Starting phenix.real_space_refine on Tue Nov 18 19:17:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dkf_7952/11_2025/6dkf_7952.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dkf_7952/11_2025/6dkf_7952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6dkf_7952/11_2025/6dkf_7952.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dkf_7952/11_2025/6dkf_7952.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6dkf_7952/11_2025/6dkf_7952.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dkf_7952/11_2025/6dkf_7952.map" } resolution = 3.7 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= 0.131 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 72 5.16 5 C 10708 2.51 5 N 2950 2.21 5 O 3330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17060 Number of models: 1 Model: "" Number of chains: 14 Chain: "B" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1285 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "D" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1285 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "C" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1285 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "A" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 829 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'PTRANS': 5, 'TRANS': 162} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 489 Unresolved non-hydrogen angles: 621 Unresolved non-hydrogen dihedrals: 393 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'TYR:plan': 5, 'ARG:plan': 7, 'ASP:plan': 11, 'GLN:plan1': 9, 'ASN:plan1': 7, 'PHE:plan': 5, 'GLU:plan': 11, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 249 Chain: "E" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1285 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "F" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1285 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "G" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1276 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 5, 'TRANS': 158} Chain breaks: 1 Chain: "I" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1285 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "K" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1285 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "J" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1285 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "H" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 829 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'PTRANS': 5, 'TRANS': 162} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 489 Unresolved non-hydrogen angles: 621 Unresolved non-hydrogen dihedrals: 393 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'TYR:plan': 5, 'ARG:plan': 7, 'ASP:plan': 11, 'GLN:plan1': 9, 'ASN:plan1': 7, 'PHE:plan': 5, 'GLU:plan': 11, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 249 Chain: "L" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1285 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "M" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1285 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "N" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1276 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 5, 'TRANS': 158} Chain breaks: 1 Time building chain proxies: 4.70, per 1000 atoms: 0.28 Number of scatterers: 17060 At special positions: 0 Unit cell: (119.78, 130.38, 113.42, 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 72 16.00 O 3330 8.00 N 2950 7.00 C 10708 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: 1.55 Conformation dependent library (CDL) restraints added in 757.7 milliseconds 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4344 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 28 sheets defined 54.8% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'B' and resid 20 through 27 removed outlier: 3.683A pdb=" N LEU B 24 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP B 27 " --> pdb=" O ARG B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 55 Processing helix chain 'B' and resid 70 through 84 removed outlier: 3.764A pdb=" N ILE B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 105 removed outlier: 3.510A pdb=" N PHE B 102 " --> pdb=" O SER B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 159 removed outlier: 3.930A pdb=" N ASN B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 147 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 150 " --> pdb=" O THR B 146 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE B 153 " --> pdb=" O LYS B 149 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG B 157 " --> pdb=" O ILE B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 169 removed outlier: 3.781A pdb=" N LYS B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 184 Processing helix chain 'D' and resid 21 through 27 removed outlier: 3.597A pdb=" N ASP D 27 " --> pdb=" O ARG D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 55 Processing helix chain 'D' and resid 70 through 84 removed outlier: 3.765A pdb=" N ILE D 77 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 105 removed outlier: 3.510A pdb=" N PHE D 102 " --> pdb=" O SER D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 159 removed outlier: 3.930A pdb=" N ASN D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG D 147 " --> pdb=" O ILE D 143 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU D 150 " --> pdb=" O THR D 146 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE D 153 " --> pdb=" O LYS D 149 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG D 157 " --> pdb=" O ILE D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 169 removed outlier: 3.782A pdb=" N LYS D 167 " --> pdb=" O GLU D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 184 Processing helix chain 'C' and resid 21 through 27 removed outlier: 3.598A pdb=" N ASP C 27 " --> pdb=" O ARG C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 55 Processing helix chain 'C' and resid 70 through 84 removed outlier: 3.764A pdb=" N ILE C 77 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 105 removed outlier: 3.510A pdb=" N PHE C 102 " --> pdb=" O SER C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 159 removed outlier: 3.930A pdb=" N ASN C 141 " --> pdb=" O GLU C 137 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG C 147 " --> pdb=" O ILE C 143 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 150 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE C 153 " --> pdb=" O LYS C 149 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG C 157 " --> pdb=" O ILE C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 169 removed outlier: 3.782A pdb=" N LYS C 167 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 184 Processing helix chain 'A' and resid 21 through 26 Processing helix chain 'A' and resid 37 through 55 Processing helix chain 'A' and resid 70 through 84 Processing helix chain 'A' and resid 98 through 106 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.670A pdb=" N ASN A 141 " --> pdb=" O GLU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 159 Processing helix chain 'A' and resid 161 through 170 Processing helix chain 'A' and resid 176 through 183 Processing helix chain 'E' and resid 21 through 27 removed outlier: 3.598A pdb=" N ASP E 27 " --> pdb=" O ARG E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 55 Processing helix chain 'E' and resid 70 through 84 removed outlier: 3.764A pdb=" N ILE E 77 " --> pdb=" O ALA E 73 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR E 80 " --> pdb=" O ALA E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 105 removed outlier: 3.512A pdb=" N PHE E 102 " --> pdb=" O SER E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 159 removed outlier: 3.929A pdb=" N ASN E 141 " --> pdb=" O GLU E 137 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG E 147 " --> pdb=" O ILE E 143 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU E 150 " --> pdb=" O THR E 146 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE E 153 " --> pdb=" O LYS E 149 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG E 157 " --> pdb=" O ILE E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 169 removed outlier: 3.782A pdb=" N LYS E 167 " --> pdb=" O GLU E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 21 through 27 removed outlier: 3.598A pdb=" N ASP F 27 " --> pdb=" O ARG F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 55 Processing helix chain 'F' and resid 70 through 84 removed outlier: 3.764A pdb=" N ILE F 77 " --> pdb=" O ALA F 73 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR F 80 " --> pdb=" O ALA F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 105 removed outlier: 3.511A pdb=" N PHE F 102 " --> pdb=" O SER F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 159 removed outlier: 3.930A pdb=" N ASN F 141 " --> pdb=" O GLU F 137 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG F 147 " --> pdb=" O ILE F 143 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU F 150 " --> pdb=" O THR F 146 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE F 153 " --> pdb=" O LYS F 149 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG F 157 " --> pdb=" O ILE F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 169 removed outlier: 3.782A pdb=" N LYS F 167 " --> pdb=" O GLU F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 184 Processing helix chain 'G' and resid 21 through 27 removed outlier: 3.598A pdb=" N ASP G 27 " --> pdb=" O ARG G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 55 Processing helix chain 'G' and resid 70 through 84 removed outlier: 3.765A pdb=" N ILE G 77 " --> pdb=" O ALA G 73 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 105 removed outlier: 3.511A pdb=" N PHE G 102 " --> pdb=" O SER G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 159 removed outlier: 3.931A pdb=" N ASN G 141 " --> pdb=" O GLU G 137 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG G 147 " --> pdb=" O ILE G 143 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU G 150 " --> pdb=" O THR G 146 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE G 153 " --> pdb=" O LYS G 149 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG G 157 " --> pdb=" O ILE G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 161 through 169 removed outlier: 3.782A pdb=" N LYS G 167 " --> pdb=" O GLU G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 184 Processing helix chain 'I' and resid 21 through 27 removed outlier: 3.598A pdb=" N ASP I 27 " --> pdb=" O ARG I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 55 Processing helix chain 'I' and resid 70 through 84 removed outlier: 3.763A pdb=" N ILE I 77 " --> pdb=" O ALA I 73 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 105 removed outlier: 3.510A pdb=" N PHE I 102 " --> pdb=" O SER I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 136 through 159 removed outlier: 3.930A pdb=" N ASN I 141 " --> pdb=" O GLU I 137 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG I 147 " --> pdb=" O ILE I 143 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU I 150 " --> pdb=" O THR I 146 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE I 153 " --> pdb=" O LYS I 149 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG I 157 " --> pdb=" O ILE I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 169 removed outlier: 3.781A pdb=" N LYS I 167 " --> pdb=" O GLU I 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 184 Processing helix chain 'K' and resid 21 through 27 removed outlier: 3.597A pdb=" N ASP K 27 " --> pdb=" O ARG K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 55 Processing helix chain 'K' and resid 70 through 84 removed outlier: 3.765A pdb=" N ILE K 77 " --> pdb=" O ALA K 73 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR K 80 " --> pdb=" O ALA K 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 105 removed outlier: 3.510A pdb=" N PHE K 102 " --> pdb=" O SER K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 136 through 159 removed outlier: 3.931A pdb=" N ASN K 141 " --> pdb=" O GLU K 137 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG K 147 " --> pdb=" O ILE K 143 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU K 150 " --> pdb=" O THR K 146 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE K 153 " --> pdb=" O LYS K 149 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG K 157 " --> pdb=" O ILE K 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 161 through 169 removed outlier: 3.782A pdb=" N LYS K 167 " --> pdb=" O GLU K 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 184 Processing helix chain 'J' and resid 21 through 27 removed outlier: 3.597A pdb=" N ASP J 27 " --> pdb=" O ARG J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 55 Processing helix chain 'J' and resid 70 through 84 removed outlier: 3.764A pdb=" N ILE J 77 " --> pdb=" O ALA J 73 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR J 80 " --> pdb=" O ALA J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 105 removed outlier: 3.511A pdb=" N PHE J 102 " --> pdb=" O SER J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 159 removed outlier: 3.929A pdb=" N ASN J 141 " --> pdb=" O GLU J 137 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG J 147 " --> pdb=" O ILE J 143 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU J 150 " --> pdb=" O THR J 146 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE J 153 " --> pdb=" O LYS J 149 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG J 157 " --> pdb=" O ILE J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 169 removed outlier: 3.781A pdb=" N LYS J 167 " --> pdb=" O GLU J 163 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 184 Processing helix chain 'H' and resid 21 through 26 Processing helix chain 'H' and resid 37 through 55 Processing helix chain 'H' and resid 70 through 84 Processing helix chain 'H' and resid 98 through 106 Processing helix chain 'H' and resid 134 through 145 removed outlier: 3.670A pdb=" N ASN H 141 " --> pdb=" O GLU H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 159 Processing helix chain 'H' and resid 161 through 170 Processing helix chain 'H' and resid 176 through 183 Processing helix chain 'L' and resid 21 through 27 removed outlier: 3.597A pdb=" N ASP L 27 " --> pdb=" O ARG L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 55 Processing helix chain 'L' and resid 70 through 84 removed outlier: 3.764A pdb=" N ILE L 77 " --> pdb=" O ALA L 73 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR L 80 " --> pdb=" O ALA L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 105 removed outlier: 3.512A pdb=" N PHE L 102 " --> pdb=" O SER L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 136 through 159 removed outlier: 3.930A pdb=" N ASN L 141 " --> pdb=" O GLU L 137 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG L 147 " --> pdb=" O ILE L 143 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU L 150 " --> pdb=" O THR L 146 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE L 153 " --> pdb=" O LYS L 149 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG L 157 " --> pdb=" O ILE L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 161 through 169 removed outlier: 3.782A pdb=" N LYS L 167 " --> pdb=" O GLU L 163 " (cutoff:3.500A) Processing helix chain 'L' and resid 177 through 184 Processing helix chain 'M' and resid 21 through 27 removed outlier: 3.597A pdb=" N ASP M 27 " --> pdb=" O ARG M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 55 Processing helix chain 'M' and resid 70 through 84 removed outlier: 3.765A pdb=" N ILE M 77 " --> pdb=" O ALA M 73 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR M 80 " --> pdb=" O ALA M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 105 removed outlier: 3.511A pdb=" N PHE M 102 " --> pdb=" O SER M 98 " (cutoff:3.500A) Processing helix chain 'M' and resid 136 through 159 removed outlier: 3.931A pdb=" N ASN M 141 " --> pdb=" O GLU M 137 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG M 147 " --> pdb=" O ILE M 143 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU M 150 " --> pdb=" O THR M 146 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE M 153 " --> pdb=" O LYS M 149 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG M 157 " --> pdb=" O ILE M 153 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 169 removed outlier: 3.782A pdb=" N LYS M 167 " --> pdb=" O GLU M 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 184 Processing helix chain 'N' and resid 21 through 27 removed outlier: 3.598A pdb=" N ASP N 27 " --> pdb=" O ARG N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 55 Processing helix chain 'N' and resid 70 through 84 removed outlier: 3.764A pdb=" N ILE N 77 " --> pdb=" O ALA N 73 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR N 80 " --> pdb=" O ALA N 76 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 105 removed outlier: 3.511A pdb=" N PHE N 102 " --> pdb=" O SER N 98 " (cutoff:3.500A) Processing helix chain 'N' and resid 136 through 159 removed outlier: 3.930A pdb=" N ASN N 141 " --> pdb=" O GLU N 137 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG N 147 " --> pdb=" O ILE N 143 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU N 150 " --> pdb=" O THR N 146 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE N 153 " --> pdb=" O LYS N 149 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG N 157 " --> pdb=" O ILE N 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 161 through 169 removed outlier: 3.782A pdb=" N LYS N 167 " --> pdb=" O GLU N 163 " (cutoff:3.500A) Processing helix chain 'N' and resid 177 through 184 Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.418A pdb=" N ILE B 30 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ASN B 65 " --> pdb=" O ILE B 30 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU B 32 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N SER B 66 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N MET B 95 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N PHE B 113 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N THR B 90 " --> pdb=" O PHE B 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B 114 " --> pdb=" O GLU B 188 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 119 through 121 Processing sheet with id=AA3, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.418A pdb=" N ILE D 30 " --> pdb=" O TYR D 63 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ASN D 65 " --> pdb=" O ILE D 30 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU D 32 " --> pdb=" O ASN D 65 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N SER D 66 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N MET D 95 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N PHE D 113 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR D 90 " --> pdb=" O PHE D 113 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA D 114 " --> pdb=" O GLU D 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 119 through 121 Processing sheet with id=AA5, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.418A pdb=" N ILE C 30 " --> pdb=" O TYR C 63 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ASN C 65 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU C 32 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N SER C 66 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N MET C 95 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N PHE C 113 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR C 90 " --> pdb=" O PHE C 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA C 114 " --> pdb=" O GLU C 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 119 through 121 Processing sheet with id=AA7, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.350A pdb=" N ILE A 60 " --> pdb=" O GLN A 89 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ILE A 91 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU A 62 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE A 93 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE A 64 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N MET A 95 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLU A 119 " --> pdb=" O CYS A 92 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLY A 94 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N MET A 121 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ALA A 96 " --> pdb=" O MET A 121 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.350A pdb=" N ILE A 60 " --> pdb=" O GLN A 89 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ILE A 91 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU A 62 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE A 93 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE A 64 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N MET A 95 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N PHE A 113 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N THR A 90 " --> pdb=" O PHE A 113 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.417A pdb=" N ILE E 30 " --> pdb=" O TYR E 63 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ASN E 65 " --> pdb=" O ILE E 30 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU E 32 " --> pdb=" O ASN E 65 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N SER E 66 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N MET E 95 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N PHE E 113 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR E 90 " --> pdb=" O PHE E 113 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA E 114 " --> pdb=" O GLU E 188 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 119 through 121 Processing sheet with id=AB2, first strand: chain 'F' and resid 29 through 32 removed outlier: 6.416A pdb=" N ILE F 30 " --> pdb=" O TYR F 63 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ASN F 65 " --> pdb=" O ILE F 30 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU F 32 " --> pdb=" O ASN F 65 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N SER F 66 " --> pdb=" O ILE F 93 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N MET F 95 " --> pdb=" O SER F 66 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N PHE F 113 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR F 90 " --> pdb=" O PHE F 113 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA F 114 " --> pdb=" O GLU F 188 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 119 through 121 Processing sheet with id=AB4, first strand: chain 'G' and resid 29 through 32 removed outlier: 6.418A pdb=" N ILE G 30 " --> pdb=" O TYR G 63 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ASN G 65 " --> pdb=" O ILE G 30 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU G 32 " --> pdb=" O ASN G 65 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N SER G 66 " --> pdb=" O ILE G 93 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N MET G 95 " --> pdb=" O SER G 66 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N PHE G 113 " --> pdb=" O VAL G 88 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR G 90 " --> pdb=" O PHE G 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA G 114 " --> pdb=" O GLU G 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 119 through 121 Processing sheet with id=AB6, first strand: chain 'I' and resid 29 through 32 removed outlier: 6.418A pdb=" N ILE I 30 " --> pdb=" O TYR I 63 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ASN I 65 " --> pdb=" O ILE I 30 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU I 32 " --> pdb=" O ASN I 65 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N SER I 66 " --> pdb=" O ILE I 93 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N MET I 95 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N PHE I 113 " --> pdb=" O VAL I 88 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N THR I 90 " --> pdb=" O PHE I 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA I 114 " --> pdb=" O GLU I 188 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 119 through 121 Processing sheet with id=AB8, first strand: chain 'K' and resid 29 through 32 removed outlier: 6.417A pdb=" N ILE K 30 " --> pdb=" O TYR K 63 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ASN K 65 " --> pdb=" O ILE K 30 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU K 32 " --> pdb=" O ASN K 65 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N SER K 66 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N MET K 95 " --> pdb=" O SER K 66 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N PHE K 113 " --> pdb=" O VAL K 88 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR K 90 " --> pdb=" O PHE K 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA K 114 " --> pdb=" O GLU K 188 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 119 through 121 Processing sheet with id=AC1, first strand: chain 'J' and resid 29 through 32 removed outlier: 6.418A pdb=" N ILE J 30 " --> pdb=" O TYR J 63 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ASN J 65 " --> pdb=" O ILE J 30 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU J 32 " --> pdb=" O ASN J 65 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N SER J 66 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N MET J 95 " --> pdb=" O SER J 66 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N PHE J 113 " --> pdb=" O VAL J 88 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR J 90 " --> pdb=" O PHE J 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA J 114 " --> pdb=" O GLU J 188 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 119 through 121 Processing sheet with id=AC3, first strand: chain 'H' and resid 29 through 32 removed outlier: 6.350A pdb=" N ILE H 60 " --> pdb=" O GLN H 89 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ILE H 91 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU H 62 " --> pdb=" O ILE H 91 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE H 93 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE H 64 " --> pdb=" O ILE H 93 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N MET H 95 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLU H 119 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLY H 94 " --> pdb=" O GLU H 119 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N MET H 121 " --> pdb=" O GLY H 94 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ALA H 96 " --> pdb=" O MET H 121 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 29 through 32 removed outlier: 6.350A pdb=" N ILE H 60 " --> pdb=" O GLN H 89 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ILE H 91 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU H 62 " --> pdb=" O ILE H 91 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE H 93 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE H 64 " --> pdb=" O ILE H 93 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N MET H 95 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N PHE H 113 " --> pdb=" O VAL H 88 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR H 90 " --> pdb=" O PHE H 113 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 29 through 32 removed outlier: 6.418A pdb=" N ILE L 30 " --> pdb=" O TYR L 63 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ASN L 65 " --> pdb=" O ILE L 30 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU L 32 " --> pdb=" O ASN L 65 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N SER L 66 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N MET L 95 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N PHE L 113 " --> pdb=" O VAL L 88 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR L 90 " --> pdb=" O PHE L 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA L 114 " --> pdb=" O GLU L 188 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 119 through 121 Processing sheet with id=AC7, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.417A pdb=" N ILE M 30 " --> pdb=" O TYR M 63 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ASN M 65 " --> pdb=" O ILE M 30 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU M 32 " --> pdb=" O ASN M 65 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N SER M 66 " --> pdb=" O ILE M 93 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N MET M 95 " --> pdb=" O SER M 66 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N PHE M 113 " --> pdb=" O VAL M 88 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N THR M 90 " --> pdb=" O PHE M 113 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA M 114 " --> pdb=" O GLU M 188 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 119 through 121 Processing sheet with id=AC9, first strand: chain 'N' and resid 29 through 32 removed outlier: 6.418A pdb=" N ILE N 30 " --> pdb=" O TYR N 63 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ASN N 65 " --> pdb=" O ILE N 30 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU N 32 " --> pdb=" O ASN N 65 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N SER N 66 " --> pdb=" O ILE N 93 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N MET N 95 " --> pdb=" O SER N 66 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N PHE N 113 " --> pdb=" O VAL N 88 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR N 90 " --> pdb=" O PHE N 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA N 114 " --> pdb=" O GLU N 188 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 119 through 121 856 hydrogen bonds defined for protein. 2568 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.92 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5815 1.34 - 1.45: 1793 1.45 - 1.57: 9508 1.57 - 1.68: 0 1.68 - 1.80: 132 Bond restraints: 17248 Sorted by residual: bond pdb=" CA LEU A 150 " pdb=" C LEU A 150 " ideal model delta sigma weight residual 1.524 1.490 0.034 1.27e-02 6.20e+03 7.09e+00 bond pdb=" CA LEU H 150 " pdb=" C LEU H 150 " ideal model delta sigma weight residual 1.524 1.490 0.034 1.27e-02 6.20e+03 7.09e+00 bond pdb=" CA THR A 146 " pdb=" C THR A 146 " ideal model delta sigma weight residual 1.523 1.492 0.032 1.30e-02 5.92e+03 5.97e+00 bond pdb=" N THR H 146 " pdb=" CA THR H 146 " ideal model delta sigma weight residual 1.459 1.430 0.029 1.21e-02 6.83e+03 5.67e+00 bond pdb=" CA THR H 146 " pdb=" C THR H 146 " ideal model delta sigma weight residual 1.523 1.492 0.031 1.30e-02 5.92e+03 5.61e+00 ... (remaining 17243 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 22230 1.74 - 3.47: 856 3.47 - 5.21: 160 5.21 - 6.94: 20 6.94 - 8.68: 42 Bond angle restraints: 23308 Sorted by residual: angle pdb=" N ILE H 143 " pdb=" CA ILE H 143 " pdb=" C ILE H 143 " ideal model delta sigma weight residual 110.62 102.83 7.79 1.02e+00 9.61e-01 5.83e+01 angle pdb=" N HIS H 142 " pdb=" CA HIS H 142 " pdb=" C HIS H 142 " ideal model delta sigma weight residual 111.28 102.96 8.32 1.09e+00 8.42e-01 5.83e+01 angle pdb=" N HIS A 142 " pdb=" CA HIS A 142 " pdb=" C HIS A 142 " ideal model delta sigma weight residual 111.28 102.96 8.32 1.09e+00 8.42e-01 5.83e+01 angle pdb=" N ILE A 143 " pdb=" CA ILE A 143 " pdb=" C ILE A 143 " ideal model delta sigma weight residual 110.62 102.87 7.75 1.02e+00 9.61e-01 5.77e+01 angle pdb=" N GLU H 137 " pdb=" CA GLU H 137 " pdb=" C GLU H 137 " ideal model delta sigma weight residual 111.28 103.97 7.31 1.09e+00 8.42e-01 4.50e+01 ... (remaining 23303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.27: 10267 15.27 - 30.54: 269 30.54 - 45.81: 36 45.81 - 61.08: 12 61.08 - 76.36: 12 Dihedral angle restraints: 10596 sinusoidal: 3906 harmonic: 6690 Sorted by residual: dihedral pdb=" CA ILE H 64 " pdb=" C ILE H 64 " pdb=" N ASN H 65 " pdb=" CA ASN H 65 " ideal model delta harmonic sigma weight residual 180.00 153.98 26.02 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA ILE A 64 " pdb=" C ILE A 64 " pdb=" N ASN A 65 " pdb=" CA ASN A 65 " ideal model delta harmonic sigma weight residual 180.00 153.98 26.02 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA ILE K 64 " pdb=" C ILE K 64 " pdb=" N ASN K 65 " pdb=" CA ASN K 65 " ideal model delta harmonic sigma weight residual 180.00 160.74 19.26 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 10593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2166 0.061 - 0.123: 546 0.123 - 0.184: 42 0.184 - 0.245: 4 0.245 - 0.307: 2 Chirality restraints: 2760 Sorted by residual: chirality pdb=" CA ILE H 143 " pdb=" N ILE H 143 " pdb=" C ILE H 143 " pdb=" CB ILE H 143 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA ILE A 143 " pdb=" N ILE A 143 " pdb=" C ILE A 143 " pdb=" CB ILE A 143 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA GLU H 137 " pdb=" N GLU H 137 " pdb=" C GLU H 137 " pdb=" CB GLU H 137 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.30e-01 ... (remaining 2757 not shown) Planarity restraints: 3052 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN M 124 " -0.023 5.00e-02 4.00e+02 3.54e-02 2.00e+00 pdb=" N PRO M 125 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO M 125 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO M 125 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 124 " 0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO B 125 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 125 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 125 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN I 124 " -0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO I 125 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO I 125 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO I 125 " -0.019 5.00e-02 4.00e+02 ... (remaining 3049 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 90 2.50 - 3.10: 14663 3.10 - 3.70: 24623 3.70 - 4.30: 36947 4.30 - 4.90: 59314 Nonbonded interactions: 135637 Sorted by model distance: nonbonded pdb=" OD1 ASP C 170 " pdb=" N GLU M 135 " model vdw 1.898 3.120 nonbonded pdb=" OD1 ASP F 170 " pdb=" N GLU J 135 " model vdw 1.904 3.120 nonbonded pdb=" OD1 ASP G 170 " pdb=" N GLU I 135 " model vdw 1.906 3.120 nonbonded pdb=" N GLU C 135 " pdb=" OD1 ASP M 170 " model vdw 1.923 3.120 nonbonded pdb=" N GLU B 135 " pdb=" OD1 ASP N 170 " model vdw 1.935 3.120 ... (remaining 135632 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 125 or resid 135 through 192)) selection = (chain 'B' and ((resid 20 through 32 and (name N or name CA or name C or name O \ or name CB )) or resid 33 or (resid 34 through 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 through 69 or (resid 70 through 73 and (n \ ame N or name CA or name C or name O or name CB )) or resid 74 or (resid 75 thro \ ugh 93 and (name N or name CA or name C or name O or name CB )) or resid 94 or ( \ resid 95 through 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 or (resid 101 through 106 and (name N or name CA or name C or name O o \ r name CB )) or (resid 107 through 109 and (name N or name CA or name C or name \ O or name CB )) or resid 110 or (resid 111 through 158 and (name N or name CA or \ name C or name O or name CB )) or resid 159 or (resid 160 through 183 and (name \ N or name CA or name C or name O or name CB )) or resid 184 or (resid 185 throu \ gh 192 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'C' and ((resid 20 through 32 and (name N or name CA or name C or name O \ or name CB )) or resid 33 or (resid 34 through 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 through 69 or (resid 70 through 73 and (n \ ame N or name CA or name C or name O or name CB )) or resid 74 or (resid 75 thro \ ugh 93 and (name N or name CA or name C or name O or name CB )) or resid 94 or ( \ resid 95 through 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 or (resid 101 through 106 and (name N or name CA or name C or name O o \ r name CB )) or (resid 107 through 109 and (name N or name CA or name C or name \ O or name CB )) or resid 110 or (resid 111 through 158 and (name N or name CA or \ name C or name O or name CB )) or resid 159 or (resid 160 through 183 and (name \ N or name CA or name C or name O or name CB )) or resid 184 or (resid 185 throu \ gh 192 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and ((resid 20 through 32 and (name N or name CA or name C or name O \ or name CB )) or resid 33 or (resid 34 through 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 through 69 or (resid 70 through 73 and (n \ ame N or name CA or name C or name O or name CB )) or resid 74 or (resid 75 thro \ ugh 93 and (name N or name CA or name C or name O or name CB )) or resid 94 or ( \ resid 95 through 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 or (resid 101 through 106 and (name N or name CA or name C or name O o \ r name CB )) or (resid 107 through 109 and (name N or name CA or name C or name \ O or name CB )) or resid 110 or (resid 111 through 158 and (name N or name CA or \ name C or name O or name CB )) or resid 159 or (resid 160 through 183 and (name \ N or name CA or name C or name O or name CB )) or resid 184 or (resid 185 throu \ gh 192 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'E' and ((resid 20 through 32 and (name N or name CA or name C or name O \ or name CB )) or resid 33 or (resid 34 through 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 through 69 or (resid 70 through 73 and (n \ ame N or name CA or name C or name O or name CB )) or resid 74 or (resid 75 thro \ ugh 93 and (name N or name CA or name C or name O or name CB )) or resid 94 or ( \ resid 95 through 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 or (resid 101 through 106 and (name N or name CA or name C or name O o \ r name CB )) or (resid 107 through 109 and (name N or name CA or name C or name \ O or name CB )) or resid 110 or (resid 111 through 158 and (name N or name CA or \ name C or name O or name CB )) or resid 159 or (resid 160 through 183 and (name \ N or name CA or name C or name O or name CB )) or resid 184 or (resid 185 throu \ gh 192 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'F' and ((resid 20 through 32 and (name N or name CA or name C or name O \ or name CB )) or resid 33 or (resid 34 through 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 through 69 or (resid 70 through 73 and (n \ ame N or name CA or name C or name O or name CB )) or resid 74 or (resid 75 thro \ ugh 93 and (name N or name CA or name C or name O or name CB )) or resid 94 or ( \ resid 95 through 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 or (resid 101 through 106 and (name N or name CA or name C or name O o \ r name CB )) or (resid 107 through 109 and (name N or name CA or name C or name \ O or name CB )) or resid 110 or (resid 111 through 158 and (name N or name CA or \ name C or name O or name CB )) or resid 159 or (resid 160 through 183 and (name \ N or name CA or name C or name O or name CB )) or resid 184 or (resid 185 throu \ gh 192 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'G' and ((resid 20 through 32 and (name N or name CA or name C or name O \ or name CB )) or resid 33 or (resid 34 through 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 through 69 or (resid 70 through 73 and (n \ ame N or name CA or name C or name O or name CB )) or resid 74 or (resid 75 thro \ ugh 93 and (name N or name CA or name C or name O or name CB )) or resid 94 or ( \ resid 95 through 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 or (resid 101 through 106 and (name N or name CA or name C or name O o \ r name CB )) or (resid 107 through 109 and (name N or name CA or name C or name \ O or name CB )) or resid 110 or (resid 111 through 158 and (name N or name CA or \ name C or name O or name CB )) or resid 159 or (resid 160 through 183 and (name \ N or name CA or name C or name O or name CB )) or resid 184 or (resid 185 throu \ gh 192 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'H' and (resid 20 through 125 or resid 135 through 192)) selection = (chain 'I' and ((resid 20 through 32 and (name N or name CA or name C or name O \ or name CB )) or resid 33 or (resid 34 through 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 through 69 or (resid 70 through 73 and (n \ ame N or name CA or name C or name O or name CB )) or resid 74 or (resid 75 thro \ ugh 93 and (name N or name CA or name C or name O or name CB )) or resid 94 or ( \ resid 95 through 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 or (resid 101 through 106 and (name N or name CA or name C or name O o \ r name CB )) or (resid 107 through 109 and (name N or name CA or name C or name \ O or name CB )) or resid 110 or (resid 111 through 158 and (name N or name CA or \ name C or name O or name CB )) or resid 159 or (resid 160 through 183 and (name \ N or name CA or name C or name O or name CB )) or resid 184 or (resid 185 throu \ gh 192 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'J' and ((resid 20 through 32 and (name N or name CA or name C or name O \ or name CB )) or resid 33 or (resid 34 through 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 through 69 or (resid 70 through 73 and (n \ ame N or name CA or name C or name O or name CB )) or resid 74 or (resid 75 thro \ ugh 93 and (name N or name CA or name C or name O or name CB )) or resid 94 or ( \ resid 95 through 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 or (resid 101 through 106 and (name N or name CA or name C or name O o \ r name CB )) or (resid 107 through 109 and (name N or name CA or name C or name \ O or name CB )) or resid 110 or (resid 111 through 158 and (name N or name CA or \ name C or name O or name CB )) or resid 159 or (resid 160 through 183 and (name \ N or name CA or name C or name O or name CB )) or resid 184 or (resid 185 throu \ gh 192 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'K' and ((resid 20 through 32 and (name N or name CA or name C or name O \ or name CB )) or resid 33 or (resid 34 through 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 through 69 or (resid 70 through 73 and (n \ ame N or name CA or name C or name O or name CB )) or resid 74 or (resid 75 thro \ ugh 93 and (name N or name CA or name C or name O or name CB )) or resid 94 or ( \ resid 95 through 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 or (resid 101 through 106 and (name N or name CA or name C or name O o \ r name CB )) or (resid 107 through 109 and (name N or name CA or name C or name \ O or name CB )) or resid 110 or (resid 111 through 158 and (name N or name CA or \ name C or name O or name CB )) or resid 159 or (resid 160 through 183 and (name \ N or name CA or name C or name O or name CB )) or resid 184 or (resid 185 throu \ gh 192 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'L' and ((resid 20 through 32 and (name N or name CA or name C or name O \ or name CB )) or resid 33 or (resid 34 through 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 through 69 or (resid 70 through 73 and (n \ ame N or name CA or name C or name O or name CB )) or resid 74 or (resid 75 thro \ ugh 93 and (name N or name CA or name C or name O or name CB )) or resid 94 or ( \ resid 95 through 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 or (resid 101 through 106 and (name N or name CA or name C or name O o \ r name CB )) or (resid 107 through 109 and (name N or name CA or name C or name \ O or name CB )) or resid 110 or (resid 111 through 158 and (name N or name CA or \ name C or name O or name CB )) or resid 159 or (resid 160 through 183 and (name \ N or name CA or name C or name O or name CB )) or resid 184 or (resid 185 throu \ gh 192 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'M' and ((resid 20 through 32 and (name N or name CA or name C or name O \ or name CB )) or resid 33 or (resid 34 through 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 through 69 or (resid 70 through 73 and (n \ ame N or name CA or name C or name O or name CB )) or resid 74 or (resid 75 thro \ ugh 93 and (name N or name CA or name C or name O or name CB )) or resid 94 or ( \ resid 95 through 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 or (resid 101 through 106 and (name N or name CA or name C or name O o \ r name CB )) or (resid 107 through 109 and (name N or name CA or name C or name \ O or name CB )) or resid 110 or (resid 111 through 158 and (name N or name CA or \ name C or name O or name CB )) or resid 159 or (resid 160 through 183 and (name \ N or name CA or name C or name O or name CB )) or resid 184 or (resid 185 throu \ gh 192 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'N' and ((resid 20 through 32 and (name N or name CA or name C or name O \ or name CB )) or resid 33 or (resid 34 through 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 through 69 or (resid 70 through 73 and (n \ ame N or name CA or name C or name O or name CB )) or resid 74 or (resid 75 thro \ ugh 93 and (name N or name CA or name C or name O or name CB )) or resid 94 or ( \ resid 95 through 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 or (resid 101 through 106 and (name N or name CA or name C or name O o \ r name CB )) or (resid 107 through 109 and (name N or name CA or name C or name \ O or name CB )) or resid 110 or (resid 111 through 158 and (name N or name CA or \ name C or name O or name CB )) or resid 159 or (resid 160 through 183 and (name \ N or name CA or name C or name O or name CB )) or resid 184 or (resid 185 throu \ gh 192 and (name N or name CA or name C or name O or name CB )))) } 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 group one per residue 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: 0.490 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.450 Find NCS groups from input model: 0.690 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 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 : 0.010 0.051 17248 Z= 0.435 Angle : 0.880 8.678 23308 Z= 0.489 Chirality : 0.053 0.307 2760 Planarity : 0.005 0.035 3052 Dihedral : 8.963 76.356 6252 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % 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: -5.10 (0.10), residues: 2258 helix: -3.85 (0.09), residues: 1190 sheet: -2.27 (0.30), residues: 168 loop : -2.66 (0.11), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 112 TYR 0.009 0.002 TYR J 183 PHE 0.009 0.002 PHE G 50 HIS 0.004 0.002 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00984 (17248) covalent geometry : angle 0.88041 (23308) hydrogen bonds : bond 0.27088 ( 844) hydrogen bonds : angle 10.70463 ( 2568) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 867 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 26 LYS cc_start: 0.8843 (tttp) cc_final: 0.8033 (tppt) REVERT: B 165 ILE cc_start: 0.8509 (mm) cc_final: 0.8115 (mt) REVERT: D 39 ASN cc_start: 0.8591 (m-40) cc_final: 0.8284 (m-40) REVERT: D 85 LYS cc_start: 0.8492 (tttt) cc_final: 0.8089 (mmtt) REVERT: D 98 SER cc_start: 0.8827 (t) cc_final: 0.8607 (m) REVERT: D 160 GLN cc_start: 0.7930 (mm-40) cc_final: 0.7717 (mm-40) REVERT: D 161 SER cc_start: 0.8605 (p) cc_final: 0.8302 (t) REVERT: C 85 LYS cc_start: 0.7826 (tttt) cc_final: 0.7577 (mptt) REVERT: C 121 MET cc_start: 0.7505 (ttp) cc_final: 0.7241 (mtp) REVERT: C 155 SER cc_start: 0.8365 (t) cc_final: 0.8087 (m) REVERT: E 26 LYS cc_start: 0.8755 (tttp) cc_final: 0.8488 (ttmt) REVERT: F 26 LYS cc_start: 0.8852 (tttp) cc_final: 0.8596 (mttp) REVERT: F 34 SER cc_start: 0.8929 (p) cc_final: 0.8583 (p) REVERT: F 35 GLN cc_start: 0.8653 (pm20) cc_final: 0.8449 (pp30) REVERT: F 160 GLN cc_start: 0.7808 (mm-40) cc_final: 0.7530 (mm-40) REVERT: F 165 ILE cc_start: 0.8250 (mm) cc_final: 0.8030 (mt) REVERT: F 179 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8182 (tt0) REVERT: G 47 GLN cc_start: 0.8149 (mt0) cc_final: 0.7915 (mt0) REVERT: G 59 ASP cc_start: 0.7312 (p0) cc_final: 0.7062 (p0) REVERT: G 165 ILE cc_start: 0.7848 (mm) cc_final: 0.7415 (mt) REVERT: G 168 ASP cc_start: 0.6193 (m-30) cc_final: 0.5752 (m-30) REVERT: I 26 LYS cc_start: 0.8766 (tttp) cc_final: 0.7962 (tppt) REVERT: I 78 TYR cc_start: 0.8757 (t80) cc_final: 0.8528 (t80) REVERT: I 163 GLU cc_start: 0.7908 (mp0) cc_final: 0.7620 (mp0) REVERT: I 165 ILE cc_start: 0.8523 (mm) cc_final: 0.8157 (mt) REVERT: I 167 LYS cc_start: 0.8927 (ttmt) cc_final: 0.8640 (tptt) REVERT: K 39 ASN cc_start: 0.8565 (m-40) cc_final: 0.8185 (m-40) REVERT: K 85 LYS cc_start: 0.8720 (tttt) cc_final: 0.8311 (mmtt) REVERT: K 121 MET cc_start: 0.6894 (ttp) cc_final: 0.6623 (ttt) REVERT: K 143 ILE cc_start: 0.8789 (tt) cc_final: 0.8571 (mt) REVERT: K 160 GLN cc_start: 0.7874 (mm-40) cc_final: 0.7629 (mm-40) REVERT: J 155 SER cc_start: 0.8293 (t) cc_final: 0.8079 (m) REVERT: L 26 LYS cc_start: 0.8940 (tttp) cc_final: 0.8738 (ttmt) REVERT: L 35 GLN cc_start: 0.8714 (pm20) cc_final: 0.8379 (pm20) REVERT: M 26 LYS cc_start: 0.9053 (tttp) cc_final: 0.8828 (ttmt) REVERT: M 30 ILE cc_start: 0.8828 (mt) cc_final: 0.8561 (pt) REVERT: M 88 VAL cc_start: 0.8494 (t) cc_final: 0.8275 (t) REVERT: M 103 LEU cc_start: 0.9033 (mt) cc_final: 0.8750 (mt) REVERT: M 188 GLU cc_start: 0.8109 (tp30) cc_final: 0.7897 (tt0) REVERT: N 59 ASP cc_start: 0.7277 (p0) cc_final: 0.7063 (p0) REVERT: N 165 ILE cc_start: 0.7971 (mm) cc_final: 0.7529 (mt) REVERT: N 168 ASP cc_start: 0.6230 (m-30) cc_final: 0.5598 (m-30) outliers start: 0 outliers final: 0 residues processed: 867 average time/residue: 0.1382 time to fit residues: 177.2273 Evaluate side-chains 645 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 645 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN B 83 HIS B 123 HIS D 42 ASN D 54 GLN D 89 GLN D 123 HIS C 123 HIS C 142 HIS E 54 GLN E 117 ASN F 39 ASN F 42 ASN F 52 GLN F 89 GLN F 141 ASN G 89 GLN G 123 HIS I 82 GLN I 83 HIS I 123 HIS K 54 GLN K 89 GLN K 123 HIS ** J 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 173 ASN L 54 GLN M 42 ASN M 52 GLN M 89 GLN M 123 HIS M 141 ASN N 54 GLN N 89 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.157656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.134686 restraints weight = 25006.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.137842 restraints weight = 13087.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.139858 restraints weight = 8168.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.141172 restraints weight = 5794.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.141882 restraints weight = 4545.711| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17248 Z= 0.135 Angle : 0.617 7.555 23308 Z= 0.323 Chirality : 0.044 0.150 2760 Planarity : 0.004 0.045 3052 Dihedral : 4.803 16.497 2430 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 5.01 % Allowed : 13.47 % Favored : 81.53 % 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: -1.82 (0.15), residues: 2258 helix: -0.82 (0.13), residues: 1284 sheet: -2.00 (0.32), residues: 168 loop : -1.41 (0.17), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 157 TYR 0.014 0.001 TYR N 183 PHE 0.020 0.002 PHE J 102 HIS 0.017 0.003 HIS B 123 Details of bonding type rmsd covalent geometry : bond 0.00294 (17248) covalent geometry : angle 0.61653 (23308) hydrogen bonds : bond 0.03166 ( 844) hydrogen bonds : angle 4.52295 ( 2568) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 726 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 66 SER cc_start: 0.9022 (t) cc_final: 0.8600 (p) REVERT: D 98 SER cc_start: 0.8424 (t) cc_final: 0.8136 (m) REVERT: D 141 ASN cc_start: 0.8400 (OUTLIER) cc_final: 0.8143 (t0) REVERT: D 160 GLN cc_start: 0.7754 (mm-40) cc_final: 0.7427 (mm-40) REVERT: D 161 SER cc_start: 0.8259 (p) cc_final: 0.8005 (t) REVERT: D 191 VAL cc_start: 0.8841 (t) cc_final: 0.8487 (m) REVERT: C 95 MET cc_start: 0.7170 (tpp) cc_final: 0.6487 (tpp) REVERT: C 99 MET cc_start: 0.8085 (tpp) cc_final: 0.7715 (mmm) REVERT: E 173 ASN cc_start: 0.7853 (t0) cc_final: 0.7586 (m-40) REVERT: F 27 ASP cc_start: 0.8226 (t0) cc_final: 0.7956 (t0) REVERT: F 34 SER cc_start: 0.8555 (p) cc_final: 0.8285 (p) REVERT: F 52 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7526 (tt0) REVERT: F 117 ASN cc_start: 0.8279 (t0) cc_final: 0.6735 (t0) REVERT: F 119 GLU cc_start: 0.7274 (tm-30) cc_final: 0.6428 (tm-30) REVERT: F 179 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8056 (tt0) REVERT: F 193 GLU cc_start: 0.6413 (pp20) cc_final: 0.5913 (pp20) REVERT: G 27 ASP cc_start: 0.7620 (p0) cc_final: 0.7023 (p0) REVERT: G 37 ASP cc_start: 0.7897 (p0) cc_final: 0.7676 (p0) REVERT: G 59 ASP cc_start: 0.7473 (p0) cc_final: 0.6769 (p0) REVERT: G 75 PHE cc_start: 0.8947 (m-10) cc_final: 0.8716 (m-10) REVERT: G 85 LYS cc_start: 0.8369 (mmmm) cc_final: 0.8053 (mmmm) REVERT: G 111 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8303 (mtpt) REVERT: G 121 MET cc_start: 0.6759 (mpp) cc_final: 0.6463 (mpp) REVERT: G 160 GLN cc_start: 0.7912 (mm-40) cc_final: 0.7543 (mp10) REVERT: G 176 THR cc_start: 0.9478 (t) cc_final: 0.9255 (t) REVERT: G 178 GLU cc_start: 0.8033 (mp0) cc_final: 0.7673 (mp0) REVERT: G 188 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7511 (tm-30) REVERT: I 70 SER cc_start: 0.7697 (t) cc_final: 0.7036 (p) REVERT: I 167 LYS cc_start: 0.8383 (ttmt) cc_final: 0.8156 (tptt) REVERT: K 66 SER cc_start: 0.8966 (t) cc_final: 0.8626 (p) REVERT: K 141 ASN cc_start: 0.8343 (m-40) cc_final: 0.8113 (t0) REVERT: K 160 GLN cc_start: 0.7810 (mm-40) cc_final: 0.7480 (mm-40) REVERT: J 99 MET cc_start: 0.8010 (tpp) cc_final: 0.7489 (mmm) REVERT: L 160 GLN cc_start: 0.7874 (mm-40) cc_final: 0.7468 (mm-40) REVERT: M 27 ASP cc_start: 0.8176 (t0) cc_final: 0.7852 (t0) REVERT: M 117 ASN cc_start: 0.8096 (t0) cc_final: 0.6546 (t0) REVERT: M 149 LYS cc_start: 0.9226 (ttmt) cc_final: 0.9007 (ttmt) REVERT: M 178 GLU cc_start: 0.7998 (tp30) cc_final: 0.7794 (mm-30) REVERT: N 27 ASP cc_start: 0.8314 (p0) cc_final: 0.7460 (p0) REVERT: N 47 GLN cc_start: 0.8715 (mt0) cc_final: 0.8450 (mp10) REVERT: N 59 ASP cc_start: 0.7597 (p0) cc_final: 0.6877 (p0) REVERT: N 60 ILE cc_start: 0.7784 (mm) cc_final: 0.7472 (mm) REVERT: N 82 GLN cc_start: 0.8209 (mp10) cc_final: 0.7979 (mp10) REVERT: N 89 GLN cc_start: 0.8823 (mt0) cc_final: 0.8349 (mt0) REVERT: N 151 ASN cc_start: 0.9175 (m-40) cc_final: 0.8872 (m-40) REVERT: N 178 GLU cc_start: 0.8057 (mp0) cc_final: 0.7802 (mp0) outliers start: 84 outliers final: 37 residues processed: 762 average time/residue: 0.1322 time to fit residues: 151.2872 Evaluate side-chains 663 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 623 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain C residue 123 HIS Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 123 HIS Chi-restraints excluded: chain F residue 52 GLN Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 123 HIS Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 123 HIS Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain I residue 191 VAL Chi-restraints excluded: chain K residue 123 HIS Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain J residue 173 ASN Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 123 HIS Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 93 ILE Chi-restraints excluded: chain M residue 123 HIS Chi-restraints excluded: chain M residue 189 VAL Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 123 HIS Chi-restraints excluded: chain N residue 189 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 194 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 chunk 152 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 HIS D 54 GLN C 117 ASN C 173 ASN E 83 HIS F 52 GLN I 83 HIS K 54 GLN ** J 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 173 ASN L 83 HIS M 42 ASN M 47 GLN M 52 GLN N 39 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.148427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.124586 restraints weight = 26047.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.127725 restraints weight = 13867.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.129701 restraints weight = 8773.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.131016 restraints weight = 6319.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.131829 restraints weight = 5013.401| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17248 Z= 0.230 Angle : 0.657 6.944 23308 Z= 0.341 Chirality : 0.047 0.175 2760 Planarity : 0.005 0.047 3052 Dihedral : 4.839 22.695 2430 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 6.73 % Allowed : 16.15 % Favored : 77.12 % 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: -1.05 (0.17), residues: 2258 helix: -0.03 (0.14), residues: 1280 sheet: -1.83 (0.32), residues: 182 loop : -1.35 (0.19), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 147 TYR 0.013 0.002 TYR D 78 PHE 0.016 0.002 PHE J 102 HIS 0.016 0.004 HIS D 123 Details of bonding type rmsd covalent geometry : bond 0.00544 (17248) covalent geometry : angle 0.65741 (23308) hydrogen bonds : bond 0.03162 ( 844) hydrogen bonds : angle 4.45019 ( 2568) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 676 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 31 MET cc_start: 0.7045 (OUTLIER) cc_final: 0.6662 (mmm) REVERT: D 85 LYS cc_start: 0.8694 (mmtt) cc_final: 0.8180 (mmtm) REVERT: D 98 SER cc_start: 0.8682 (t) cc_final: 0.8345 (m) REVERT: E 42 ASN cc_start: 0.8509 (m-40) cc_final: 0.8267 (m-40) REVERT: E 113 PHE cc_start: 0.8518 (m-80) cc_final: 0.8305 (m-80) REVERT: E 145 LYS cc_start: 0.8703 (mtpp) cc_final: 0.8268 (mtmm) REVERT: F 51 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8437 (mp) REVERT: G 40 VAL cc_start: 0.9343 (m) cc_final: 0.8989 (p) REVERT: G 59 ASP cc_start: 0.7447 (p0) cc_final: 0.6619 (p0) REVERT: G 89 GLN cc_start: 0.8762 (mt0) cc_final: 0.8346 (mt0) REVERT: G 147 ARG cc_start: 0.8930 (tpt-90) cc_final: 0.8628 (tpp-160) REVERT: G 160 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7405 (mp10) REVERT: G 170 ASP cc_start: 0.7191 (t0) cc_final: 0.6259 (t0) REVERT: G 176 THR cc_start: 0.9419 (t) cc_final: 0.9152 (t) REVERT: G 178 GLU cc_start: 0.8000 (mp0) cc_final: 0.7538 (mp0) REVERT: G 188 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7531 (tm-30) REVERT: I 70 SER cc_start: 0.8116 (t) cc_final: 0.7617 (p) REVERT: I 78 TYR cc_start: 0.8513 (t80) cc_final: 0.8282 (t80) REVERT: I 113 PHE cc_start: 0.8037 (m-10) cc_final: 0.7807 (m-80) REVERT: I 173 ASN cc_start: 0.8319 (t0) cc_final: 0.8112 (t0) REVERT: L 113 PHE cc_start: 0.8488 (m-80) cc_final: 0.8288 (m-80) REVERT: M 117 ASN cc_start: 0.8133 (t0) cc_final: 0.7775 (t0) REVERT: M 119 GLU cc_start: 0.7473 (tm-30) cc_final: 0.7172 (tm-30) REVERT: M 178 GLU cc_start: 0.8186 (tp30) cc_final: 0.7953 (mm-30) REVERT: N 27 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.8199 (p0) REVERT: N 28 ARG cc_start: 0.8479 (mtp85) cc_final: 0.7954 (mtt-85) REVERT: N 59 ASP cc_start: 0.7598 (p0) cc_final: 0.7011 (p0) REVERT: N 89 GLN cc_start: 0.8767 (mt0) cc_final: 0.8537 (mt0) REVERT: N 111 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8497 (mmmm) REVERT: N 151 ASN cc_start: 0.9233 (m-40) cc_final: 0.8944 (m-40) REVERT: N 160 GLN cc_start: 0.8096 (mm110) cc_final: 0.7638 (mp10) REVERT: N 165 ILE cc_start: 0.7800 (mm) cc_final: 0.7414 (mm) REVERT: N 178 GLU cc_start: 0.8229 (mp0) cc_final: 0.7922 (mp0) REVERT: N 183 TYR cc_start: 0.8316 (t80) cc_final: 0.8018 (t80) outliers start: 113 outliers final: 82 residues processed: 727 average time/residue: 0.1290 time to fit residues: 143.2562 Evaluate side-chains 727 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 641 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 31 MET Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 123 HIS Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 123 HIS Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain I residue 148 GLU Chi-restraints excluded: chain I residue 191 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain K residue 161 SER Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 123 HIS Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 168 ASP Chi-restraints excluded: chain J residue 173 ASN Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 123 HIS Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 93 ILE Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 138 ILE Chi-restraints excluded: chain M residue 189 VAL Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 98 SER Chi-restraints excluded: chain N residue 111 LYS Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 123 HIS Chi-restraints excluded: chain N residue 146 THR Chi-restraints excluded: chain N residue 148 GLU Chi-restraints excluded: chain N residue 155 SER Chi-restraints excluded: chain N residue 162 ILE Chi-restraints excluded: chain N residue 189 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 103 optimal weight: 9.9990 chunk 192 optimal weight: 7.9990 chunk 113 optimal weight: 0.4980 chunk 78 optimal weight: 10.0000 chunk 222 optimal weight: 20.0000 chunk 76 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 126 optimal weight: 8.9990 chunk 147 optimal weight: 2.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 HIS D 42 ASN C 42 ASN C 89 GLN C 123 HIS C 166 GLN C 173 ASN F 52 GLN I 83 HIS K 123 HIS J 42 ASN J 166 GLN J 173 ASN L 42 ASN M 42 ASN M 47 GLN M 52 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.147836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.124271 restraints weight = 25995.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.127389 restraints weight = 13813.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.129363 restraints weight = 8675.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.130612 restraints weight = 6227.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.131472 restraints weight = 4944.426| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17248 Z= 0.191 Angle : 0.619 9.545 23308 Z= 0.321 Chirality : 0.045 0.197 2760 Planarity : 0.005 0.060 3052 Dihedral : 4.689 20.610 2430 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 7.33 % Allowed : 18.65 % Favored : 74.02 % 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: -0.69 (0.17), residues: 2258 helix: 0.19 (0.14), residues: 1300 sheet: -1.49 (0.34), residues: 182 loop : -1.13 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 171 TYR 0.012 0.001 TYR D 78 PHE 0.015 0.002 PHE N 102 HIS 0.013 0.003 HIS J 123 Details of bonding type rmsd covalent geometry : bond 0.00453 (17248) covalent geometry : angle 0.61933 (23308) hydrogen bonds : bond 0.02976 ( 844) hydrogen bonds : angle 4.16958 ( 2568) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 665 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 65 ASN cc_start: 0.7801 (t0) cc_final: 0.7569 (t0) REVERT: D 98 SER cc_start: 0.8715 (t) cc_final: 0.8433 (m) REVERT: E 42 ASN cc_start: 0.8406 (m-40) cc_final: 0.8196 (m-40) REVERT: F 27 ASP cc_start: 0.8276 (t0) cc_final: 0.7832 (t0) REVERT: F 117 ASN cc_start: 0.8354 (t0) cc_final: 0.6247 (t0) REVERT: G 27 ASP cc_start: 0.8197 (p0) cc_final: 0.7530 (p0) REVERT: G 47 GLN cc_start: 0.8672 (mt0) cc_final: 0.8308 (mp10) REVERT: G 59 ASP cc_start: 0.7550 (p0) cc_final: 0.6905 (p0) REVERT: G 75 PHE cc_start: 0.8897 (m-10) cc_final: 0.8622 (m-80) REVERT: G 89 GLN cc_start: 0.8735 (mt0) cc_final: 0.8358 (mt0) REVERT: G 95 MET cc_start: 0.7266 (tpp) cc_final: 0.6606 (tpp) REVERT: G 160 GLN cc_start: 0.7884 (mm-40) cc_final: 0.7387 (mp10) REVERT: G 176 THR cc_start: 0.9305 (t) cc_final: 0.9008 (t) REVERT: G 178 GLU cc_start: 0.7981 (mp0) cc_final: 0.7538 (mp0) REVERT: G 183 TYR cc_start: 0.8492 (t80) cc_final: 0.8203 (t80) REVERT: G 188 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7688 (tm-30) REVERT: I 20 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.7913 (mt) REVERT: I 70 SER cc_start: 0.8180 (t) cc_final: 0.7675 (p) REVERT: I 113 PHE cc_start: 0.7957 (m-10) cc_final: 0.7714 (m-80) REVERT: I 167 LYS cc_start: 0.8598 (tptt) cc_final: 0.8178 (tptt) REVERT: J 34 SER cc_start: 0.9112 (p) cc_final: 0.8725 (m) REVERT: J 85 LYS cc_start: 0.7809 (mptt) cc_final: 0.7308 (mtmm) REVERT: L 27 ASP cc_start: 0.8041 (t70) cc_final: 0.7553 (t0) REVERT: L 64 ILE cc_start: 0.9159 (mm) cc_final: 0.8834 (mt) REVERT: M 27 ASP cc_start: 0.8309 (t0) cc_final: 0.7984 (t0) REVERT: M 47 GLN cc_start: 0.8340 (mt0) cc_final: 0.8109 (mt0) REVERT: M 117 ASN cc_start: 0.8058 (t0) cc_final: 0.7691 (t0) REVERT: N 28 ARG cc_start: 0.8645 (mtp85) cc_final: 0.8145 (mtt-85) REVERT: N 59 ASP cc_start: 0.7600 (p0) cc_final: 0.6823 (p0) REVERT: N 78 TYR cc_start: 0.9171 (t80) cc_final: 0.8550 (t80) REVERT: N 82 GLN cc_start: 0.8267 (mp10) cc_final: 0.7783 (mp10) REVERT: N 89 GLN cc_start: 0.8646 (mt0) cc_final: 0.8258 (mt0) REVERT: N 111 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8404 (mmmm) REVERT: N 151 ASN cc_start: 0.9125 (m-40) cc_final: 0.8910 (m-40) REVERT: N 160 GLN cc_start: 0.8048 (mm110) cc_final: 0.7588 (mp10) REVERT: N 165 ILE cc_start: 0.7867 (mm) cc_final: 0.7434 (mm) REVERT: N 178 GLU cc_start: 0.8196 (mp0) cc_final: 0.7912 (mp0) outliers start: 123 outliers final: 92 residues processed: 715 average time/residue: 0.1298 time to fit residues: 141.8247 Evaluate side-chains 738 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 644 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 123 HIS Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 123 HIS Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 123 HIS Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 123 HIS Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain I residue 122 ILE Chi-restraints excluded: chain I residue 148 GLU Chi-restraints excluded: chain I residue 191 VAL Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 123 HIS Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain J residue 42 ASN Chi-restraints excluded: chain J residue 43 SER Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 123 HIS Chi-restraints excluded: chain J residue 161 SER Chi-restraints excluded: chain J residue 168 ASP Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 121 MET Chi-restraints excluded: chain L residue 123 HIS Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 148 GLU Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 93 ILE Chi-restraints excluded: chain M residue 115 LEU Chi-restraints excluded: chain M residue 123 HIS Chi-restraints excluded: chain M residue 138 ILE Chi-restraints excluded: chain M residue 189 VAL Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 98 SER Chi-restraints excluded: chain N residue 111 LYS Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 123 HIS Chi-restraints excluded: chain N residue 146 THR Chi-restraints excluded: chain N residue 148 GLU Chi-restraints excluded: chain N residue 155 SER Chi-restraints excluded: chain N residue 162 ILE Chi-restraints excluded: chain N residue 189 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 5 optimal weight: 6.9990 chunk 201 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 137 optimal weight: 4.9990 chunk 35 optimal weight: 0.0970 chunk 191 optimal weight: 5.9990 chunk 173 optimal weight: 30.0000 chunk 140 optimal weight: 5.9990 chunk 174 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 HIS C 42 ASN C 123 HIS E 142 HIS F 52 GLN ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 HIS ** K 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 123 HIS J 42 ASN ** J 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 142 HIS J 166 GLN M 52 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.144957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.121400 restraints weight = 25927.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.124382 restraints weight = 14119.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.126279 restraints weight = 9028.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.127463 restraints weight = 6533.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.128291 restraints weight = 5218.066| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 17248 Z= 0.272 Angle : 0.687 8.725 23308 Z= 0.356 Chirality : 0.048 0.223 2760 Planarity : 0.005 0.057 3052 Dihedral : 4.953 19.608 2430 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 9.06 % Allowed : 20.02 % Favored : 70.92 % 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: -1.02 (0.17), residues: 2258 helix: 0.06 (0.14), residues: 1316 sheet: -1.66 (0.30), residues: 258 loop : -1.50 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 171 TYR 0.014 0.002 TYR D 78 PHE 0.029 0.003 PHE L 113 HIS 0.015 0.003 HIS J 123 Details of bonding type rmsd covalent geometry : bond 0.00639 (17248) covalent geometry : angle 0.68708 (23308) hydrogen bonds : bond 0.03260 ( 844) hydrogen bonds : angle 4.45151 ( 2568) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 684 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8261 (tp) REVERT: D 20 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.8063 (tp) REVERT: D 98 SER cc_start: 0.8789 (t) cc_final: 0.8490 (m) REVERT: E 22 SER cc_start: 0.9036 (m) cc_final: 0.8604 (p) REVERT: E 27 ASP cc_start: 0.7924 (t70) cc_final: 0.7476 (t0) REVERT: F 27 ASP cc_start: 0.8380 (t0) cc_final: 0.7996 (t0) REVERT: F 47 GLN cc_start: 0.8388 (mt0) cc_final: 0.7870 (mt0) REVERT: F 51 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8479 (mp) REVERT: F 52 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.7494 (tt0) REVERT: F 117 ASN cc_start: 0.8412 (t0) cc_final: 0.8052 (t0) REVERT: F 188 GLU cc_start: 0.8109 (tt0) cc_final: 0.7905 (tt0) REVERT: G 27 ASP cc_start: 0.8276 (p0) cc_final: 0.7674 (p0) REVERT: G 47 GLN cc_start: 0.8728 (mt0) cc_final: 0.8384 (mp10) REVERT: G 59 ASP cc_start: 0.7557 (p0) cc_final: 0.6918 (p0) REVERT: G 89 GLN cc_start: 0.8768 (mt0) cc_final: 0.8403 (mt0) REVERT: G 160 GLN cc_start: 0.7928 (mm-40) cc_final: 0.7402 (mp10) REVERT: G 167 LYS cc_start: 0.8702 (mtmm) cc_final: 0.8499 (mtmm) REVERT: G 168 ASP cc_start: 0.7837 (p0) cc_final: 0.7585 (p0) REVERT: G 176 THR cc_start: 0.9379 (t) cc_final: 0.9108 (t) REVERT: G 178 GLU cc_start: 0.8045 (mp0) cc_final: 0.7595 (mp0) REVERT: I 70 SER cc_start: 0.8306 (t) cc_final: 0.7811 (p) REVERT: I 167 LYS cc_start: 0.8648 (tptt) cc_final: 0.8263 (ttpp) REVERT: K 20 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8101 (tp) REVERT: K 102 PHE cc_start: 0.8683 (t80) cc_final: 0.8360 (t80) REVERT: J 34 SER cc_start: 0.9333 (OUTLIER) cc_final: 0.9040 (m) REVERT: J 85 LYS cc_start: 0.7696 (mptt) cc_final: 0.7204 (mtmm) REVERT: L 22 SER cc_start: 0.9032 (m) cc_final: 0.8699 (p) REVERT: L 27 ASP cc_start: 0.7986 (t70) cc_final: 0.7515 (t0) REVERT: L 64 ILE cc_start: 0.9191 (mm) cc_final: 0.8830 (mt) REVERT: L 167 LYS cc_start: 0.8637 (ttmt) cc_final: 0.8380 (mtmt) REVERT: M 27 ASP cc_start: 0.8347 (t0) cc_final: 0.8009 (t0) REVERT: M 43 SER cc_start: 0.9245 (t) cc_final: 0.8866 (t) REVERT: M 47 GLN cc_start: 0.8456 (mt0) cc_final: 0.8215 (mt0) REVERT: M 117 ASN cc_start: 0.8146 (t0) cc_final: 0.7699 (t0) REVERT: M 156 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7184 (tt0) REVERT: M 178 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7535 (mm-30) REVERT: N 27 ASP cc_start: 0.8378 (p0) cc_final: 0.7599 (p0) REVERT: N 28 ARG cc_start: 0.8655 (mtp85) cc_final: 0.8179 (mtt90) REVERT: N 47 GLN cc_start: 0.8807 (mt0) cc_final: 0.8602 (mp10) REVERT: N 59 ASP cc_start: 0.7607 (p0) cc_final: 0.6866 (p0) REVERT: N 89 GLN cc_start: 0.8703 (mt0) cc_final: 0.8359 (mt0) REVERT: N 95 MET cc_start: 0.7395 (tpp) cc_final: 0.6957 (tpp) REVERT: N 98 SER cc_start: 0.9002 (OUTLIER) cc_final: 0.8678 (t) REVERT: N 111 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8369 (mmmm) REVERT: N 160 GLN cc_start: 0.8103 (mm110) cc_final: 0.7601 (mp10) REVERT: N 170 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7941 (m-30) outliers start: 152 outliers final: 114 residues processed: 743 average time/residue: 0.1291 time to fit residues: 147.0281 Evaluate side-chains 768 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 645 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 31 MET Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain C residue 31 MET Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 123 HIS Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 123 HIS Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 52 GLN Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 123 HIS Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 123 HIS Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 164 LYS Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain I residue 122 ILE Chi-restraints excluded: chain I residue 148 GLU Chi-restraints excluded: chain I residue 161 SER Chi-restraints excluded: chain I residue 191 VAL Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 123 HIS Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain K residue 156 GLU Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 42 ASN Chi-restraints excluded: chain J residue 43 SER Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 123 HIS Chi-restraints excluded: chain J residue 161 SER Chi-restraints excluded: chain J residue 168 ASP Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 121 MET Chi-restraints excluded: chain L residue 123 HIS Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 148 GLU Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 93 ILE Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 115 LEU Chi-restraints excluded: chain M residue 123 HIS Chi-restraints excluded: chain M residue 138 ILE Chi-restraints excluded: chain M residue 189 VAL Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 98 SER Chi-restraints excluded: chain N residue 111 LYS Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 123 HIS Chi-restraints excluded: chain N residue 146 THR Chi-restraints excluded: chain N residue 148 GLU Chi-restraints excluded: chain N residue 155 SER Chi-restraints excluded: chain N residue 162 ILE Chi-restraints excluded: chain N residue 170 ASP Chi-restraints excluded: chain N residue 189 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 221 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 191 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 168 optimal weight: 30.0000 chunk 216 optimal weight: 10.0000 chunk 35 optimal weight: 0.1980 chunk 218 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 212 optimal weight: 6.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 HIS B 124 GLN C 42 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 GLN G 142 HIS ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 HIS ** I 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 42 ASN L 42 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.149543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.126218 restraints weight = 25770.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.129319 restraints weight = 13684.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.131278 restraints weight = 8582.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.132564 restraints weight = 6143.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.133301 restraints weight = 4860.304| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.5403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17248 Z= 0.133 Angle : 0.583 9.004 23308 Z= 0.303 Chirality : 0.044 0.233 2760 Planarity : 0.004 0.060 3052 Dihedral : 4.452 20.229 2430 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 6.20 % Allowed : 23.72 % Favored : 70.08 % 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: -0.44 (0.18), residues: 2258 helix: 0.47 (0.15), residues: 1316 sheet: -1.57 (0.30), residues: 268 loop : -1.03 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 23 TYR 0.011 0.001 TYR D 78 PHE 0.021 0.002 PHE L 113 HIS 0.017 0.003 HIS I 123 Details of bonding type rmsd covalent geometry : bond 0.00312 (17248) covalent geometry : angle 0.58335 (23308) hydrogen bonds : bond 0.02725 ( 844) hydrogen bonds : angle 3.91131 ( 2568) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 663 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8211 (tp) REVERT: D 20 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8045 (tp) REVERT: D 98 SER cc_start: 0.8653 (t) cc_final: 0.8371 (m) REVERT: D 156 GLU cc_start: 0.6608 (OUTLIER) cc_final: 0.6129 (tt0) REVERT: D 181 LYS cc_start: 0.7531 (tttp) cc_final: 0.7082 (ttpt) REVERT: C 171 ARG cc_start: 0.8304 (ptm-80) cc_final: 0.7909 (ptm-80) REVERT: E 27 ASP cc_start: 0.7941 (t70) cc_final: 0.7471 (t0) REVERT: E 54 GLN cc_start: 0.8274 (mm110) cc_final: 0.7211 (tt0) REVERT: F 27 ASP cc_start: 0.8374 (t0) cc_final: 0.7853 (t0) REVERT: F 51 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8347 (mp) REVERT: F 52 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7406 (tt0) REVERT: F 111 LYS cc_start: 0.7899 (mmmm) cc_final: 0.7696 (mmmm) REVERT: F 117 ASN cc_start: 0.8413 (t0) cc_final: 0.6588 (t0) REVERT: F 165 ILE cc_start: 0.8111 (mm) cc_final: 0.7855 (mm) REVERT: F 189 VAL cc_start: 0.9009 (OUTLIER) cc_final: 0.8789 (m) REVERT: G 27 ASP cc_start: 0.8251 (p0) cc_final: 0.7596 (p0) REVERT: G 28 ARG cc_start: 0.8528 (mtp85) cc_final: 0.8244 (mtt90) REVERT: G 49 LEU cc_start: 0.9170 (mp) cc_final: 0.8939 (mm) REVERT: G 59 ASP cc_start: 0.7594 (p0) cc_final: 0.6962 (p0) REVERT: G 75 PHE cc_start: 0.8924 (m-10) cc_final: 0.8478 (m-10) REVERT: G 78 TYR cc_start: 0.9109 (t80) cc_final: 0.8890 (t80) REVERT: G 82 GLN cc_start: 0.8127 (mp10) cc_final: 0.7875 (mp10) REVERT: G 89 GLN cc_start: 0.8728 (mt0) cc_final: 0.8387 (mt0) REVERT: G 160 GLN cc_start: 0.7842 (mm-40) cc_final: 0.7402 (mp10) REVERT: G 178 GLU cc_start: 0.7980 (mp0) cc_final: 0.7558 (mp0) REVERT: G 183 TYR cc_start: 0.8431 (t80) cc_final: 0.8118 (t80) REVERT: G 188 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7718 (tm-30) REVERT: I 113 PHE cc_start: 0.7949 (m-10) cc_final: 0.7661 (m-80) REVERT: I 167 LYS cc_start: 0.8565 (tptt) cc_final: 0.8134 (ttpp) REVERT: K 20 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8120 (tp) REVERT: K 146 THR cc_start: 0.8554 (m) cc_final: 0.8278 (m) REVERT: J 85 LYS cc_start: 0.7862 (mptt) cc_final: 0.7385 (mtmm) REVERT: L 22 SER cc_start: 0.8983 (m) cc_final: 0.8609 (p) REVERT: L 27 ASP cc_start: 0.7982 (t70) cc_final: 0.7499 (t0) REVERT: L 64 ILE cc_start: 0.9139 (mm) cc_final: 0.8810 (mt) REVERT: L 167 LYS cc_start: 0.8698 (ttmt) cc_final: 0.8300 (mtmt) REVERT: L 182 GLU cc_start: 0.6745 (OUTLIER) cc_final: 0.5896 (mp0) REVERT: M 27 ASP cc_start: 0.8300 (t0) cc_final: 0.7813 (t0) REVERT: M 117 ASN cc_start: 0.8081 (t0) cc_final: 0.7458 (t0) REVERT: M 156 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7258 (tt0) REVERT: N 27 ASP cc_start: 0.8342 (p0) cc_final: 0.7563 (p0) REVERT: N 28 ARG cc_start: 0.8583 (mtp85) cc_final: 0.7755 (mmt90) REVERT: N 47 GLN cc_start: 0.8687 (mt0) cc_final: 0.8479 (mp10) REVERT: N 59 ASP cc_start: 0.7392 (p0) cc_final: 0.6968 (p0) REVERT: N 89 GLN cc_start: 0.8689 (mt0) cc_final: 0.8322 (mt0) REVERT: N 98 SER cc_start: 0.9047 (OUTLIER) cc_final: 0.8728 (t) REVERT: N 111 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8340 (mmmm) REVERT: N 160 GLN cc_start: 0.8053 (mm110) cc_final: 0.7522 (mp10) REVERT: N 170 ASP cc_start: 0.8329 (OUTLIER) cc_final: 0.7987 (m-30) REVERT: N 178 GLU cc_start: 0.8211 (mp0) cc_final: 0.7747 (mp0) outliers start: 104 outliers final: 68 residues processed: 705 average time/residue: 0.1321 time to fit residues: 140.8569 Evaluate side-chains 711 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 632 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 123 HIS Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 52 GLN Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 123 HIS Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 123 HIS Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 164 LYS Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain I residue 148 GLU Chi-restraints excluded: chain I residue 191 VAL Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain J residue 38 ASP Chi-restraints excluded: chain J residue 43 SER Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 123 HIS Chi-restraints excluded: chain J residue 161 SER Chi-restraints excluded: chain J residue 176 THR Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 123 HIS Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 148 GLU Chi-restraints excluded: chain L residue 182 GLU Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain M residue 75 PHE Chi-restraints excluded: chain M residue 123 HIS Chi-restraints excluded: chain M residue 138 ILE Chi-restraints excluded: chain M residue 189 VAL Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 98 SER Chi-restraints excluded: chain N residue 111 LYS Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 119 GLU Chi-restraints excluded: chain N residue 123 HIS Chi-restraints excluded: chain N residue 155 SER Chi-restraints excluded: chain N residue 170 ASP Chi-restraints excluded: chain N residue 189 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 78 optimal weight: 10.0000 chunk 189 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 chunk 212 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 223 optimal weight: 20.0000 chunk 205 optimal weight: 0.0060 chunk 0 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 overall best weight: 1.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 HIS B 124 GLN C 42 ASN C 142 HIS ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 GLN ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 HIS ** I 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 123 HIS J 42 ASN J 166 GLN L 142 HIS M 47 GLN M 52 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.148804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.125515 restraints weight = 25732.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.128531 restraints weight = 13808.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.130498 restraints weight = 8786.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.131763 restraints weight = 6294.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.132497 restraints weight = 4990.283| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.5532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17248 Z= 0.157 Angle : 0.606 10.774 23308 Z= 0.312 Chirality : 0.045 0.254 2760 Planarity : 0.004 0.053 3052 Dihedral : 4.411 18.343 2430 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 6.38 % Allowed : 23.48 % Favored : 70.14 % 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: -0.38 (0.18), residues: 2258 helix: 0.49 (0.15), residues: 1326 sheet: -1.48 (0.31), residues: 268 loop : -1.00 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 152 TYR 0.016 0.001 TYR K 78 PHE 0.026 0.002 PHE G 50 HIS 0.020 0.004 HIS K 123 Details of bonding type rmsd covalent geometry : bond 0.00373 (17248) covalent geometry : angle 0.60574 (23308) hydrogen bonds : bond 0.02758 ( 844) hydrogen bonds : angle 3.94763 ( 2568) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 660 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 LYS cc_start: 0.7188 (mmtm) cc_final: 0.6867 (mmtp) REVERT: D 20 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.8090 (tp) REVERT: D 31 MET cc_start: 0.7024 (OUTLIER) cc_final: 0.6637 (mmm) REVERT: D 98 SER cc_start: 0.8699 (t) cc_final: 0.8359 (m) REVERT: D 156 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.6134 (tt0) REVERT: D 181 LYS cc_start: 0.7578 (tttp) cc_final: 0.7117 (ttpt) REVERT: C 171 ARG cc_start: 0.8240 (ptm-80) cc_final: 0.7850 (ptm-80) REVERT: E 27 ASP cc_start: 0.7967 (t70) cc_final: 0.7504 (t0) REVERT: E 54 GLN cc_start: 0.8337 (mm110) cc_final: 0.7288 (tt0) REVERT: E 167 LYS cc_start: 0.8703 (ttmt) cc_final: 0.8063 (mtmm) REVERT: F 27 ASP cc_start: 0.8410 (t0) cc_final: 0.7851 (t0) REVERT: F 47 GLN cc_start: 0.8331 (mt0) cc_final: 0.7851 (mt0) REVERT: F 51 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8393 (mp) REVERT: F 52 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7522 (tt0) REVERT: F 117 ASN cc_start: 0.8430 (t0) cc_final: 0.6432 (t0) REVERT: F 156 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7290 (tt0) REVERT: G 27 ASP cc_start: 0.8290 (p0) cc_final: 0.7634 (p0) REVERT: G 28 ARG cc_start: 0.8506 (mtp85) cc_final: 0.8273 (mtt90) REVERT: G 47 GLN cc_start: 0.8702 (mt0) cc_final: 0.8321 (mp10) REVERT: G 59 ASP cc_start: 0.7610 (p0) cc_final: 0.7035 (p0) REVERT: G 75 PHE cc_start: 0.8917 (m-10) cc_final: 0.8393 (m-80) REVERT: G 78 TYR cc_start: 0.9080 (t80) cc_final: 0.8861 (t80) REVERT: G 82 GLN cc_start: 0.8138 (mp10) cc_final: 0.7807 (mp10) REVERT: G 89 GLN cc_start: 0.8743 (mt0) cc_final: 0.8403 (mt0) REVERT: G 160 GLN cc_start: 0.7858 (mm-40) cc_final: 0.7409 (mp10) REVERT: G 178 GLU cc_start: 0.8020 (mp0) cc_final: 0.7587 (mp0) REVERT: G 183 TYR cc_start: 0.8484 (t80) cc_final: 0.8119 (t80) REVERT: G 188 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7567 (tm-30) REVERT: G 190 MET cc_start: 0.6851 (ttm) cc_final: 0.6631 (tpp) REVERT: I 167 LYS cc_start: 0.8671 (tptt) cc_final: 0.8241 (ttpp) REVERT: K 20 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8143 (tp) REVERT: K 31 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.6806 (mmm) REVERT: K 146 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8357 (m) REVERT: J 85 LYS cc_start: 0.7845 (mptt) cc_final: 0.7392 (mtmm) REVERT: L 22 SER cc_start: 0.9007 (m) cc_final: 0.8651 (p) REVERT: L 27 ASP cc_start: 0.8015 (t70) cc_final: 0.7466 (t0) REVERT: L 64 ILE cc_start: 0.9194 (mm) cc_final: 0.8823 (mt) REVERT: L 167 LYS cc_start: 0.8670 (ttmt) cc_final: 0.8320 (mtmt) REVERT: L 182 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.5919 (mp0) REVERT: M 27 ASP cc_start: 0.8358 (t0) cc_final: 0.7861 (t0) REVERT: M 47 GLN cc_start: 0.8375 (mt0) cc_final: 0.8086 (mt0) REVERT: M 117 ASN cc_start: 0.8382 (t0) cc_final: 0.7973 (t0) REVERT: M 156 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7260 (tt0) REVERT: N 27 ASP cc_start: 0.8426 (p0) cc_final: 0.7670 (p0) REVERT: N 28 ARG cc_start: 0.8594 (mtp85) cc_final: 0.8315 (mtt90) REVERT: N 59 ASP cc_start: 0.7405 (p0) cc_final: 0.6791 (p0) REVERT: N 78 TYR cc_start: 0.9092 (t80) cc_final: 0.8683 (t80) REVERT: N 82 GLN cc_start: 0.8168 (mm-40) cc_final: 0.7596 (mp10) REVERT: N 89 GLN cc_start: 0.8673 (mt0) cc_final: 0.8299 (mt0) REVERT: N 160 GLN cc_start: 0.8112 (mm110) cc_final: 0.7526 (mp10) REVERT: N 170 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.7997 (m-30) REVERT: N 173 ASN cc_start: 0.7976 (m110) cc_final: 0.7326 (m-40) outliers start: 107 outliers final: 86 residues processed: 706 average time/residue: 0.1296 time to fit residues: 140.2196 Evaluate side-chains 723 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 627 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 31 MET Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 123 HIS Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 52 GLN Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 123 HIS Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 123 HIS Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 148 GLU Chi-restraints excluded: chain G residue 164 LYS Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain I residue 148 GLU Chi-restraints excluded: chain I residue 150 LEU Chi-restraints excluded: chain I residue 161 SER Chi-restraints excluded: chain I residue 191 VAL Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 31 MET Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 146 THR Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain J residue 42 ASN Chi-restraints excluded: chain J residue 43 SER Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 123 HIS Chi-restraints excluded: chain J residue 161 SER Chi-restraints excluded: chain J residue 168 ASP Chi-restraints excluded: chain J residue 176 THR Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 123 HIS Chi-restraints excluded: chain L residue 148 GLU Chi-restraints excluded: chain L residue 182 GLU Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 75 PHE Chi-restraints excluded: chain M residue 115 LEU Chi-restraints excluded: chain M residue 123 HIS Chi-restraints excluded: chain M residue 138 ILE Chi-restraints excluded: chain M residue 189 VAL Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 111 LYS Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 119 GLU Chi-restraints excluded: chain N residue 136 ILE Chi-restraints excluded: chain N residue 148 GLU Chi-restraints excluded: chain N residue 155 SER Chi-restraints excluded: chain N residue 162 ILE Chi-restraints excluded: chain N residue 170 ASP Chi-restraints excluded: chain N residue 189 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 192 optimal weight: 6.9990 chunk 212 optimal weight: 20.0000 chunk 26 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 96 optimal weight: 20.0000 chunk 208 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 223 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 HIS ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 ASN ** C 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 GLN I 83 HIS ** I 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 GLN J 42 ASN J 117 ASN ** J 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 166 GLN L 42 ASN ** L 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.142860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.119018 restraints weight = 26231.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.122013 restraints weight = 14315.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.123903 restraints weight = 9149.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.125213 restraints weight = 6631.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.126010 restraints weight = 5241.113| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.5614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.064 17248 Z= 0.364 Angle : 0.798 12.960 23308 Z= 0.416 Chirality : 0.052 0.301 2760 Planarity : 0.006 0.068 3052 Dihedral : 5.278 22.543 2430 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 7.99 % Allowed : 23.36 % Favored : 68.65 % 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: -1.11 (0.18), residues: 2258 helix: 0.08 (0.15), residues: 1294 sheet: -1.81 (0.31), residues: 258 loop : -1.65 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 152 TYR 0.019 0.002 TYR D 78 PHE 0.021 0.003 PHE B 174 HIS 0.018 0.004 HIS B 123 Details of bonding type rmsd covalent geometry : bond 0.00850 (17248) covalent geometry : angle 0.79760 (23308) hydrogen bonds : bond 0.03608 ( 844) hydrogen bonds : angle 4.77431 ( 2568) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 667 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 PHE cc_start: 0.8137 (m-10) cc_final: 0.7868 (m-80) REVERT: D 20 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8151 (tp) REVERT: D 98 SER cc_start: 0.8783 (t) cc_final: 0.8464 (m) REVERT: D 167 LYS cc_start: 0.8657 (ttmt) cc_final: 0.7897 (ttpp) REVERT: D 181 LYS cc_start: 0.7841 (tttp) cc_final: 0.7469 (ttpt) REVERT: C 171 ARG cc_start: 0.8310 (ptm-80) cc_final: 0.8104 (ptm160) REVERT: E 22 SER cc_start: 0.9074 (m) cc_final: 0.8660 (p) REVERT: E 27 ASP cc_start: 0.7965 (t70) cc_final: 0.7345 (t0) REVERT: E 167 LYS cc_start: 0.8885 (ttmt) cc_final: 0.8284 (mtmm) REVERT: F 51 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8485 (mp) REVERT: F 52 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7559 (tt0) REVERT: F 117 ASN cc_start: 0.8503 (t0) cc_final: 0.8091 (t0) REVERT: F 121 MET cc_start: 0.7917 (mmm) cc_final: 0.7611 (mtt) REVERT: G 27 ASP cc_start: 0.8403 (p0) cc_final: 0.7898 (p0) REVERT: G 28 ARG cc_start: 0.8510 (mtp85) cc_final: 0.8201 (mtt90) REVERT: G 59 ASP cc_start: 0.7594 (p0) cc_final: 0.7052 (p0) REVERT: G 87 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.6843 (p0) REVERT: G 89 GLN cc_start: 0.8792 (mt0) cc_final: 0.8350 (mt0) REVERT: G 95 MET cc_start: 0.7236 (tpp) cc_final: 0.6566 (tpp) REVERT: G 160 GLN cc_start: 0.7984 (mm-40) cc_final: 0.7405 (mp10) REVERT: G 168 ASP cc_start: 0.7899 (p0) cc_final: 0.7691 (p0) REVERT: G 178 GLU cc_start: 0.8068 (mp0) cc_final: 0.7666 (mp0) REVERT: G 188 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7286 (tm-30) REVERT: I 70 SER cc_start: 0.8395 (t) cc_final: 0.7902 (p) REVERT: I 167 LYS cc_start: 0.8598 (tptt) cc_final: 0.8391 (tptp) REVERT: K 20 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8167 (tp) REVERT: K 146 THR cc_start: 0.8649 (m) cc_final: 0.8392 (m) REVERT: J 85 LYS cc_start: 0.7641 (mptt) cc_final: 0.7192 (mtmm) REVERT: L 22 SER cc_start: 0.9113 (m) cc_final: 0.8764 (p) REVERT: L 27 ASP cc_start: 0.7987 (t70) cc_final: 0.7450 (t0) REVERT: L 64 ILE cc_start: 0.9236 (mm) cc_final: 0.8913 (mt) REVERT: L 167 LYS cc_start: 0.8720 (ttmt) cc_final: 0.8385 (mtmt) REVERT: L 182 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.5958 (mp0) REVERT: M 27 ASP cc_start: 0.8379 (t0) cc_final: 0.7870 (t0) REVERT: M 117 ASN cc_start: 0.8362 (t0) cc_final: 0.7882 (t0) REVERT: M 156 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7321 (tt0) REVERT: N 28 ARG cc_start: 0.8641 (mtp85) cc_final: 0.7825 (mmt90) REVERT: N 47 GLN cc_start: 0.8858 (mt0) cc_final: 0.8617 (mp10) REVERT: N 59 ASP cc_start: 0.7374 (p0) cc_final: 0.7067 (p0) REVERT: N 89 GLN cc_start: 0.8706 (mt0) cc_final: 0.8289 (mt0) REVERT: N 115 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8118 (tt) REVERT: N 121 MET cc_start: 0.7038 (mmm) cc_final: 0.6811 (mmt) REVERT: N 160 GLN cc_start: 0.8113 (mm110) cc_final: 0.7534 (mp10) REVERT: N 170 ASP cc_start: 0.8237 (m-30) cc_final: 0.7968 (m-30) REVERT: N 183 TYR cc_start: 0.8366 (t80) cc_final: 0.7904 (t80) outliers start: 134 outliers final: 105 residues processed: 729 average time/residue: 0.1275 time to fit residues: 141.2429 Evaluate side-chains 736 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 624 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 31 MET Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 123 HIS Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 123 HIS Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 52 GLN Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 123 HIS Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 123 HIS Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 148 GLU Chi-restraints excluded: chain G residue 162 ILE Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain I residue 148 GLU Chi-restraints excluded: chain I residue 161 SER Chi-restraints excluded: chain I residue 162 ILE Chi-restraints excluded: chain I residue 191 VAL Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 31 MET Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 161 SER Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain J residue 43 SER Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 123 HIS Chi-restraints excluded: chain J residue 161 SER Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 123 HIS Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 148 GLU Chi-restraints excluded: chain L residue 182 GLU Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 81 ILE Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 115 LEU Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 123 HIS Chi-restraints excluded: chain M residue 138 ILE Chi-restraints excluded: chain M residue 189 VAL Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 37 ASP Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 119 GLU Chi-restraints excluded: chain N residue 123 HIS Chi-restraints excluded: chain N residue 148 GLU Chi-restraints excluded: chain N residue 155 SER Chi-restraints excluded: chain N residue 162 ILE Chi-restraints excluded: chain N residue 188 GLU Chi-restraints excluded: chain N residue 189 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 178 optimal weight: 0.7980 chunk 155 optimal weight: 0.0770 chunk 179 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 77 optimal weight: 0.0670 chunk 220 optimal weight: 3.9990 overall best weight: 0.5676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN B 83 HIS ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN C 42 ASN C 65 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 GLN F 89 GLN ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 HIS I 89 GLN I 123 HIS K 42 ASN J 42 ASN J 89 GLN J 123 HIS J 166 GLN L 42 ASN L 117 ASN M 166 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.150985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.128145 restraints weight = 25645.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.131242 restraints weight = 13554.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.133178 restraints weight = 8449.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.134447 restraints weight = 6009.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.135151 restraints weight = 4730.974| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.5927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17248 Z= 0.123 Angle : 0.629 9.785 23308 Z= 0.326 Chirality : 0.045 0.347 2760 Planarity : 0.004 0.061 3052 Dihedral : 4.464 17.774 2430 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.46 % Allowed : 28.37 % Favored : 68.18 % 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: -0.10 (0.18), residues: 2258 helix: 0.71 (0.15), residues: 1276 sheet: -1.33 (0.32), residues: 258 loop : -0.80 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 152 TYR 0.013 0.001 TYR D 78 PHE 0.027 0.002 PHE D 102 HIS 0.013 0.003 HIS E 142 Details of bonding type rmsd covalent geometry : bond 0.00282 (17248) covalent geometry : angle 0.62851 (23308) hydrogen bonds : bond 0.02704 ( 844) hydrogen bonds : angle 3.89847 ( 2568) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 681 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 149 LYS cc_start: 0.9059 (ttpt) cc_final: 0.8681 (tttt) REVERT: B 170 ASP cc_start: 0.8040 (t0) cc_final: 0.7783 (t0) REVERT: D 20 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.8066 (tp) REVERT: D 42 ASN cc_start: 0.8426 (m-40) cc_final: 0.8060 (t0) REVERT: D 98 SER cc_start: 0.8639 (t) cc_final: 0.8257 (m) REVERT: D 156 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.6299 (tt0) REVERT: D 181 LYS cc_start: 0.7515 (tttp) cc_final: 0.7029 (ttpt) REVERT: E 27 ASP cc_start: 0.7967 (t70) cc_final: 0.7500 (t0) REVERT: E 54 GLN cc_start: 0.8183 (mm110) cc_final: 0.7186 (tt0) REVERT: E 167 LYS cc_start: 0.8653 (ttmt) cc_final: 0.8007 (mtmm) REVERT: F 27 ASP cc_start: 0.8416 (t0) cc_final: 0.7969 (t0) REVERT: F 47 GLN cc_start: 0.8260 (mt0) cc_final: 0.7732 (mt0) REVERT: F 51 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8393 (mp) REVERT: F 117 ASN cc_start: 0.8489 (t0) cc_final: 0.6663 (t0) REVERT: F 121 MET cc_start: 0.7552 (mmm) cc_final: 0.7283 (mtt) REVERT: F 156 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7279 (tt0) REVERT: F 193 GLU cc_start: 0.6931 (pm20) cc_final: 0.6672 (pm20) REVERT: G 27 ASP cc_start: 0.8275 (p0) cc_final: 0.7719 (p0) REVERT: G 28 ARG cc_start: 0.8414 (mtp85) cc_final: 0.8171 (mtt90) REVERT: G 59 ASP cc_start: 0.7574 (p0) cc_final: 0.7125 (p0) REVERT: G 75 PHE cc_start: 0.8929 (m-10) cc_final: 0.8242 (m-80) REVERT: G 87 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.6841 (p0) REVERT: G 89 GLN cc_start: 0.8731 (mt0) cc_final: 0.8416 (mt0) REVERT: G 160 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7384 (mp10) REVERT: G 178 GLU cc_start: 0.7972 (mp0) cc_final: 0.7594 (mp0) REVERT: G 188 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7490 (tm-30) REVERT: I 23 ARG cc_start: 0.8418 (tpt90) cc_final: 0.8085 (tpt90) REVERT: K 20 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.8080 (tp) REVERT: K 146 THR cc_start: 0.8534 (OUTLIER) cc_final: 0.8266 (m) REVERT: J 85 LYS cc_start: 0.7849 (mptt) cc_final: 0.7386 (mtmm) REVERT: J 171 ARG cc_start: 0.8297 (ptm-80) cc_final: 0.7792 (ptm-80) REVERT: J 173 ASN cc_start: 0.8242 (m110) cc_final: 0.7223 (m110) REVERT: L 22 SER cc_start: 0.8968 (m) cc_final: 0.8616 (p) REVERT: L 27 ASP cc_start: 0.7995 (t70) cc_final: 0.7405 (t0) REVERT: L 64 ILE cc_start: 0.9190 (mm) cc_final: 0.8885 (mt) REVERT: L 167 LYS cc_start: 0.8605 (ttmt) cc_final: 0.8324 (mtmt) REVERT: L 182 GLU cc_start: 0.6676 (OUTLIER) cc_final: 0.5767 (mp0) REVERT: M 27 ASP cc_start: 0.8379 (t0) cc_final: 0.7884 (t0) REVERT: M 43 SER cc_start: 0.8890 (t) cc_final: 0.8632 (t) REVERT: M 47 GLN cc_start: 0.8281 (mt0) cc_final: 0.7926 (mt0) REVERT: M 117 ASN cc_start: 0.8189 (t0) cc_final: 0.7765 (t0) REVERT: M 149 LYS cc_start: 0.9351 (tttt) cc_final: 0.9109 (tttm) REVERT: M 182 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7757 (tm-30) REVERT: N 27 ASP cc_start: 0.8265 (p0) cc_final: 0.7439 (p0) REVERT: N 28 ARG cc_start: 0.8498 (mtp85) cc_final: 0.7593 (mmt90) REVERT: N 59 ASP cc_start: 0.7444 (p0) cc_final: 0.7111 (p0) REVERT: N 89 GLN cc_start: 0.8625 (mt0) cc_final: 0.8307 (mt0) REVERT: N 121 MET cc_start: 0.6974 (mmm) cc_final: 0.6602 (mmt) REVERT: N 160 GLN cc_start: 0.7937 (mm110) cc_final: 0.7482 (mp10) REVERT: N 178 GLU cc_start: 0.8229 (mp0) cc_final: 0.7786 (mp0) outliers start: 58 outliers final: 38 residues processed: 705 average time/residue: 0.1303 time to fit residues: 139.6885 Evaluate side-chains 671 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 626 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 123 HIS Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 123 HIS Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 148 GLU Chi-restraints excluded: chain G residue 164 LYS Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain I residue 161 SER Chi-restraints excluded: chain I residue 191 VAL Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 146 THR Chi-restraints excluded: chain J residue 42 ASN Chi-restraints excluded: chain J residue 123 HIS Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 123 HIS Chi-restraints excluded: chain L residue 182 GLU Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 123 HIS Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 34 optimal weight: 5.9990 chunk 142 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 119 optimal weight: 8.9990 chunk 169 optimal weight: 30.0000 chunk 138 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 221 optimal weight: 5.9990 chunk 202 optimal weight: 0.9990 chunk 105 optimal weight: 0.0980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 HIS ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 ASN C 54 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 HIS I 89 GLN K 89 GLN J 42 ASN J 123 HIS J 166 GLN L 42 ASN ** N 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 HIS ** N 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.149441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.126300 restraints weight = 25544.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.129266 restraints weight = 13645.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.131183 restraints weight = 8629.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.132375 restraints weight = 6194.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.133087 restraints weight = 4926.251| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.5990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17248 Z= 0.191 Angle : 0.678 10.743 23308 Z= 0.353 Chirality : 0.046 0.347 2760 Planarity : 0.005 0.067 3052 Dihedral : 4.613 19.517 2430 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.64 % Allowed : 29.08 % Favored : 67.28 % 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: -0.29 (0.18), residues: 2258 helix: 0.57 (0.15), residues: 1298 sheet: -1.41 (0.31), residues: 262 loop : -0.94 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 152 TYR 0.016 0.001 TYR D 78 PHE 0.031 0.002 PHE D 102 HIS 0.017 0.003 HIS E 142 Details of bonding type rmsd covalent geometry : bond 0.00455 (17248) covalent geometry : angle 0.67782 (23308) hydrogen bonds : bond 0.02908 ( 844) hydrogen bonds : angle 4.11465 ( 2568) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4516 Ramachandran restraints generated. 2258 Oldfield, 0 Emsley, 2258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 642 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 ARG cc_start: 0.8486 (mmm160) cc_final: 0.8038 (tpt90) REVERT: B 113 PHE cc_start: 0.7940 (m-10) cc_final: 0.7660 (m-80) REVERT: D 20 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.8076 (tp) REVERT: D 98 SER cc_start: 0.8726 (t) cc_final: 0.8426 (m) REVERT: D 156 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.6146 (tt0) REVERT: D 167 LYS cc_start: 0.8608 (ttmt) cc_final: 0.7801 (ttpp) REVERT: D 181 LYS cc_start: 0.7676 (tttp) cc_final: 0.7224 (ttpt) REVERT: C 171 ARG cc_start: 0.8287 (ptm-80) cc_final: 0.8018 (ptt90) REVERT: C 173 ASN cc_start: 0.8175 (OUTLIER) cc_final: 0.7789 (m110) REVERT: E 27 ASP cc_start: 0.7990 (t70) cc_final: 0.7519 (t0) REVERT: E 54 GLN cc_start: 0.8198 (mm110) cc_final: 0.7212 (tt0) REVERT: E 167 LYS cc_start: 0.8696 (ttmt) cc_final: 0.8035 (mtmm) REVERT: F 27 ASP cc_start: 0.8366 (t0) cc_final: 0.7891 (t0) REVERT: F 47 GLN cc_start: 0.8268 (mt0) cc_final: 0.7771 (mt0) REVERT: F 51 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8531 (mp) REVERT: F 117 ASN cc_start: 0.8534 (t0) cc_final: 0.6978 (t0) REVERT: F 121 MET cc_start: 0.7633 (mmm) cc_final: 0.7394 (mtt) REVERT: G 27 ASP cc_start: 0.8272 (p0) cc_final: 0.7756 (p0) REVERT: G 28 ARG cc_start: 0.8458 (mtp85) cc_final: 0.8139 (mtt90) REVERT: G 47 GLN cc_start: 0.8748 (mt0) cc_final: 0.8429 (mp10) REVERT: G 59 ASP cc_start: 0.7615 (p0) cc_final: 0.7118 (p0) REVERT: G 75 PHE cc_start: 0.8886 (m-10) cc_final: 0.8318 (m-10) REVERT: G 87 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.6764 (p0) REVERT: G 89 GLN cc_start: 0.8761 (mt0) cc_final: 0.8417 (mt0) REVERT: G 121 MET cc_start: 0.7253 (mpp) cc_final: 0.6985 (mpp) REVERT: G 160 GLN cc_start: 0.7824 (mm-40) cc_final: 0.7344 (mp10) REVERT: G 178 GLU cc_start: 0.8005 (mp0) cc_final: 0.7593 (mp0) REVERT: G 188 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7524 (tm-30) REVERT: I 167 LYS cc_start: 0.8358 (tptp) cc_final: 0.8026 (ttpp) REVERT: K 20 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8165 (tp) REVERT: K 146 THR cc_start: 0.8495 (m) cc_final: 0.8272 (m) REVERT: K 156 GLU cc_start: 0.6544 (OUTLIER) cc_final: 0.6330 (tt0) REVERT: J 85 LYS cc_start: 0.7833 (mptt) cc_final: 0.7377 (mtmm) REVERT: J 171 ARG cc_start: 0.8396 (ptm-80) cc_final: 0.7811 (ptm-80) REVERT: L 22 SER cc_start: 0.9061 (m) cc_final: 0.8688 (p) REVERT: L 27 ASP cc_start: 0.7997 (t70) cc_final: 0.7437 (t0) REVERT: L 64 ILE cc_start: 0.9231 (mm) cc_final: 0.8914 (mt) REVERT: L 167 LYS cc_start: 0.8617 (ttmt) cc_final: 0.8351 (mtmt) REVERT: L 182 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.5906 (mp0) REVERT: M 27 ASP cc_start: 0.8393 (t0) cc_final: 0.7886 (t0) REVERT: M 43 SER cc_start: 0.8918 (t) cc_final: 0.8713 (t) REVERT: M 47 GLN cc_start: 0.8395 (mt0) cc_final: 0.8173 (mt0) REVERT: M 117 ASN cc_start: 0.8326 (t0) cc_final: 0.7897 (t0) REVERT: N 28 ARG cc_start: 0.8492 (mtp85) cc_final: 0.7613 (mmt90) REVERT: N 59 ASP cc_start: 0.7558 (p0) cc_final: 0.7275 (p0) REVERT: N 89 GLN cc_start: 0.8679 (mt0) cc_final: 0.8326 (mt0) REVERT: N 111 LYS cc_start: 0.8570 (mmmm) cc_final: 0.8118 (mmmm) REVERT: N 121 MET cc_start: 0.6934 (mmm) cc_final: 0.6662 (mmt) REVERT: N 160 GLN cc_start: 0.8074 (mm110) cc_final: 0.7503 (mp10) REVERT: N 170 ASP cc_start: 0.8332 (m-30) cc_final: 0.8047 (m-30) REVERT: N 183 TYR cc_start: 0.8336 (t80) cc_final: 0.7956 (t80) outliers start: 61 outliers final: 47 residues processed: 667 average time/residue: 0.1319 time to fit residues: 133.1867 Evaluate side-chains 675 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 620 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 123 HIS Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 123 HIS Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 148 GLU Chi-restraints excluded: chain G residue 164 LYS Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain I residue 161 SER Chi-restraints excluded: chain I residue 191 VAL Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 156 GLU Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 161 SER Chi-restraints excluded: chain J residue 176 THR Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 123 HIS Chi-restraints excluded: chain L residue 148 GLU Chi-restraints excluded: chain L residue 182 GLU Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 123 HIS Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 37 ASP Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 123 HIS Chi-restraints excluded: chain N residue 162 ILE Chi-restraints excluded: chain N residue 188 GLU Chi-restraints excluded: chain N residue 189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 142 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 219 optimal weight: 10.0000 chunk 191 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 141 optimal weight: 0.7980 chunk 206 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 HIS ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 ASN C 65 ASN E 42 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 HIS ** F 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 54 GLN ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 HIS I 89 GLN K 42 ASN J 42 ASN J 142 HIS L 42 ASN M 166 GLN ** N 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 HIS ** N 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.151876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.128905 restraints weight = 25360.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.131820 restraints weight = 13616.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.133723 restraints weight = 8543.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.134964 restraints weight = 6135.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.135686 restraints weight = 4885.684| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.6096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17248 Z= 0.142 Angle : 0.663 11.237 23308 Z= 0.340 Chirality : 0.045 0.356 2760 Planarity : 0.004 0.064 3052 Dihedral : 4.488 18.615 2430 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.40 % Allowed : 29.56 % Favored : 67.04 % 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: -0.01 (0.18), residues: 2258 helix: 0.73 (0.15), residues: 1298 sheet: -1.24 (0.32), residues: 262 loop : -0.71 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 152 TYR 0.015 0.001 TYR D 78 PHE 0.027 0.002 PHE D 102 HIS 0.014 0.003 HIS L 142 Details of bonding type rmsd covalent geometry : bond 0.00339 (17248) covalent geometry : angle 0.66270 (23308) hydrogen bonds : bond 0.02709 ( 844) hydrogen bonds : angle 3.94036 ( 2568) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3492.82 seconds wall clock time: 60 minutes 47.55 seconds (3647.55 seconds total)