" O LYS G 102 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LYS G 102 " --> pdb=" O LEU G 98 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N PHE G 103 " --> pdb=" O GLY G 131 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 53 through 56 Processing sheet with id=AB7, first strand: chain 'H' and resid 84 through 99 removed outlier: 5.341A pdb=" N HIS H 86 " --> pdb=" O GLN H 114 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLN H 114 " --> pdb=" O HIS H 86 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ILE H 88 " --> pdb=" O ARG H 112 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ARG H 112 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN H 90 " --> pdb=" O PHE H 110 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLY H 106 " --> pdb=" O ASP H 94 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL H 96 " --> pdb=" O TYR H 104 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TYR H 104 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU H 98 " --> pdb=" O LYS H 102 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LYS H 102 " --> pdb=" O LEU H 98 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N PHE H 103 " --> pdb=" O GLY H 131 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 53 through 56 Processing sheet with id=AB9, first strand: chain 'I' and resid 84 through 99 removed outlier: 5.351A pdb=" N HIS I 86 " --> pdb=" O GLN I 114 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N GLN I 114 " --> pdb=" O HIS I 86 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ILE I 88 " --> pdb=" O ARG I 112 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ARG I 112 " --> pdb=" O ILE I 88 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN I 90 " --> pdb=" O PHE I 110 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLY I 106 " --> pdb=" O ASP I 94 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL I 96 " --> pdb=" O TYR I 104 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR I 104 " --> pdb=" O VAL I 96 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU I 98 " --> pdb=" O LYS I 102 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LYS I 102 " --> pdb=" O LEU I 98 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N PHE I 103 " --> pdb=" O GLY I 131 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 53 through 56 Processing sheet with id=AC2, first strand: chain 'J' and resid 84 through 99 removed outlier: 5.353A pdb=" N HIS J 86 " --> pdb=" O GLN J 114 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLN J 114 " --> pdb=" O HIS J 86 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ILE J 88 " --> pdb=" O ARG J 112 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG J 112 " --> pdb=" O ILE J 88 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN J 90 " --> pdb=" O PHE J 110 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLY J 106 " --> pdb=" O ASP J 94 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL J 96 " --> pdb=" O TYR J 104 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TYR J 104 " --> pdb=" O VAL J 96 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU J 98 " --> pdb=" O LYS J 102 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LYS J 102 " --> pdb=" O LEU J 98 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N PHE J 103 " --> pdb=" O GLY J 131 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 53 through 56 Processing sheet with id=AC4, first strand: chain 'K' and resid 84 through 99 removed outlier: 5.369A pdb=" N HIS K 86 " --> pdb=" O GLN K 114 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLN K 114 " --> pdb=" O HIS K 86 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ILE K 88 " --> pdb=" O ARG K 112 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ARG K 112 " --> pdb=" O ILE K 88 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN K 90 " --> pdb=" O PHE K 110 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLY K 106 " --> pdb=" O ASP K 94 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL K 96 " --> pdb=" O TYR K 104 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TYR K 104 " --> pdb=" O VAL K 96 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU K 98 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LYS K 102 " --> pdb=" O LEU K 98 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N PHE K 103 " --> pdb=" O GLY K 131 " (cutoff:3.500A) 822 hydrogen bonds defined for protein. 2271 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: 3.18 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3186 1.32 - 1.45: 3905 1.45 - 1.57: 9220 1.57 - 1.69: 0 1.69 - 1.81: 110 Bond restraints: 16421 Sorted by residual: bond pdb=" C TYR K 171 " pdb=" O TYR K 171 " ideal model delta sigma weight residual 1.237 1.202 0.035 1.19e-02 7.06e+03 8.69e+00 bond pdb=" C TYR H 171 " pdb=" O TYR H 171 " ideal model delta sigma weight residual 1.237 1.206 0.031 1.19e-02 7.06e+03 6.65e+00 bond pdb=" C TYR H 171 " pdb=" N LEU H 172 " ideal model delta sigma weight residual 1.335 1.315 0.020 1.31e-02 5.83e+03 2.33e+00 bond pdb=" C ASP K 170 " pdb=" N TYR K 171 " ideal model delta sigma weight residual 1.335 1.315 0.019 1.36e-02 5.41e+03 2.01e+00 bond pdb=" C TYR K 171 " pdb=" N LEU K 172 " ideal model delta sigma weight residual 1.335 1.317 0.018 1.31e-02 5.83e+03 1.94e+00 ... (remaining 16416 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.96: 20520 0.96 - 1.93: 1279 1.93 - 2.89: 197 2.89 - 3.85: 68 3.85 - 4.82: 10 Bond angle restraints: 22074 Sorted by residual: angle pdb=" N TYR H 171 " pdb=" CA TYR H 171 " pdb=" C TYR H 171 " ideal model delta sigma weight residual 111.36 108.79 2.57 1.09e+00 8.42e-01 5.55e+00 angle pdb=" CA TYR H 36 " pdb=" CB TYR H 36 " pdb=" CG TYR H 36 " ideal model delta sigma weight residual 113.90 109.79 4.11 1.80e+00 3.09e-01 5.20e+00 angle pdb=" CA TYR F 36 " pdb=" CB TYR F 36 " pdb=" CG TYR F 36 " ideal model delta sigma weight residual 113.90 109.81 4.09 1.80e+00 3.09e-01 5.16e+00 angle pdb=" CA TYR J 36 " pdb=" CB TYR J 36 " pdb=" CG TYR J 36 " ideal model delta sigma weight residual 113.90 109.98 3.92 1.80e+00 3.09e-01 4.75e+00 angle pdb=" C ALA F 85 " pdb=" N HIS F 86 " pdb=" CA HIS F 86 " ideal model delta sigma weight residual 121.94 118.13 3.81 1.76e+00 3.23e-01 4.70e+00 ... (remaining 22069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 9189 17.59 - 35.17: 540 35.17 - 52.76: 120 52.76 - 70.35: 62 70.35 - 87.93: 21 Dihedral angle restraints: 9932 sinusoidal: 4057 harmonic: 5875 Sorted by residual: dihedral pdb=" CB ARG I 193 " pdb=" CG ARG I 193 " pdb=" CD ARG I 193 " pdb=" NE ARG I 193 " ideal model delta sinusoidal sigma weight residual 60.00 119.40 -59.40 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N LEU B 178 " pdb=" CA LEU B 178 " pdb=" CB LEU B 178 " pdb=" CG LEU B 178 " ideal model delta sinusoidal sigma weight residual -180.00 -122.09 -57.91 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CB GLU D 145 " pdb=" CG GLU D 145 " pdb=" CD GLU D 145 " pdb=" OE1 GLU D 145 " ideal model delta sinusoidal sigma weight residual 0.00 83.45 -83.45 1 3.00e+01 1.11e-03 9.45e+00 ... (remaining 9929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1272 0.028 - 0.057: 658 0.057 - 0.085: 274 0.085 - 0.113: 109 0.113 - 0.142: 34 Chirality restraints: 2347 Sorted by residual: chirality pdb=" CA VAL H 96 " pdb=" N VAL H 96 " pdb=" C VAL H 96 " pdb=" CB VAL H 96 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA VAL E 96 " pdb=" N VAL E 96 " pdb=" C VAL E 96 " pdb=" CB VAL E 96 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA VAL D 96 " pdb=" N VAL D 96 " pdb=" C VAL D 96 " pdb=" CB VAL D 96 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.94e-01 ... (remaining 2344 not shown) Planarity restraints: 2910 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 36 " 0.024 2.00e-02 2.50e+03 1.27e-02 3.23e+00 pdb=" CG TYR F 36 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR F 36 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR F 36 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR F 36 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR F 36 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR F 36 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR F 36 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 36 " -0.023 2.00e-02 2.50e+03 1.22e-02 3.00e+00 pdb=" CG TYR H 36 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR H 36 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR H 36 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR H 36 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR H 36 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR H 36 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR H 36 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 36 " 0.023 2.00e-02 2.50e+03 1.22e-02 2.97e+00 pdb=" CG TYR C 36 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR C 36 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR C 36 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR C 36 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 36 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 36 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR C 36 " 0.006 2.00e-02 2.50e+03 ... (remaining 2907 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1412 2.74 - 3.28: 15913 3.28 - 3.82: 31105 3.82 - 4.36: 37928 4.36 - 4.90: 60876 Nonbonded interactions: 147234 Sorted by model distance: nonbonded pdb=" O LEU E 47 " pdb=" OH TYR E 171 " model vdw 2.200 3.040 nonbonded pdb=" OD2 ASP B 123 " pdb=" O HOH B 501 " model vdw 2.211 3.040 nonbonded pdb=" O LEU B 47 " pdb=" OH TYR B 171 " model vdw 2.213 3.040 nonbonded pdb=" OD2 ASP E 123 " pdb=" O HOH E 501 " model vdw 2.214 3.040 nonbonded pdb=" OE1 GLU B 35 " pdb=" O HOH B 502 " model vdw 2.218 3.040 ... (remaining 147229 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 23 through 37 or (resid 38 and (name N or name CA or name \ C or name CB )) or resid 39 through 51 or (resid 52 and (name N or name CA or na \ me C or name CB or name CG1 or name CG2 or name CD1)) or resid 53 through 208)) selection = (chain 'B' and (resid 23 through 37 or (resid 38 and (name N or name CA or name \ C or name CB )) or resid 39 through 51 or (resid 52 and (name N or name CA or na \ me C or name CB or name CG1 or name CG2 or name CD1)) or resid 53 through 208)) selection = (chain 'C' and (resid 23 through 37 or (resid 38 and (name N or name CA or name \ C or name CB )) or resid 39 through 51 or (resid 52 and (name N or name CA or na \ me C or name CB or name CG1 or name CG2 or name CD1)) or resid 53 through 208)) selection = (chain 'D' and (resid 23 through 37 or (resid 38 and (name N or name CA or name \ C or name CB )) or resid 39 through 208)) selection = (chain 'E' and (resid 23 through 37 or (resid 38 and (name N or name CA or name \ C or name CB )) or resid 39 through 51 or (resid 52 and (name N or name CA or na \ me C or name CB or name CG1 or name CG2 or name CD1)) or resid 53 through 208)) selection = (chain 'F' and (resid 23 through 37 or (resid 38 and (name N or name CA or name \ C or name CB )) or resid 39 through 51 or (resid 52 and (name N or name CA or na \ me C or name CB or name CG1 or name CG2 or name CD1)) or resid 53 through 208)) selection = (chain 'G' and (resid 23 through 37 or (resid 38 and (name N or name CA or name \ C or name CB )) or resid 39 through 51 or (resid 52 and (name N or name CA or na \ me C or name CB or name CG1 or name CG2 or name CD1)) or resid 53 through 208)) selection = (chain 'H' and (resid 23 through 37 or (resid 38 and (name N or name CA or name \ C or name CB )) or resid 39 through 51 or (resid 52 and (name N or name CA or na \ me C or name CB or name CG1 or name CG2 or name CD1)) or resid 53 through 208)) selection = (chain 'I' and (resid 23 through 51 or (resid 52 and (name N or name CA or name \ C or name CB or name CG1 or name CG2 or name CD1)) or resid 53 through 208)) selection = (chain 'J' and (resid 23 through 37 or (resid 38 and (name N or name CA or name \ C or name CB )) or resid 39 through 51 or (resid 52 and (name N or name CA or na \ me C or name CB or name CG1 or name CG2 or name CD1)) or resid 53 through 208)) selection = (chain 'K' and (resid 23 through 37 or (resid 38 and (name N or name CA or name \ C or name CB )) or resid 39 through 51 or (resid 52 and (name N or name CA or na \ me C or name CB or name CG1 or name CG2 or name CD1)) or resid 53 through 208)) } 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: 0.870 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.400 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 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 : 0.005 0.035 16421 Z= 0.223 Angle : 0.548 4.817 22074 Z= 0.311 Chirality : 0.043 0.142 2347 Planarity : 0.004 0.043 2910 Dihedral : 13.854 87.934 6206 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 1.17 % Allowed : 4.86 % Favored : 93.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.18), residues: 2028 helix: 1.92 (0.18), residues: 777 sheet: 1.90 (0.23), residues: 424 loop : 0.69 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 112 TYR 0.024 0.003 TYR F 36 PHE 0.012 0.002 PHE K 110 TRP 0.004 0.002 TRP D 84 HIS 0.006 0.002 HIS F 86 Details of bonding type rmsd covalent geometry : bond 0.00477 (16421) covalent geometry : angle 0.54812 (22074) hydrogen bonds : bond 0.14650 ( 822) hydrogen bonds : angle 6.49052 ( 2271) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 287 time to evaluate : 0.671 Fit side-chains REVERT: B 41 LYS cc_start: 0.9005 (mttp) cc_final: 0.8469 (mppt) REVERT: C 133 LYS cc_start: 0.8670 (mptm) cc_final: 0.8097 (mppt) REVERT: C 194 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.6837 (pp30) REVERT: C 196 LEU cc_start: 0.8214 (mt) cc_final: 0.7725 (mm) REVERT: C 206 ASN cc_start: 0.8725 (m-40) cc_final: 0.8493 (m-40) REVERT: E 192 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7424 (tttm) REVERT: H 196 LEU cc_start: 0.8190 (mt) cc_final: 0.7828 (mm) REVERT: I 192 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7620 (tttm) REVERT: J 196 LEU cc_start: 0.8619 (mt) cc_final: 0.8417 (mm) outliers start: 20 outliers final: 2 residues processed: 299 average time/residue: 0.7698 time to fit residues: 251.0055 Evaluate side-chains 259 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 254 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain I residue 192 LYS Chi-restraints excluded: chain K residue 175 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 45 GLN A 69 HIS A 90 GLN A 114 GLN A 164 ASN B 30 GLN B 40 GLN B 90 GLN B 114 GLN B 176 ASN C 28 GLN C 40 GLN C 114 GLN C 176 ASN D 90 GLN D 114 GLN D 194 GLN E 30 GLN E 40 GLN E 90 GLN E 114 GLN E 176 ASN F 40 GLN F 45 GLN F 90 GLN F 114 GLN G 28 GLN G 40 GLN G 90 GLN G 100 ASN G 114 GLN G 194 GLN H 40 GLN H 90 GLN H 99 ASN H 114 GLN I 30 GLN I 40 GLN I 90 GLN I 114 GLN J 28 GLN J 30 GLN J 40 GLN J 90 GLN J 114 GLN K 28 GLN K 40 GLN K 45 GLN K 114 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.147760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.112374 restraints weight = 17053.893| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.43 r_work: 0.3075 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16421 Z= 0.194 Angle : 0.536 4.579 22074 Z= 0.295 Chirality : 0.042 0.131 2347 Planarity : 0.004 0.034 2910 Dihedral : 5.143 68.048 2299 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 1.81 % Allowed : 8.19 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.18), residues: 2028 helix: 2.15 (0.18), residues: 783 sheet: 1.84 (0.23), residues: 424 loop : 0.65 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 112 TYR 0.025 0.003 TYR F 36 PHE 0.012 0.002 PHE F 110 TRP 0.003 0.001 TRP A 84 HIS 0.005 0.002 HIS D 86 Details of bonding type rmsd covalent geometry : bond 0.00423 (16421) covalent geometry : angle 0.53550 (22074) hydrogen bonds : bond 0.04969 ( 822) hydrogen bonds : angle 5.12083 ( 2271) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 273 time to evaluate : 0.657 Fit side-chains REVERT: A 130 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7908 (mt-10) REVERT: B 41 LYS cc_start: 0.9151 (mttp) cc_final: 0.8659 (mppt) REVERT: C 175 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8614 (mm) REVERT: C 196 LEU cc_start: 0.8270 (mt) cc_final: 0.7971 (mm) REVERT: C 206 ASN cc_start: 0.8681 (m-40) cc_final: 0.8439 (m-40) REVERT: D 56 MET cc_start: 0.8221 (tpp) cc_final: 0.7965 (tpp) REVERT: F 174 SER cc_start: 0.8034 (m) cc_final: 0.7796 (t) REVERT: G 56 MET cc_start: 0.7900 (tpp) cc_final: 0.7468 (mmm) REVERT: H 56 MET cc_start: 0.7769 (tpp) cc_final: 0.7284 (tpp) REVERT: H 196 LEU cc_start: 0.8294 (mt) cc_final: 0.7951 (mm) REVERT: I 56 MET cc_start: 0.8040 (mmm) cc_final: 0.7750 (tpp) REVERT: I 192 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7723 (tttm) outliers start: 31 outliers final: 8 residues processed: 285 average time/residue: 0.7360 time to fit residues: 229.9934 Evaluate side-chains 276 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 265 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain I residue 192 LYS Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 194 GLN Chi-restraints excluded: chain K residue 208 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 46 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 157 optimal weight: 9.9990 chunk 172 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 119 optimal weight: 9.9990 chunk 173 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 175 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 194 optimal weight: 7.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN B 30 GLN B 90 GLN B 176 ASN C 176 ASN D 90 GLN E 90 GLN E 176 ASN F 28 GLN F 90 GLN F 176 ASN G 90 GLN G 100 ASN G 194 GLN H 28 GLN H 90 GLN H 206 ASN I 30 GLN I 90 GLN J 30 GLN J 90 GLN K 176 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.148378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.112714 restraints weight = 17140.106| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.40 r_work: 0.3084 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16421 Z= 0.174 Angle : 0.509 5.657 22074 Z= 0.280 Chirality : 0.041 0.126 2347 Planarity : 0.003 0.031 2910 Dihedral : 4.546 57.925 2291 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 2.22 % Allowed : 9.30 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.18), residues: 2028 helix: 2.30 (0.18), residues: 783 sheet: 1.84 (0.23), residues: 424 loop : 0.68 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 44 TYR 0.024 0.002 TYR F 36 PHE 0.011 0.002 PHE F 110 TRP 0.003 0.001 TRP A 84 HIS 0.005 0.001 HIS D 86 Details of bonding type rmsd covalent geometry : bond 0.00377 (16421) covalent geometry : angle 0.50944 (22074) hydrogen bonds : bond 0.04569 ( 822) hydrogen bonds : angle 4.90413 ( 2271) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 274 time to evaluate : 0.749 Fit side-chains REVERT: A 130 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7907 (mt-10) REVERT: B 41 LYS cc_start: 0.9152 (mttp) cc_final: 0.8663 (mppt) REVERT: C 194 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7029 (pp30) REVERT: C 196 LEU cc_start: 0.8281 (mt) cc_final: 0.7775 (mm) REVERT: C 206 ASN cc_start: 0.8648 (m-40) cc_final: 0.8401 (m-40) REVERT: D 56 MET cc_start: 0.8289 (tpp) cc_final: 0.8034 (tpp) REVERT: F 56 MET cc_start: 0.7702 (tpp) cc_final: 0.7414 (mmm) REVERT: G 56 MET cc_start: 0.7922 (tpp) cc_final: 0.7462 (mmm) REVERT: H 56 MET cc_start: 0.7705 (tpp) cc_final: 0.7184 (tpp) REVERT: H 175 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8759 (mm) REVERT: H 196 LEU cc_start: 0.8278 (mt) cc_final: 0.7945 (mm) REVERT: J 56 MET cc_start: 0.7695 (tpp) cc_final: 0.7379 (tpp) REVERT: K 56 MET cc_start: 0.7382 (tpp) cc_final: 0.7023 (tpp) outliers start: 38 outliers final: 6 residues processed: 289 average time/residue: 0.7711 time to fit residues: 243.5174 Evaluate side-chains 272 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 263 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain H residue 102 LYS Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain K residue 208 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 162 optimal weight: 10.0000 chunk 69 optimal weight: 0.0670 chunk 155 optimal weight: 0.8980 chunk 126 optimal weight: 20.0000 chunk 161 optimal weight: 5.9990 chunk 177 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 194 optimal weight: 10.0000 chunk 142 optimal weight: 40.0000 chunk 89 optimal weight: 8.9990 overall best weight: 4.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 90 GLN B 30 GLN B 90 GLN B 176 ASN C 176 ASN D 90 GLN E 90 GLN E 176 ASN F 28 GLN F 176 ASN G 90 GLN G 100 ASN G 194 GLN H 90 GLN H 99 ASN H 176 ASN I 30 GLN I 90 GLN J 30 GLN K 90 GLN K 176 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.148318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.112788 restraints weight = 16995.856| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.38 r_work: 0.3085 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16421 Z= 0.179 Angle : 0.511 7.726 22074 Z= 0.281 Chirality : 0.041 0.125 2347 Planarity : 0.003 0.031 2910 Dihedral : 4.266 30.725 2287 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 2.40 % Allowed : 9.89 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.18), residues: 2028 helix: 2.36 (0.18), residues: 783 sheet: 1.86 (0.23), residues: 424 loop : 0.69 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 44 TYR 0.024 0.002 TYR F 36 PHE 0.011 0.002 PHE F 110 TRP 0.003 0.001 TRP A 84 HIS 0.005 0.001 HIS D 86 Details of bonding type rmsd covalent geometry : bond 0.00390 (16421) covalent geometry : angle 0.51142 (22074) hydrogen bonds : bond 0.04557 ( 822) hydrogen bonds : angle 4.83616 ( 2271) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 273 time to evaluate : 0.677 Fit side-chains REVERT: A 130 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7929 (mt-10) REVERT: B 41 LYS cc_start: 0.9149 (mttp) cc_final: 0.8676 (mppt) REVERT: B 194 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.6862 (pp30) REVERT: C 194 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7071 (pp30) REVERT: C 196 LEU cc_start: 0.8288 (mt) cc_final: 0.7779 (mm) REVERT: C 206 ASN cc_start: 0.8657 (m-40) cc_final: 0.8390 (m-40) REVERT: D 56 MET cc_start: 0.8316 (tpp) cc_final: 0.8055 (tpp) REVERT: F 56 MET cc_start: 0.7657 (tpp) cc_final: 0.7307 (mmm) REVERT: F 192 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.5974 (tptt) REVERT: H 56 MET cc_start: 0.7643 (tpp) cc_final: 0.7159 (tpp) REVERT: H 175 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8737 (mm) REVERT: H 196 LEU cc_start: 0.8296 (mt) cc_final: 0.7945 (mm) REVERT: I 56 MET cc_start: 0.7774 (tpp) cc_final: 0.7461 (tpp) REVERT: I 194 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.6645 (pp30) REVERT: J 56 MET cc_start: 0.7716 (tpp) cc_final: 0.7463 (tpp) REVERT: K 56 MET cc_start: 0.7458 (tpp) cc_final: 0.6874 (tpp) outliers start: 41 outliers final: 10 residues processed: 291 average time/residue: 0.7686 time to fit residues: 244.6558 Evaluate side-chains 284 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 268 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain H residue 102 LYS Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain I residue 194 GLN Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain J residue 182 LEU Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain K residue 208 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 93 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 142 optimal weight: 40.0000 chunk 98 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 16 optimal weight: 30.0000 chunk 137 optimal weight: 2.9990 chunk 191 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 90 GLN B 30 GLN B 90 GLN B 176 ASN C 176 ASN D 28 GLN D 90 GLN E 90 GLN E 176 ASN F 176 ASN G 90 GLN G 100 ASN G 194 GLN H 90 GLN H 176 ASN I 30 GLN I 90 GLN J 30 GLN K 176 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.148598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.113593 restraints weight = 17025.877| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.36 r_work: 0.3090 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 16421 Z= 0.167 Angle : 0.503 8.325 22074 Z= 0.275 Chirality : 0.040 0.124 2347 Planarity : 0.003 0.029 2910 Dihedral : 4.216 30.383 2287 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 2.22 % Allowed : 10.71 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.18), residues: 2028 helix: 2.39 (0.18), residues: 786 sheet: 1.89 (0.23), residues: 421 loop : 0.66 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 44 TYR 0.023 0.002 TYR F 36 PHE 0.011 0.002 PHE F 110 TRP 0.003 0.001 TRP A 84 HIS 0.005 0.001 HIS D 86 Details of bonding type rmsd covalent geometry : bond 0.00363 (16421) covalent geometry : angle 0.50331 (22074) hydrogen bonds : bond 0.04396 ( 822) hydrogen bonds : angle 4.76290 ( 2271) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 273 time to evaluate : 0.741 Fit side-chains REVERT: A 130 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7916 (mt-10) REVERT: A 196 LEU cc_start: 0.8257 (mm) cc_final: 0.7985 (mt) REVERT: B 41 LYS cc_start: 0.9160 (mttp) cc_final: 0.8678 (mppt) REVERT: B 194 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.6820 (pp30) REVERT: C 194 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7044 (pp30) REVERT: C 196 LEU cc_start: 0.8272 (mt) cc_final: 0.7744 (mm) REVERT: C 206 ASN cc_start: 0.8635 (m-40) cc_final: 0.8353 (m-40) REVERT: D 56 MET cc_start: 0.8354 (tpp) cc_final: 0.8088 (tpp) REVERT: F 56 MET cc_start: 0.7622 (tpp) cc_final: 0.7278 (mmm) REVERT: F 192 LYS cc_start: 0.7680 (OUTLIER) cc_final: 0.5925 (tptt) REVERT: H 56 MET cc_start: 0.7678 (tpp) cc_final: 0.7155 (tpp) REVERT: H 196 LEU cc_start: 0.8275 (mt) cc_final: 0.7926 (mm) REVERT: I 192 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7669 (tttm) REVERT: I 194 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.6405 (pp30) REVERT: J 56 MET cc_start: 0.7629 (tpp) cc_final: 0.7362 (tpp) REVERT: K 56 MET cc_start: 0.7405 (tpp) cc_final: 0.6925 (tpp) outliers start: 38 outliers final: 12 residues processed: 287 average time/residue: 0.7486 time to fit residues: 235.2485 Evaluate side-chains 286 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 268 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain H residue 102 LYS Chi-restraints excluded: chain I residue 192 LYS Chi-restraints excluded: chain I residue 194 GLN Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain J residue 182 LEU Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain K residue 208 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 107 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 188 optimal weight: 5.9990 chunk 111 optimal weight: 40.0000 chunk 46 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 56 optimal weight: 0.3980 chunk 190 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 90 GLN B 28 GLN B 30 GLN B 90 GLN B 176 ASN C 176 ASN D 28 GLN D 90 GLN E 90 GLN E 176 ASN F 45 GLN F 176 ASN G 100 ASN G 194 GLN H 90 GLN H 99 ASN H 176 ASN I 30 GLN I 90 GLN J 30 GLN K 90 GLN K 176 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.149228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.114269 restraints weight = 17015.667| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.33 r_work: 0.3105 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16421 Z= 0.148 Angle : 0.495 9.285 22074 Z= 0.268 Chirality : 0.040 0.124 2347 Planarity : 0.003 0.025 2910 Dihedral : 4.130 30.053 2287 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 2.05 % Allowed : 11.29 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.18), residues: 2028 helix: 2.48 (0.18), residues: 786 sheet: 1.92 (0.23), residues: 421 loop : 0.69 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 44 TYR 0.022 0.002 TYR F 36 PHE 0.010 0.002 PHE F 110 TRP 0.002 0.001 TRP D 84 HIS 0.004 0.001 HIS D 86 Details of bonding type rmsd covalent geometry : bond 0.00320 (16421) covalent geometry : angle 0.49478 (22074) hydrogen bonds : bond 0.04142 ( 822) hydrogen bonds : angle 4.65886 ( 2271) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 285 time to evaluate : 0.808 Fit side-chains REVERT: A 130 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7894 (mt-10) REVERT: A 196 LEU cc_start: 0.8251 (mm) cc_final: 0.7978 (mt) REVERT: B 41 LYS cc_start: 0.9156 (mttp) cc_final: 0.8680 (mppt) REVERT: B 194 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.7017 (pp30) REVERT: C 194 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7038 (pp30) REVERT: C 196 LEU cc_start: 0.8222 (mt) cc_final: 0.7683 (mm) REVERT: C 206 ASN cc_start: 0.8626 (m-40) cc_final: 0.8334 (m-40) REVERT: D 56 MET cc_start: 0.8311 (tpp) cc_final: 0.8034 (tpp) REVERT: E 56 MET cc_start: 0.7399 (mmm) cc_final: 0.7142 (mmm) REVERT: F 56 MET cc_start: 0.7592 (tpp) cc_final: 0.7236 (mmm) REVERT: F 192 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.5939 (tptt) REVERT: G 56 MET cc_start: 0.7594 (mmm) cc_final: 0.6972 (tpp) REVERT: H 56 MET cc_start: 0.7707 (tpp) cc_final: 0.7156 (tpp) REVERT: H 175 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8779 (mm) REVERT: H 196 LEU cc_start: 0.8275 (mt) cc_final: 0.7936 (mm) REVERT: I 56 MET cc_start: 0.7640 (tpp) cc_final: 0.7124 (tpp) REVERT: I 192 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7682 (tttm) REVERT: I 194 GLN cc_start: 0.7434 (OUTLIER) cc_final: 0.6445 (pp30) REVERT: J 56 MET cc_start: 0.7654 (tpp) cc_final: 0.7338 (tpp) REVERT: J 192 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.7180 (tttt) REVERT: K 56 MET cc_start: 0.7381 (tpp) cc_final: 0.6887 (tpp) outliers start: 35 outliers final: 10 residues processed: 298 average time/residue: 0.7604 time to fit residues: 248.2472 Evaluate side-chains 293 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 275 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain H residue 102 LYS Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain I residue 192 LYS Chi-restraints excluded: chain I residue 194 GLN Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain J residue 182 LEU Chi-restraints excluded: chain J residue 192 LYS Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 208 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 27 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 124 optimal weight: 40.0000 chunk 34 optimal weight: 30.0000 chunk 146 optimal weight: 0.0670 chunk 149 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 170 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 overall best weight: 4.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 90 GLN B 28 GLN B 30 GLN B 90 GLN B 176 ASN C 176 ASN D 28 GLN D 90 GLN E 45 GLN E 90 GLN E 176 ASN F 176 ASN G 90 GLN G 100 ASN G 194 GLN H 28 GLN H 90 GLN H 176 ASN I 30 GLN I 90 GLN J 30 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.148318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.112803 restraints weight = 17023.326| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.36 r_work: 0.3085 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16421 Z= 0.181 Angle : 0.527 10.889 22074 Z= 0.286 Chirality : 0.041 0.125 2347 Planarity : 0.003 0.030 2910 Dihedral : 4.236 30.303 2287 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 2.28 % Allowed : 11.41 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.18), residues: 2028 helix: 2.41 (0.18), residues: 786 sheet: 1.88 (0.23), residues: 424 loop : 0.65 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 156 TYR 0.024 0.003 TYR F 36 PHE 0.011 0.002 PHE I 110 TRP 0.003 0.001 TRP A 84 HIS 0.005 0.001 HIS D 86 Details of bonding type rmsd covalent geometry : bond 0.00397 (16421) covalent geometry : angle 0.52663 (22074) hydrogen bonds : bond 0.04553 ( 822) hydrogen bonds : angle 4.75285 ( 2271) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 276 time to evaluate : 0.669 Fit side-chains REVERT: A 130 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7944 (mt-10) REVERT: A 196 LEU cc_start: 0.8292 (mm) cc_final: 0.8022 (mt) REVERT: B 194 GLN cc_start: 0.7466 (OUTLIER) cc_final: 0.6986 (pp30) REVERT: B 201 GLU cc_start: 0.8167 (tp30) cc_final: 0.7495 (mm-30) REVERT: C 194 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7050 (pp30) REVERT: C 196 LEU cc_start: 0.8267 (mt) cc_final: 0.7742 (mm) REVERT: C 206 ASN cc_start: 0.8636 (m-40) cc_final: 0.8350 (m-40) REVERT: D 56 MET cc_start: 0.8367 (tpp) cc_final: 0.8097 (tpp) REVERT: E 192 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7451 (tttm) REVERT: F 56 MET cc_start: 0.7641 (tpp) cc_final: 0.6735 (tpp) REVERT: F 192 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.5913 (tptt) REVERT: G 56 MET cc_start: 0.7562 (mmm) cc_final: 0.7056 (tpp) REVERT: H 56 MET cc_start: 0.7748 (tpp) cc_final: 0.7173 (tpp) REVERT: H 175 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8787 (mm) REVERT: H 196 LEU cc_start: 0.8280 (mt) cc_final: 0.7917 (mm) REVERT: I 192 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7670 (tttm) REVERT: I 194 GLN cc_start: 0.7412 (OUTLIER) cc_final: 0.6387 (pp30) REVERT: J 56 MET cc_start: 0.7719 (tpp) cc_final: 0.7368 (tpp) REVERT: J 192 LYS cc_start: 0.7427 (OUTLIER) cc_final: 0.7149 (tttt) REVERT: K 56 MET cc_start: 0.7441 (tpp) cc_final: 0.6880 (tpp) outliers start: 39 outliers final: 12 residues processed: 295 average time/residue: 0.7701 time to fit residues: 248.5938 Evaluate side-chains 294 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 273 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain I residue 192 LYS Chi-restraints excluded: chain I residue 194 GLN Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain J residue 182 LEU Chi-restraints excluded: chain J residue 192 LYS Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain K residue 208 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 105 optimal weight: 40.0000 chunk 92 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 140 optimal weight: 8.9990 chunk 171 optimal weight: 7.9990 chunk 189 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 90 GLN B 30 GLN B 90 GLN B 176 ASN C 176 ASN D 28 GLN D 90 GLN E 90 GLN E 176 ASN F 45 GLN F 176 ASN G 100 ASN G 194 GLN H 28 GLN H 90 GLN H 99 ASN H 176 ASN I 30 GLN I 90 GLN J 30 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.148266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.112961 restraints weight = 17085.585| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.41 r_work: 0.3087 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16421 Z= 0.175 Angle : 0.533 11.483 22074 Z= 0.287 Chirality : 0.041 0.125 2347 Planarity : 0.003 0.029 2910 Dihedral : 4.212 30.060 2287 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 2.05 % Allowed : 11.59 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.18), residues: 2028 helix: 2.43 (0.18), residues: 786 sheet: 1.89 (0.23), residues: 424 loop : 0.66 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 156 TYR 0.024 0.002 TYR F 36 PHE 0.011 0.002 PHE F 110 TRP 0.003 0.001 TRP A 84 HIS 0.005 0.001 HIS D 86 Details of bonding type rmsd covalent geometry : bond 0.00383 (16421) covalent geometry : angle 0.53289 (22074) hydrogen bonds : bond 0.04457 ( 822) hydrogen bonds : angle 4.71853 ( 2271) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 277 time to evaluate : 0.697 Fit side-chains REVERT: A 130 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7934 (mt-10) REVERT: A 196 LEU cc_start: 0.8249 (mm) cc_final: 0.7970 (mt) REVERT: B 194 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.6998 (pp30) REVERT: B 201 GLU cc_start: 0.8181 (tp30) cc_final: 0.7507 (mm-30) REVERT: C 194 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7046 (pp30) REVERT: C 196 LEU cc_start: 0.8268 (mt) cc_final: 0.7745 (mm) REVERT: C 206 ASN cc_start: 0.8649 (m-40) cc_final: 0.8362 (m-40) REVERT: D 56 MET cc_start: 0.8370 (tpp) cc_final: 0.8094 (tpp) REVERT: D 192 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8164 (tttm) REVERT: E 192 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7451 (tttm) REVERT: F 56 MET cc_start: 0.7637 (tpp) cc_final: 0.7213 (mmm) REVERT: F 192 LYS cc_start: 0.7638 (OUTLIER) cc_final: 0.5859 (tptt) REVERT: G 56 MET cc_start: 0.7563 (mmm) cc_final: 0.7089 (tpp) REVERT: H 56 MET cc_start: 0.7747 (tpp) cc_final: 0.7207 (tpp) REVERT: H 175 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8784 (mm) REVERT: H 196 LEU cc_start: 0.8256 (mt) cc_final: 0.7897 (mm) REVERT: I 56 MET cc_start: 0.7596 (tpp) cc_final: 0.6951 (tpp) REVERT: I 192 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7676 (tttm) REVERT: I 194 GLN cc_start: 0.7408 (OUTLIER) cc_final: 0.6385 (pp30) REVERT: J 56 MET cc_start: 0.7729 (tpp) cc_final: 0.7374 (tpp) REVERT: J 192 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.7153 (tttt) REVERT: K 56 MET cc_start: 0.7438 (tpp) cc_final: 0.6870 (tpp) outliers start: 35 outliers final: 12 residues processed: 294 average time/residue: 0.7623 time to fit residues: 245.3043 Evaluate side-chains 291 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 269 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 192 LYS Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain I residue 192 LYS Chi-restraints excluded: chain I residue 194 GLN Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain J residue 182 LEU Chi-restraints excluded: chain J residue 192 LYS Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 208 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 152 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 126 optimal weight: 20.0000 chunk 101 optimal weight: 0.0970 chunk 117 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 156 optimal weight: 0.9990 chunk 180 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 185 optimal weight: 7.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN B 28 GLN B 30 GLN B 90 GLN B 176 ASN C 37 GLN C 45 GLN C 176 ASN D 28 GLN D 90 GLN E 45 GLN E 90 GLN E 176 ASN F 176 ASN G 100 ASN G 194 GLN H 28 GLN H 90 GLN H 176 ASN I 30 GLN I 90 GLN J 30 GLN K 28 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.151877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.117328 restraints weight = 17241.072| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.35 r_work: 0.3159 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16421 Z= 0.092 Angle : 0.473 11.964 22074 Z= 0.247 Chirality : 0.038 0.124 2347 Planarity : 0.002 0.022 2910 Dihedral : 3.823 29.318 2287 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 1.46 % Allowed : 12.52 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.64 (0.19), residues: 2028 helix: 2.66 (0.18), residues: 793 sheet: 2.05 (0.23), residues: 421 loop : 0.74 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 55 TYR 0.015 0.001 TYR F 36 PHE 0.007 0.001 PHE I 110 TRP 0.001 0.000 TRP C 84 HIS 0.003 0.001 HIS D 69 Details of bonding type rmsd covalent geometry : bond 0.00202 (16421) covalent geometry : angle 0.47270 (22074) hydrogen bonds : bond 0.03038 ( 822) hydrogen bonds : angle 4.29103 ( 2271) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 300 time to evaluate : 0.652 Fit side-chains REVERT: A 196 LEU cc_start: 0.8266 (mm) cc_final: 0.8000 (mt) REVERT: B 194 GLN cc_start: 0.7322 (OUTLIER) cc_final: 0.6945 (pp30) REVERT: B 201 GLU cc_start: 0.8207 (tp30) cc_final: 0.7496 (mm-30) REVERT: C 196 LEU cc_start: 0.8130 (mt) cc_final: 0.7810 (mm) REVERT: D 56 MET cc_start: 0.8209 (tpp) cc_final: 0.7947 (tpp) REVERT: D 133 LYS cc_start: 0.7898 (mppt) cc_final: 0.7503 (mptm) REVERT: F 56 MET cc_start: 0.7588 (tpp) cc_final: 0.7214 (mmm) REVERT: F 192 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.5989 (tptt) REVERT: G 56 MET cc_start: 0.7446 (mmm) cc_final: 0.6904 (tpp) REVERT: H 169 LYS cc_start: 0.8938 (mttm) cc_final: 0.8731 (mttp) REVERT: H 175 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8809 (mm) REVERT: H 196 LEU cc_start: 0.8276 (mt) cc_final: 0.8002 (mm) REVERT: I 56 MET cc_start: 0.7502 (tpp) cc_final: 0.6880 (tpp) REVERT: J 56 MET cc_start: 0.7555 (tpp) cc_final: 0.7225 (tpp) REVERT: K 56 MET cc_start: 0.7388 (tpp) cc_final: 0.6873 (tpp) REVERT: K 133 LYS cc_start: 0.8142 (mppt) cc_final: 0.7850 (mmtp) outliers start: 25 outliers final: 5 residues processed: 310 average time/residue: 0.7312 time to fit residues: 247.5958 Evaluate side-chains 296 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 288 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain J residue 182 LEU Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 208 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 10 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 173 optimal weight: 0.0980 chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 121 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 194 optimal weight: 0.4980 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 90 GLN B 30 GLN B 176 ASN C 28 GLN C 37 GLN C 90 GLN C 176 ASN D 90 GLN D 176 ASN E 90 GLN E 176 ASN F 45 GLN F 90 GLN F 176 ASN G 28 GLN G 176 ASN H 90 GLN H 99 ASN H 176 ASN I 30 GLN I 37 GLN I 90 GLN J 28 GLN J 30 GLN J 176 ASN K 176 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.149386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.114892 restraints weight = 16978.058| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.37 r_work: 0.3110 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16421 Z= 0.145 Angle : 0.524 12.597 22074 Z= 0.277 Chirality : 0.039 0.124 2347 Planarity : 0.003 0.024 2910 Dihedral : 4.022 29.788 2287 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 1.23 % Allowed : 13.52 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.61 (0.18), residues: 2028 helix: 2.61 (0.18), residues: 787 sheet: 2.03 (0.23), residues: 421 loop : 0.77 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 46 TYR 0.021 0.002 TYR F 36 PHE 0.009 0.002 PHE K 110 TRP 0.002 0.001 TRP A 84 HIS 0.004 0.001 HIS D 86 Details of bonding type rmsd covalent geometry : bond 0.00320 (16421) covalent geometry : angle 0.52364 (22074) hydrogen bonds : bond 0.04009 ( 822) hydrogen bonds : angle 4.52414 ( 2271) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 279 time to evaluate : 0.725 Fit side-chains REVERT: A 196 LEU cc_start: 0.8219 (mm) cc_final: 0.7944 (mt) REVERT: B 194 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.6983 (pp30) REVERT: C 196 LEU cc_start: 0.8158 (mt) cc_final: 0.7813 (mm) REVERT: D 56 MET cc_start: 0.8215 (tpp) cc_final: 0.7944 (tpp) REVERT: F 56 MET cc_start: 0.7531 (tpp) cc_final: 0.7123 (mmm) REVERT: F 192 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.5858 (tptt) REVERT: G 56 MET cc_start: 0.7527 (mmm) cc_final: 0.6988 (tpp) REVERT: H 169 LYS cc_start: 0.8957 (mttm) cc_final: 0.8734 (mttp) REVERT: H 175 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8782 (mm) REVERT: H 196 LEU cc_start: 0.8260 (mt) cc_final: 0.7918 (mm) REVERT: I 56 MET cc_start: 0.7592 (tpp) cc_final: 0.6965 (tpp) REVERT: J 56 MET cc_start: 0.7673 (tpp) cc_final: 0.7314 (tpp) REVERT: K 56 MET cc_start: 0.7424 (tpp) cc_final: 0.6859 (tpp) outliers start: 21 outliers final: 7 residues processed: 285 average time/residue: 0.7709 time to fit residues: 240.2373 Evaluate side-chains 280 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 270 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain H residue 102 LYS Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain J residue 182 LEU Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 208 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 47 optimal weight: 6.9990 chunk 68 optimal weight: 0.6980 chunk 75 optimal weight: 9.9990 chunk 196 optimal weight: 20.0000 chunk 197 optimal weight: 0.1980 chunk 27 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 183 optimal weight: 20.0000 chunk 134 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 90 GLN B 28 GLN B 30 GLN B 176 ASN C 28 GLN C 90 GLN C 91 GLN C 176 ASN D 90 GLN E 45 GLN E 90 GLN E 176 ASN F 45 GLN F 90 GLN F 176 ASN G 100 ASN H 90 GLN H 99 ASN H 176 ASN I 30 GLN I 90 GLN J 30 GLN J 176 ASN K 176 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.150342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.115523 restraints weight = 17036.473| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.40 r_work: 0.3123 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16421 Z= 0.125 Angle : 0.517 12.599 22074 Z= 0.270 Chirality : 0.039 0.123 2347 Planarity : 0.003 0.023 2910 Dihedral : 3.957 29.570 2287 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 1.11 % Allowed : 13.63 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.18), residues: 2028 helix: 2.62 (0.18), residues: 787 sheet: 2.03 (0.23), residues: 421 loop : 0.79 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 46 TYR 0.019 0.002 TYR F 36 PHE 0.009 0.001 PHE F 110 TRP 0.002 0.001 TRP K 84 HIS 0.003 0.001 HIS D 86 Details of bonding type rmsd covalent geometry : bond 0.00275 (16421) covalent geometry : angle 0.51722 (22074) hydrogen bonds : bond 0.03732 ( 822) hydrogen bonds : angle 4.44473 ( 2271) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8402.53 seconds wall clock time: 143 minutes 16.63 seconds (8596.63 seconds total)