Starting phenix.real_space_refine on Wed Feb 4 08:39:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qvd_53394/02_2026/9qvd_53394.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qvd_53394/02_2026/9qvd_53394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qvd_53394/02_2026/9qvd_53394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qvd_53394/02_2026/9qvd_53394.map" model { file = "/net/cci-nas-00/data/ceres_data/9qvd_53394/02_2026/9qvd_53394.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qvd_53394/02_2026/9qvd_53394.cif" } resolution = 3.52 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= 0.001 sd= 0.027 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 37 5.16 5 C 6215 2.51 5 N 1642 2.21 5 O 1676 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9570 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1703 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1703 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1703 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1703 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1703 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 181 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "G" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 181 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 231 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "I" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 231 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "J" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 231 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Time building chain proxies: 2.21, per 1000 atoms: 0.23 Number of scatterers: 9570 At special positions: 0 Unit cell: (93.5, 97.9, 118.8, 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 37 16.00 O 1676 8.00 N 1642 7.00 C 6215 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: 0.77 Conformation dependent library (CDL) restraints added in 310.8 milliseconds 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2300 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 0 sheets defined 91.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 Processing helix chain 'A' and resid 17 through 57 removed outlier: 4.097A pdb=" N ARG A 40 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A 41 " --> pdb=" O GLN A 37 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TRP A 57 " --> pdb=" O GLU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 73 Processing helix chain 'A' and resid 78 through 97 removed outlier: 3.672A pdb=" N ALA A 96 " --> pdb=" O ARG A 92 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN A 97 " --> pdb=" O LEU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 124 removed outlier: 3.515A pdb=" N ALA A 111 " --> pdb=" O GLY A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 159 removed outlier: 4.232A pdb=" N LEU A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY A 131 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Proline residue: A 138 - end of helix removed outlier: 3.523A pdb=" N GLY A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY A 157 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 175 removed outlier: 3.885A pdb=" N ALA A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU A 175 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 221 removed outlier: 3.858A pdb=" N ALA A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Proline residue: A 187 - end of helix removed outlier: 4.582A pdb=" N MET A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 204 " --> pdb=" O ASN A 200 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN A 205 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 12 Processing helix chain 'B' and resid 14 through 57 removed outlier: 3.889A pdb=" N THR B 39 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ARG B 40 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE B 41 " --> pdb=" O GLN B 37 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TRP B 57 " --> pdb=" O GLU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 73 Processing helix chain 'B' and resid 78 through 96 removed outlier: 3.893A pdb=" N ILE B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG B 92 " --> pdb=" O LYS B 88 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ARG B 95 " --> pdb=" O VAL B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 124 removed outlier: 3.523A pdb=" N VAL B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 157 removed outlier: 3.737A pdb=" N GLY B 131 " --> pdb=" O ILE B 127 " (cutoff:3.500A) Proline residue: B 138 - end of helix removed outlier: 3.592A pdb=" N GLY B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY B 157 " --> pdb=" O PHE B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 219 removed outlier: 3.715A pdb=" N VAL B 167 " --> pdb=" O THR B 163 " (cutoff:3.500A) Proline residue: B 169 - end of helix removed outlier: 3.528A pdb=" N ALA B 172 " --> pdb=" O ALA B 168 " (cutoff:3.500A) Proline residue: B 187 - end of helix removed outlier: 4.197A pdb=" N ASN B 193 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG B 198 " --> pdb=" O ARG B 194 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 199 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS B 201 " --> pdb=" O GLN B 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 13 Processing helix chain 'C' and resid 14 through 57 removed outlier: 4.030A pdb=" N ARG C 40 " --> pdb=" O ILE C 36 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE C 41 " --> pdb=" O GLN C 37 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N TRP C 57 " --> pdb=" O GLU C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 70 Processing helix chain 'C' and resid 71 through 76 removed outlier: 5.848A pdb=" N ASP C 74 " --> pdb=" O GLY C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 97 Processing helix chain 'C' and resid 100 through 124 removed outlier: 3.924A pdb=" N VAL C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL C 105 " --> pdb=" O PRO C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 159 removed outlier: 4.012A pdb=" N GLY C 131 " --> pdb=" O ILE C 127 " (cutoff:3.500A) Proline residue: C 138 - end of helix removed outlier: 3.684A pdb=" N GLY C 148 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA C 158 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL C 159 " --> pdb=" O ALA C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 221 removed outlier: 3.785A pdb=" N ILE C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA C 177 " --> pdb=" O GLU C 173 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR C 178 " --> pdb=" O ALA C 174 " (cutoff:3.500A) Proline residue: C 187 - end of helix removed outlier: 4.024A pdb=" N MET C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN C 193 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU C 204 " --> pdb=" O ASN C 200 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASN C 205 " --> pdb=" O LYS C 201 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR C 206 " --> pdb=" O LEU C 202 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG C 219 " --> pdb=" O ALA C 215 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN C 220 " --> pdb=" O ILE C 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 13 Processing helix chain 'D' and resid 14 through 57 removed outlier: 3.940A pdb=" N ALA D 33 " --> pdb=" O ILE D 29 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE D 34 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE D 41 " --> pdb=" O GLN D 37 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TRP D 57 " --> pdb=" O GLU D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 73 removed outlier: 3.781A pdb=" N GLY D 71 " --> pdb=" O GLN D 67 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG D 73 " --> pdb=" O SER D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 77 removed outlier: 5.237A pdb=" N THR D 77 " --> pdb=" O ASP D 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 74 through 77' Processing helix chain 'D' and resid 78 through 96 removed outlier: 3.601A pdb=" N ILE D 82 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA D 96 " --> pdb=" O ARG D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 124 Processing helix chain 'D' and resid 127 through 157 removed outlier: 4.289A pdb=" N GLY D 131 " --> pdb=" O ILE D 127 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR D 132 " --> pdb=" O PRO D 128 " (cutoff:3.500A) Proline residue: D 138 - end of helix removed outlier: 3.586A pdb=" N GLY D 141 " --> pdb=" O SER D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 175 removed outlier: 3.922A pdb=" N VAL D 167 " --> pdb=" O THR D 163 " (cutoff:3.500A) Proline residue: D 169 - end of helix Processing helix chain 'D' and resid 175 through 221 removed outlier: 3.967A pdb=" N ALA D 179 " --> pdb=" O LEU D 175 " (cutoff:3.500A) Proline residue: D 187 - end of helix removed outlier: 4.371A pdb=" N ASN D 193 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ARG D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASN D 205 " --> pdb=" O LYS D 201 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR D 206 " --> pdb=" O LEU D 202 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS D 218 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ARG D 219 " --> pdb=" O ALA D 215 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN D 220 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 14 through 57 removed outlier: 4.130A pdb=" N THR E 39 " --> pdb=" O ILE E 35 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ARG E 40 " --> pdb=" O ILE E 36 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE E 41 " --> pdb=" O GLN E 37 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS E 55 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TRP E 57 " --> pdb=" O GLU E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 72 removed outlier: 3.899A pdb=" N GLY E 71 " --> pdb=" O GLN E 67 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYS E 72 " --> pdb=" O GLU E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 77 removed outlier: 6.797A pdb=" N THR E 77 " --> pdb=" O ASP E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 96 removed outlier: 4.270A pdb=" N ILE E 82 " --> pdb=" O GLY E 78 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE E 83 " --> pdb=" O SER E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 124 Processing helix chain 'E' and resid 126 through 157 removed outlier: 3.683A pdb=" N LEU E 130 " --> pdb=" O HIS E 126 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY E 131 " --> pdb=" O ILE E 127 " (cutoff:3.500A) Proline residue: E 138 - end of helix removed outlier: 3.932A pdb=" N GLY E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 184 removed outlier: 3.572A pdb=" N VAL E 167 " --> pdb=" O THR E 163 " (cutoff:3.500A) Proline residue: E 169 - end of helix Processing helix chain 'E' and resid 185 through 221 removed outlier: 3.548A pdb=" N VAL E 189 " --> pdb=" O ALA E 185 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ASN E 193 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ARG E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG E 198 " --> pdb=" O ARG E 194 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL E 199 " --> pdb=" O LEU E 195 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU E 202 " --> pdb=" O ARG E 198 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU E 204 " --> pdb=" O ASN E 200 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN E 205 " --> pdb=" O LYS E 201 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG E 219 " --> pdb=" O ALA E 215 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN E 220 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 35 removed outlier: 3.794A pdb=" N VAL F 24 " --> pdb=" O PRO F 20 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE F 31 " --> pdb=" O VAL F 27 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE F 32 " --> pdb=" O LEU F 28 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET F 33 " --> pdb=" O LEU F 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 35 removed outlier: 3.551A pdb=" N THR G 35 " --> pdb=" O ILE G 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 35 removed outlier: 3.551A pdb=" N SER H 33 " --> pdb=" O LEU H 29 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE H 34 " --> pdb=" O ILE H 30 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASP H 35 " --> pdb=" O TRP H 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 35 removed outlier: 3.721A pdb=" N ASP I 35 " --> pdb=" O TRP I 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 35 removed outlier: 3.634A pdb=" N PHE J 34 " --> pdb=" O ILE J 30 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP J 35 " --> pdb=" O TRP J 31 " (cutoff:3.500A) 784 hydrogen bonds defined for protein. 2343 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: 1.42 Time building geometry restraints manager: 1.01 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: 3073 1.34 - 1.45: 1125 1.45 - 1.57: 5479 1.57 - 1.69: 0 1.69 - 1.80: 74 Bond restraints: 9751 Sorted by residual: bond pdb=" CB GLN A 67 " pdb=" CG GLN A 67 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.25e+00 bond pdb=" N ILE B 186 " pdb=" CA ILE B 186 " ideal model delta sigma weight residual 1.463 1.476 -0.013 1.20e-02 6.94e+03 1.17e+00 bond pdb=" C ASN B 196 " pdb=" O ASN B 196 " ideal model delta sigma weight residual 1.236 1.250 -0.013 1.25e-02 6.40e+03 1.17e+00 bond pdb=" CA ILE B 186 " pdb=" C ILE B 186 " ideal model delta sigma weight residual 1.523 1.532 -0.009 9.20e-03 1.18e+04 1.04e+00 bond pdb=" CA ILE A 186 " pdb=" C ILE A 186 " ideal model delta sigma weight residual 1.523 1.532 -0.009 9.20e-03 1.18e+04 9.56e-01 ... (remaining 9746 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 13027 1.47 - 2.94: 119 2.94 - 4.42: 23 4.42 - 5.89: 21 5.89 - 7.36: 3 Bond angle restraints: 13193 Sorted by residual: angle pdb=" C ARG A 73 " pdb=" CA ARG A 73 " pdb=" CB ARG A 73 " ideal model delta sigma weight residual 116.63 109.27 7.36 1.16e+00 7.43e-01 4.03e+01 angle pdb=" CA ARG A 73 " pdb=" C ARG A 73 " pdb=" N ASP A 74 " ideal model delta sigma weight residual 119.63 116.26 3.37 8.10e-01 1.52e+00 1.73e+01 angle pdb=" N ARG A 73 " pdb=" CA ARG A 73 " pdb=" C ARG A 73 " ideal model delta sigma weight residual 108.08 113.84 -5.76 1.69e+00 3.50e-01 1.16e+01 angle pdb=" N GLN A 67 " pdb=" CA GLN A 67 " pdb=" CB GLN A 67 " ideal model delta sigma weight residual 110.22 114.82 -4.60 1.54e+00 4.22e-01 8.94e+00 angle pdb=" C ILE A 186 " pdb=" CA ILE A 186 " pdb=" CB ILE A 186 " ideal model delta sigma weight residual 114.00 110.41 3.59 1.31e+00 5.83e-01 7.52e+00 ... (remaining 13188 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 5388 17.92 - 35.84: 317 35.84 - 53.76: 46 53.76 - 71.68: 45 71.68 - 89.60: 24 Dihedral angle restraints: 5820 sinusoidal: 2285 harmonic: 3535 Sorted by residual: dihedral pdb=" CA ALA B 185 " pdb=" C ALA B 185 " pdb=" N ILE B 186 " pdb=" CA ILE B 186 " ideal model delta harmonic sigma weight residual -180.00 -162.59 -17.41 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ILE A 136 " pdb=" C ILE A 136 " pdb=" N SER A 137 " pdb=" CA SER A 137 " ideal model delta harmonic sigma weight residual 180.00 -163.42 -16.58 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CG ARG C 113 " pdb=" CD ARG C 113 " pdb=" NE ARG C 113 " pdb=" CZ ARG C 113 " ideal model delta sinusoidal sigma weight residual 90.00 134.18 -44.18 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 5817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1085 0.030 - 0.060: 276 0.060 - 0.090: 125 0.090 - 0.120: 47 0.120 - 0.150: 3 Chirality restraints: 1536 Sorted by residual: chirality pdb=" CA GLN A 67 " pdb=" N GLN A 67 " pdb=" C GLN A 67 " pdb=" CB GLN A 67 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.59e-01 chirality pdb=" CB ILE F 18 " pdb=" CA ILE F 18 " pdb=" CG1 ILE F 18 " pdb=" CG2 ILE F 18 " both_signs ideal model delta sigma weight residual False 2.64 2.78 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CB ILE E 136 " pdb=" CA ILE E 136 " pdb=" CG1 ILE E 136 " pdb=" CG2 ILE E 136 " both_signs ideal model delta sigma weight residual False 2.64 2.77 -0.12 2.00e-01 2.50e+01 3.73e-01 ... (remaining 1533 not shown) Planarity restraints: 1664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 100 " -0.021 5.00e-02 4.00e+02 3.20e-02 1.64e+00 pdb=" N PRO A 101 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 101 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 101 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 127 " 0.018 5.00e-02 4.00e+02 2.72e-02 1.18e+00 pdb=" N PRO D 128 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO D 128 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 128 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 127 " -0.017 5.00e-02 4.00e+02 2.52e-02 1.01e+00 pdb=" N PRO B 128 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO B 128 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 128 " -0.014 5.00e-02 4.00e+02 ... (remaining 1661 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2598 2.83 - 3.34: 9888 3.34 - 3.86: 14781 3.86 - 4.38: 14923 4.38 - 4.90: 28323 Nonbonded interactions: 70513 Sorted by model distance: nonbonded pdb=" OG1 THR C 178 " pdb=" OD2 ASP F 23 " model vdw 2.307 3.040 nonbonded pdb=" O VAL D 133 " pdb=" OG SER D 137 " model vdw 2.359 3.040 nonbonded pdb=" NH1 ARG A 38 " pdb=" O THR A 125 " model vdw 2.391 3.120 nonbonded pdb=" OD1 ASN B 43 " pdb=" NH2 ARG B 198 " model vdw 2.408 3.120 nonbonded pdb=" O SER A 63 " pdb=" OE1 GLN A 67 " model vdw 2.411 3.040 ... (remaining 70508 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 1.100 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.300 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 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 : 0.002 0.033 9751 Z= 0.125 Angle : 0.437 7.362 13193 Z= 0.250 Chirality : 0.035 0.150 1536 Planarity : 0.003 0.032 1664 Dihedral : 14.890 89.600 3520 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: 4.99 (0.24), residues: 1200 helix: 3.85 (0.15), residues: 1012 sheet: None (None), residues: 0 loop : -0.32 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 64 TYR 0.012 0.001 TYR A 192 PHE 0.013 0.001 PHE D 52 TRP 0.010 0.001 TRP C 147 HIS 0.004 0.000 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 9751) covalent geometry : angle 0.43728 (13193) hydrogen bonds : bond 0.13519 ( 784) hydrogen bonds : angle 3.46327 ( 2343) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 381 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO G 37 " (corrupted residue). Skipping it. Corrupt residue: chain: G residue: PRO 37 >>> skipping TARDY: cannot create tardy model for: "ASP H 35 " (corrupted residue). Skipping it. REVERT: A 36 ILE cc_start: 0.8536 (mt) cc_final: 0.7672 (tp) REVERT: A 37 GLN cc_start: 0.8184 (tp40) cc_final: 0.7765 (tp40) REVERT: A 40 ARG cc_start: 0.7252 (mtm-85) cc_final: 0.6967 (mtm-85) REVERT: A 61 GLU cc_start: 0.6942 (mt-10) cc_final: 0.6467 (mt-10) REVERT: A 63 SER cc_start: 0.6899 (p) cc_final: 0.5815 (m) REVERT: A 88 LYS cc_start: 0.8360 (tttp) cc_final: 0.8053 (tttp) REVERT: A 120 LEU cc_start: 0.8497 (mt) cc_final: 0.8119 (mt) REVERT: A 121 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7540 (mt-10) REVERT: A 124 GLU cc_start: 0.7325 (mt-10) cc_final: 0.7096 (mt-10) REVERT: A 151 HIS cc_start: 0.7738 (t70) cc_final: 0.7536 (t70) REVERT: A 166 MET cc_start: 0.7352 (ptm) cc_final: 0.7089 (ptm) REVERT: A 204 LEU cc_start: 0.8437 (mt) cc_final: 0.8195 (mm) REVERT: B 7 LEU cc_start: 0.7789 (tp) cc_final: 0.7512 (tp) REVERT: B 15 LEU cc_start: 0.6376 (tp) cc_final: 0.6088 (tp) REVERT: B 19 LEU cc_start: 0.8283 (mt) cc_final: 0.8073 (mt) REVERT: B 38 ARG cc_start: 0.8694 (tpp-160) cc_final: 0.8405 (mmp80) REVERT: B 64 ARG cc_start: 0.7840 (mmt180) cc_final: 0.7565 (mmt180) REVERT: B 89 GLU cc_start: 0.7544 (tp30) cc_final: 0.6950 (tp30) REVERT: B 110 ARG cc_start: 0.7650 (mtt90) cc_final: 0.7303 (mtt90) REVERT: B 113 ARG cc_start: 0.7978 (mtm110) cc_final: 0.7616 (mtm180) REVERT: C 11 LEU cc_start: 0.8187 (mt) cc_final: 0.7856 (mt) REVERT: C 21 MET cc_start: 0.7375 (mtp) cc_final: 0.7029 (mtt) REVERT: C 52 PHE cc_start: 0.8217 (t80) cc_final: 0.7945 (t80) REVERT: C 55 LYS cc_start: 0.7999 (tptt) cc_final: 0.7791 (tptt) REVERT: C 183 PHE cc_start: 0.8856 (t80) cc_final: 0.8621 (t80) REVERT: C 213 PHE cc_start: 0.8544 (t80) cc_final: 0.8331 (t80) REVERT: D 89 GLU cc_start: 0.7908 (tt0) cc_final: 0.7668 (tt0) REVERT: D 112 MET cc_start: 0.8245 (mtt) cc_final: 0.7871 (mtp) REVERT: D 135 SER cc_start: 0.8810 (t) cc_final: 0.8265 (p) REVERT: D 201 LYS cc_start: 0.8036 (mtpt) cc_final: 0.7616 (mtpt) REVERT: E 35 ILE cc_start: 0.8749 (mt) cc_final: 0.8532 (tp) REVERT: E 38 ARG cc_start: 0.8251 (tpp-160) cc_final: 0.7970 (mmp-170) REVERT: E 48 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7156 (mt-10) REVERT: E 61 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6688 (mt-10) REVERT: E 64 ARG cc_start: 0.7780 (mtt180) cc_final: 0.7517 (mtt180) REVERT: E 76 LEU cc_start: 0.8250 (mt) cc_final: 0.7972 (mm) REVERT: E 83 PHE cc_start: 0.8469 (t80) cc_final: 0.8217 (t80) outliers start: 0 outliers final: 0 residues processed: 381 average time/residue: 0.1120 time to fit residues: 56.2594 Evaluate side-chains 325 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.1980 chunk 113 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN B 165 GLN B 218 HIS C 70 GLN E 37 GLN E 75 ASN E 200 ASN E 208 ASN I 8 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.143897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.120794 restraints weight = 14358.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.125163 restraints weight = 6363.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.128161 restraints weight = 3764.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.129861 restraints weight = 2706.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.131165 restraints weight = 2231.071| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9751 Z= 0.153 Angle : 0.519 6.897 13193 Z= 0.277 Chirality : 0.037 0.152 1536 Planarity : 0.003 0.029 1664 Dihedral : 3.446 17.047 1303 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.52 % Allowed : 14.29 % Favored : 83.20 % 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: 4.83 (0.24), residues: 1200 helix: 3.67 (0.15), residues: 1033 sheet: None (None), residues: 0 loop : -0.44 (0.50), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 219 TYR 0.015 0.001 TYR A 66 PHE 0.024 0.001 PHE C 56 TRP 0.014 0.001 TRP C 147 HIS 0.006 0.001 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9751) covalent geometry : angle 0.51865 (13193) hydrogen bonds : bond 0.07000 ( 784) hydrogen bonds : angle 3.28404 ( 2343) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 328 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO G 37 " (corrupted residue). Skipping it. Corrupt residue: chain: G residue: PRO 37 >>> skipping TARDY: cannot create tardy model for: "ASP H 35 " (corrupted residue). Skipping it. REVERT: A 36 ILE cc_start: 0.8452 (mt) cc_final: 0.7550 (tp) REVERT: A 37 GLN cc_start: 0.7902 (tp40) cc_final: 0.7437 (tp40) REVERT: A 43 ASN cc_start: 0.7998 (m-40) cc_final: 0.7770 (m-40) REVERT: A 48 GLU cc_start: 0.7312 (tm-30) cc_final: 0.7110 (tm-30) REVERT: A 80 GLU cc_start: 0.7246 (mt-10) cc_final: 0.7038 (mm-30) REVERT: A 88 LYS cc_start: 0.8153 (tttp) cc_final: 0.7847 (tttp) REVERT: A 124 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6854 (mt-10) REVERT: A 151 HIS cc_start: 0.7325 (t70) cc_final: 0.7009 (t70) REVERT: A 176 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8224 (tp) REVERT: A 201 LYS cc_start: 0.8364 (mttm) cc_final: 0.8044 (tttm) REVERT: A 204 LEU cc_start: 0.8301 (mt) cc_final: 0.7988 (mm) REVERT: B 15 LEU cc_start: 0.5865 (tp) cc_final: 0.5653 (tp) REVERT: B 21 MET cc_start: 0.7571 (mmt) cc_final: 0.7311 (mmt) REVERT: B 37 GLN cc_start: 0.8327 (tm-30) cc_final: 0.7619 (tm-30) REVERT: B 38 ARG cc_start: 0.8539 (tpp-160) cc_final: 0.7723 (mmp80) REVERT: B 48 GLU cc_start: 0.7070 (mt-10) cc_final: 0.6855 (tt0) REVERT: B 64 ARG cc_start: 0.7691 (mmt180) cc_final: 0.7438 (mmt180) REVERT: B 89 GLU cc_start: 0.7400 (tp30) cc_final: 0.6891 (tp30) REVERT: B 110 ARG cc_start: 0.7393 (mtt90) cc_final: 0.7146 (mtt90) REVERT: C 21 MET cc_start: 0.7018 (mtp) cc_final: 0.6806 (mtt) REVERT: C 52 PHE cc_start: 0.8283 (t80) cc_final: 0.8029 (t80) REVERT: D 90 PHE cc_start: 0.8647 (t80) cc_final: 0.8439 (t80) REVERT: D 112 MET cc_start: 0.7771 (mtt) cc_final: 0.7492 (mtp) REVERT: D 132 THR cc_start: 0.8363 (p) cc_final: 0.8079 (t) REVERT: D 135 SER cc_start: 0.8510 (t) cc_final: 0.8087 (p) REVERT: D 201 LYS cc_start: 0.7874 (mtpt) cc_final: 0.7443 (mtpt) REVERT: E 35 ILE cc_start: 0.8679 (mt) cc_final: 0.8454 (tp) REVERT: E 38 ARG cc_start: 0.8175 (tpp-160) cc_final: 0.7778 (mmp-170) REVERT: E 48 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6824 (mt-10) REVERT: E 64 ARG cc_start: 0.7451 (mtt180) cc_final: 0.7209 (mtt180) REVERT: E 210 MET cc_start: 0.8103 (ttm) cc_final: 0.7882 (ttm) outliers start: 25 outliers final: 11 residues processed: 339 average time/residue: 0.1218 time to fit residues: 53.2449 Evaluate side-chains 333 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 321 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 79 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 67 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 84 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 111 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 ASN E 37 GLN E 75 ASN E 205 ASN E 208 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.140793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.117556 restraints weight = 14172.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.121818 restraints weight = 6249.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.124789 restraints weight = 3691.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.126556 restraints weight = 2655.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.127764 restraints weight = 2181.128| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9751 Z= 0.192 Angle : 0.545 7.949 13193 Z= 0.292 Chirality : 0.038 0.140 1536 Planarity : 0.003 0.032 1664 Dihedral : 3.539 18.262 1303 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 4.43 % Allowed : 15.69 % Favored : 79.88 % 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: 4.55 (0.24), residues: 1200 helix: 3.47 (0.15), residues: 1033 sheet: None (None), residues: 0 loop : -0.46 (0.51), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 219 TYR 0.023 0.002 TYR E 84 PHE 0.026 0.001 PHE E 90 TRP 0.014 0.001 TRP C 147 HIS 0.006 0.001 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 9751) covalent geometry : angle 0.54539 (13193) hydrogen bonds : bond 0.08114 ( 784) hydrogen bonds : angle 3.40976 ( 2343) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 339 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO G 37 " (corrupted residue). Skipping it. Corrupt residue: chain: G residue: PRO 37 >>> skipping TARDY: cannot create tardy model for: "ASP H 35 " (corrupted residue). Skipping it. REVERT: A 21 MET cc_start: 0.7077 (mtm) cc_final: 0.6872 (mtm) REVERT: A 37 GLN cc_start: 0.7875 (tp40) cc_final: 0.7482 (tp40) REVERT: A 43 ASN cc_start: 0.8006 (m-40) cc_final: 0.7787 (m-40) REVERT: A 88 LYS cc_start: 0.8138 (tttp) cc_final: 0.7874 (tttp) REVERT: A 121 GLU cc_start: 0.7298 (mt-10) cc_final: 0.7029 (mt-10) REVERT: A 124 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6902 (mt-10) REVERT: A 151 HIS cc_start: 0.7367 (t70) cc_final: 0.7086 (t70) REVERT: A 201 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8091 (tttm) REVERT: A 204 LEU cc_start: 0.8276 (mt) cc_final: 0.8010 (mm) REVERT: B 21 MET cc_start: 0.7592 (mmt) cc_final: 0.7389 (mmt) REVERT: B 37 GLN cc_start: 0.8428 (tm-30) cc_final: 0.7702 (tm-30) REVERT: B 38 ARG cc_start: 0.8527 (tpp-160) cc_final: 0.7700 (mmp80) REVERT: B 47 ARG cc_start: 0.7138 (ptt-90) cc_final: 0.6936 (ptt-90) REVERT: B 63 SER cc_start: 0.8251 (m) cc_final: 0.8028 (p) REVERT: B 64 ARG cc_start: 0.7687 (mmt180) cc_final: 0.7457 (mmt180) REVERT: B 85 SER cc_start: 0.8191 (m) cc_final: 0.7933 (t) REVERT: B 89 GLU cc_start: 0.7465 (tp30) cc_final: 0.6885 (tp30) REVERT: B 110 ARG cc_start: 0.7387 (mtt90) cc_final: 0.7100 (mtt90) REVERT: B 156 LEU cc_start: 0.8869 (tp) cc_final: 0.8650 (tt) REVERT: C 21 MET cc_start: 0.7079 (mtp) cc_final: 0.6878 (mtt) REVERT: C 132 THR cc_start: 0.8650 (p) cc_final: 0.8428 (t) REVERT: D 36 ILE cc_start: 0.8469 (tp) cc_final: 0.8232 (tp) REVERT: D 112 MET cc_start: 0.7726 (mtt) cc_final: 0.7493 (mtp) REVERT: D 122 ASN cc_start: 0.8569 (t0) cc_final: 0.8359 (t0) REVERT: D 135 SER cc_start: 0.8547 (t) cc_final: 0.8167 (p) REVERT: D 164 LEU cc_start: 0.8691 (tp) cc_final: 0.8175 (mp) REVERT: D 201 LYS cc_start: 0.7896 (mtpt) cc_final: 0.7390 (mtpt) REVERT: E 38 ARG cc_start: 0.8233 (tpp-160) cc_final: 0.7872 (mmp-170) REVERT: E 64 ARG cc_start: 0.7444 (mtt180) cc_final: 0.7240 (mtt180) REVERT: E 66 TYR cc_start: 0.8460 (t80) cc_final: 0.8146 (t80) REVERT: E 89 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7176 (mm-30) REVERT: E 93 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8081 (mp) REVERT: E 153 PHE cc_start: 0.8507 (m-80) cc_final: 0.8234 (m-80) REVERT: E 210 MET cc_start: 0.8072 (ttm) cc_final: 0.7871 (ttm) outliers start: 44 outliers final: 25 residues processed: 352 average time/residue: 0.1208 time to fit residues: 55.0011 Evaluate side-chains 358 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 331 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 154 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 109 optimal weight: 5.9990 chunk 105 optimal weight: 0.4980 chunk 21 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 GLN B 196 ASN C 122 ASN C 208 ASN E 37 GLN E 75 ASN E 208 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.140654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.117238 restraints weight = 14250.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.121516 restraints weight = 6283.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.124509 restraints weight = 3685.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.126236 restraints weight = 2645.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.127475 restraints weight = 2186.235| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9751 Z= 0.184 Angle : 0.526 7.254 13193 Z= 0.285 Chirality : 0.038 0.141 1536 Planarity : 0.003 0.044 1664 Dihedral : 3.572 17.803 1303 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 4.73 % Allowed : 18.01 % Favored : 77.26 % 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: 4.46 (0.24), residues: 1200 helix: 3.42 (0.15), residues: 1032 sheet: None (None), residues: 0 loop : -0.56 (0.50), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 219 TYR 0.021 0.002 TYR E 84 PHE 0.019 0.001 PHE E 143 TRP 0.014 0.001 TRP C 147 HIS 0.005 0.001 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 9751) covalent geometry : angle 0.52576 (13193) hydrogen bonds : bond 0.07947 ( 784) hydrogen bonds : angle 3.38014 ( 2343) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 334 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO G 37 " (corrupted residue). Skipping it. Corrupt residue: chain: G residue: PRO 37 >>> skipping TARDY: cannot create tardy model for: "ASP H 35 " (corrupted residue). Skipping it. REVERT: A 37 GLN cc_start: 0.7917 (tp40) cc_final: 0.7526 (tp40) REVERT: A 76 LEU cc_start: 0.8230 (mt) cc_final: 0.8001 (mp) REVERT: A 80 GLU cc_start: 0.7240 (mt-10) cc_final: 0.6829 (mm-30) REVERT: A 88 LYS cc_start: 0.8139 (tttp) cc_final: 0.7882 (tttp) REVERT: A 121 GLU cc_start: 0.7278 (mt-10) cc_final: 0.7023 (mt-10) REVERT: A 124 GLU cc_start: 0.7111 (mt-10) cc_final: 0.6870 (mt-10) REVERT: A 151 HIS cc_start: 0.7389 (t70) cc_final: 0.7076 (t70) REVERT: A 201 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8094 (tttm) REVERT: A 204 LEU cc_start: 0.8295 (mt) cc_final: 0.8021 (mm) REVERT: B 37 GLN cc_start: 0.8381 (tm-30) cc_final: 0.7533 (tm-30) REVERT: B 38 ARG cc_start: 0.8534 (tpp-160) cc_final: 0.7562 (mmt-90) REVERT: B 47 ARG cc_start: 0.7156 (ptt-90) cc_final: 0.6927 (ptt-90) REVERT: B 63 SER cc_start: 0.8260 (m) cc_final: 0.8031 (p) REVERT: B 64 ARG cc_start: 0.7676 (mmt180) cc_final: 0.7447 (mmt180) REVERT: B 85 SER cc_start: 0.8191 (m) cc_final: 0.7907 (t) REVERT: B 89 GLU cc_start: 0.7489 (tp30) cc_final: 0.6879 (tp30) REVERT: B 110 ARG cc_start: 0.7295 (mtt90) cc_final: 0.7029 (mtt90) REVERT: B 116 MET cc_start: 0.8361 (ttp) cc_final: 0.8005 (ttm) REVERT: B 196 ASN cc_start: 0.8343 (m-40) cc_final: 0.8130 (m-40) REVERT: C 21 MET cc_start: 0.7103 (mtp) cc_final: 0.6849 (mtt) REVERT: C 132 THR cc_start: 0.8625 (p) cc_final: 0.8405 (t) REVERT: D 112 MET cc_start: 0.7771 (mtt) cc_final: 0.7516 (mtp) REVERT: D 135 SER cc_start: 0.8473 (t) cc_final: 0.8098 (p) REVERT: D 164 LEU cc_start: 0.8681 (tp) cc_final: 0.8224 (mp) REVERT: D 198 ARG cc_start: 0.7425 (mtt180) cc_final: 0.7082 (mtt180) REVERT: D 201 LYS cc_start: 0.7881 (mtpt) cc_final: 0.7407 (mtpt) REVERT: E 38 ARG cc_start: 0.8255 (tpp-160) cc_final: 0.7876 (mmp-170) REVERT: E 40 ARG cc_start: 0.7051 (ptp-110) cc_final: 0.6830 (ptp-110) REVERT: E 66 TYR cc_start: 0.8434 (t80) cc_final: 0.8208 (t80) REVERT: E 89 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7174 (mm-30) REVERT: E 93 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8071 (mp) REVERT: E 190 MET cc_start: 0.7624 (tmm) cc_final: 0.7366 (tmm) REVERT: E 210 MET cc_start: 0.8156 (ttm) cc_final: 0.7931 (ttm) outliers start: 47 outliers final: 36 residues processed: 344 average time/residue: 0.1182 time to fit residues: 52.6712 Evaluate side-chains 367 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 329 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 151 HIS Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain H residue 23 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 77 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 81 optimal weight: 0.0170 chunk 54 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 100 optimal weight: 0.0030 chunk 64 optimal weight: 0.7980 overall best weight: 0.4628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 HIS C 208 ASN E 37 GLN E 208 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.143675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.120433 restraints weight = 14222.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.124738 restraints weight = 6247.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.127658 restraints weight = 3663.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.129413 restraints weight = 2652.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.130494 restraints weight = 2180.149| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9751 Z= 0.145 Angle : 0.504 7.077 13193 Z= 0.267 Chirality : 0.036 0.132 1536 Planarity : 0.003 0.042 1664 Dihedral : 3.548 17.548 1303 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 4.63 % Allowed : 19.22 % Favored : 76.16 % 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: 4.68 (0.24), residues: 1200 helix: 3.58 (0.15), residues: 1032 sheet: None (None), residues: 0 loop : -0.62 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 219 TYR 0.020 0.001 TYR E 84 PHE 0.024 0.001 PHE E 90 TRP 0.015 0.001 TRP C 147 HIS 0.004 0.000 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 9751) covalent geometry : angle 0.50425 (13193) hydrogen bonds : bond 0.06858 ( 784) hydrogen bonds : angle 3.20263 ( 2343) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 333 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO G 37 " (corrupted residue). Skipping it. Corrupt residue: chain: G residue: PRO 37 >>> skipping TARDY: cannot create tardy model for: "ASP H 35 " (corrupted residue). Skipping it. REVERT: A 21 MET cc_start: 0.7029 (mtm) cc_final: 0.6671 (mtm) REVERT: A 37 GLN cc_start: 0.7826 (tp40) cc_final: 0.7432 (tp40) REVERT: A 76 LEU cc_start: 0.8177 (mt) cc_final: 0.7971 (mp) REVERT: A 80 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6818 (mm-30) REVERT: A 88 LYS cc_start: 0.8150 (tttp) cc_final: 0.7915 (tttp) REVERT: A 121 GLU cc_start: 0.7295 (mt-10) cc_final: 0.7053 (mt-10) REVERT: A 124 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6774 (mt-10) REVERT: A 151 HIS cc_start: 0.7410 (t70) cc_final: 0.7026 (t70) REVERT: A 201 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8056 (tttm) REVERT: A 204 LEU cc_start: 0.8311 (mt) cc_final: 0.8012 (mm) REVERT: B 37 GLN cc_start: 0.8320 (tm-30) cc_final: 0.7988 (tm-30) REVERT: B 38 ARG cc_start: 0.8476 (tpp-160) cc_final: 0.8045 (mmt-90) REVERT: B 48 GLU cc_start: 0.7305 (tt0) cc_final: 0.6842 (tt0) REVERT: B 63 SER cc_start: 0.8228 (m) cc_final: 0.7985 (p) REVERT: B 64 ARG cc_start: 0.7672 (mmt180) cc_final: 0.7425 (mmt180) REVERT: B 85 SER cc_start: 0.8108 (m) cc_final: 0.7813 (t) REVERT: B 89 GLU cc_start: 0.7457 (tp30) cc_final: 0.6844 (tp30) REVERT: B 110 ARG cc_start: 0.7318 (mtt90) cc_final: 0.7001 (mtt90) REVERT: B 150 MET cc_start: 0.7466 (ttp) cc_final: 0.7249 (ttp) REVERT: C 21 MET cc_start: 0.7076 (mtp) cc_final: 0.6805 (mtt) REVERT: C 132 THR cc_start: 0.8555 (p) cc_final: 0.8337 (t) REVERT: D 89 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7021 (tt0) REVERT: D 135 SER cc_start: 0.8430 (t) cc_final: 0.8061 (p) REVERT: D 164 LEU cc_start: 0.8642 (tp) cc_final: 0.8186 (mp) REVERT: D 198 ARG cc_start: 0.7454 (mtt180) cc_final: 0.7049 (mtt180) REVERT: D 201 LYS cc_start: 0.7866 (mtpt) cc_final: 0.7392 (mtpt) REVERT: E 38 ARG cc_start: 0.8209 (tpp-160) cc_final: 0.7901 (mmp-170) REVERT: E 40 ARG cc_start: 0.7071 (ptp-110) cc_final: 0.6809 (ptp-110) REVERT: E 66 TYR cc_start: 0.8431 (t80) cc_final: 0.8129 (t80) REVERT: E 70 GLN cc_start: 0.7946 (mm-40) cc_final: 0.7618 (tp40) REVERT: E 89 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7179 (mm-30) REVERT: E 210 MET cc_start: 0.8166 (ttm) cc_final: 0.7938 (ttm) outliers start: 46 outliers final: 30 residues processed: 347 average time/residue: 0.1120 time to fit residues: 50.2126 Evaluate side-chains 358 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 326 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain H residue 23 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 109 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 113 optimal weight: 9.9990 chunk 56 optimal weight: 0.6980 chunk 57 optimal weight: 7.9990 chunk 91 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 70 optimal weight: 0.0770 chunk 61 optimal weight: 0.0770 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 ASN C 122 ASN C 208 ASN E 37 GLN E 75 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.143529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.120115 restraints weight = 14107.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.124428 restraints weight = 6207.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.127379 restraints weight = 3679.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.129272 restraints weight = 2659.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.130209 restraints weight = 2165.512| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9751 Z= 0.141 Angle : 0.502 8.096 13193 Z= 0.265 Chirality : 0.036 0.132 1536 Planarity : 0.003 0.047 1664 Dihedral : 3.518 17.175 1303 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 4.33 % Allowed : 20.42 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.70 (0.24), residues: 1200 helix: 3.60 (0.15), residues: 1032 sheet: None (None), residues: 0 loop : -0.61 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 219 TYR 0.021 0.001 TYR E 84 PHE 0.025 0.001 PHE E 90 TRP 0.013 0.001 TRP C 147 HIS 0.015 0.001 HIS B 151 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9751) covalent geometry : angle 0.50218 (13193) hydrogen bonds : bond 0.06608 ( 784) hydrogen bonds : angle 3.16226 ( 2343) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 327 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO G 37 " (corrupted residue). Skipping it. Corrupt residue: chain: G residue: PRO 37 >>> skipping TARDY: cannot create tardy model for: "ASP H 35 " (corrupted residue). Skipping it. REVERT: A 21 MET cc_start: 0.7081 (mtm) cc_final: 0.6870 (mtm) REVERT: A 37 GLN cc_start: 0.7808 (tp40) cc_final: 0.7401 (tp40) REVERT: A 80 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6798 (mm-30) REVERT: A 88 LYS cc_start: 0.8145 (tttp) cc_final: 0.7917 (tttp) REVERT: A 120 LEU cc_start: 0.8359 (mt) cc_final: 0.7447 (mt) REVERT: A 121 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6915 (mt-10) REVERT: A 124 GLU cc_start: 0.7026 (mt-10) cc_final: 0.6755 (mt-10) REVERT: A 151 HIS cc_start: 0.7407 (t70) cc_final: 0.7007 (t70) REVERT: A 201 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8062 (tttm) REVERT: A 204 LEU cc_start: 0.8277 (mt) cc_final: 0.7978 (mm) REVERT: B 21 MET cc_start: 0.7621 (mmm) cc_final: 0.7114 (mmm) REVERT: B 38 ARG cc_start: 0.8489 (tpp-160) cc_final: 0.8206 (mmt-90) REVERT: B 48 GLU cc_start: 0.7288 (tt0) cc_final: 0.6845 (tt0) REVERT: B 63 SER cc_start: 0.8227 (m) cc_final: 0.7989 (p) REVERT: B 64 ARG cc_start: 0.7668 (mmt180) cc_final: 0.7420 (mmt180) REVERT: B 85 SER cc_start: 0.8098 (m) cc_final: 0.7792 (t) REVERT: B 89 GLU cc_start: 0.7437 (tp30) cc_final: 0.6827 (tp30) REVERT: B 110 ARG cc_start: 0.7316 (mtt90) cc_final: 0.6999 (mtt90) REVERT: B 150 MET cc_start: 0.7462 (ttp) cc_final: 0.7261 (ttp) REVERT: B 156 LEU cc_start: 0.8841 (tp) cc_final: 0.8637 (tt) REVERT: B 180 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8253 (tt) REVERT: C 21 MET cc_start: 0.7067 (mtp) cc_final: 0.6831 (mtt) REVERT: C 132 THR cc_start: 0.8511 (p) cc_final: 0.8303 (t) REVERT: D 89 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7005 (tt0) REVERT: D 112 MET cc_start: 0.7908 (mtt) cc_final: 0.7706 (mtt) REVERT: D 135 SER cc_start: 0.8436 (t) cc_final: 0.8064 (p) REVERT: D 164 LEU cc_start: 0.8596 (tp) cc_final: 0.8143 (mp) REVERT: D 198 ARG cc_start: 0.7461 (mtt180) cc_final: 0.7060 (mtt180) REVERT: D 201 LYS cc_start: 0.7857 (mtpt) cc_final: 0.7409 (mtpt) REVERT: E 38 ARG cc_start: 0.8221 (tpp-160) cc_final: 0.7894 (mmp-170) REVERT: E 40 ARG cc_start: 0.7100 (ptp-110) cc_final: 0.6832 (ptp-110) REVERT: E 64 ARG cc_start: 0.7569 (mtt180) cc_final: 0.7250 (mtm180) REVERT: E 89 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7193 (mm-30) REVERT: E 198 ARG cc_start: 0.8453 (mmm-85) cc_final: 0.7753 (mtt180) REVERT: E 210 MET cc_start: 0.8166 (ttm) cc_final: 0.7929 (ttm) outliers start: 43 outliers final: 30 residues processed: 339 average time/residue: 0.1140 time to fit residues: 50.1389 Evaluate side-chains 360 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 327 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain H residue 23 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 78 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 95 optimal weight: 0.0470 chunk 9 optimal weight: 0.9980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 ASN C 208 ASN E 37 GLN E 75 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.143918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.120644 restraints weight = 14170.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.124984 restraints weight = 6258.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.127834 restraints weight = 3694.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.129790 restraints weight = 2668.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.130822 restraints weight = 2172.636| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9751 Z= 0.142 Angle : 0.507 7.845 13193 Z= 0.266 Chirality : 0.036 0.133 1536 Planarity : 0.003 0.052 1664 Dihedral : 3.512 16.986 1303 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 4.43 % Allowed : 20.42 % Favored : 75.15 % 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: 4.65 (0.24), residues: 1200 helix: 3.57 (0.15), residues: 1032 sheet: None (None), residues: 0 loop : -0.63 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 219 TYR 0.022 0.001 TYR E 84 PHE 0.026 0.001 PHE E 90 TRP 0.012 0.001 TRP C 147 HIS 0.003 0.000 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9751) covalent geometry : angle 0.50746 (13193) hydrogen bonds : bond 0.06614 ( 784) hydrogen bonds : angle 3.15201 ( 2343) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 327 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO G 37 " (corrupted residue). Skipping it. Corrupt residue: chain: G residue: PRO 37 >>> skipping TARDY: cannot create tardy model for: "ASP H 35 " (corrupted residue). Skipping it. REVERT: A 21 MET cc_start: 0.7091 (mtm) cc_final: 0.6856 (mtm) REVERT: A 37 GLN cc_start: 0.7794 (tp40) cc_final: 0.7390 (tp40) REVERT: A 80 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6820 (mm-30) REVERT: A 88 LYS cc_start: 0.8149 (tttp) cc_final: 0.7919 (tttp) REVERT: A 120 LEU cc_start: 0.8352 (mt) cc_final: 0.7493 (mt) REVERT: A 121 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6879 (mt-10) REVERT: A 124 GLU cc_start: 0.7027 (mt-10) cc_final: 0.6755 (mt-10) REVERT: A 151 HIS cc_start: 0.7418 (t70) cc_final: 0.6999 (t70) REVERT: A 201 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8068 (tttm) REVERT: A 204 LEU cc_start: 0.8313 (mt) cc_final: 0.7990 (mm) REVERT: B 21 MET cc_start: 0.7619 (mmm) cc_final: 0.7123 (mmm) REVERT: B 38 ARG cc_start: 0.8534 (tpp-160) cc_final: 0.8216 (mmt-90) REVERT: B 48 GLU cc_start: 0.7305 (tt0) cc_final: 0.6881 (tt0) REVERT: B 63 SER cc_start: 0.8229 (m) cc_final: 0.7989 (p) REVERT: B 64 ARG cc_start: 0.7667 (mmt180) cc_final: 0.7420 (mmt180) REVERT: B 85 SER cc_start: 0.8088 (m) cc_final: 0.7779 (t) REVERT: B 89 GLU cc_start: 0.7445 (tp30) cc_final: 0.6836 (tp30) REVERT: B 110 ARG cc_start: 0.7315 (mtt90) cc_final: 0.7006 (mtt90) REVERT: B 180 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8246 (tt) REVERT: C 21 MET cc_start: 0.7051 (mtp) cc_final: 0.6808 (mtt) REVERT: C 132 THR cc_start: 0.8518 (p) cc_final: 0.8307 (t) REVERT: D 89 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7006 (tt0) REVERT: D 135 SER cc_start: 0.8364 (t) cc_final: 0.7997 (p) REVERT: D 164 LEU cc_start: 0.8629 (tp) cc_final: 0.8195 (mp) REVERT: D 198 ARG cc_start: 0.7460 (mtt180) cc_final: 0.7107 (mtt180) REVERT: D 201 LYS cc_start: 0.7854 (mtpt) cc_final: 0.7380 (mtpt) REVERT: E 35 ILE cc_start: 0.8748 (tp) cc_final: 0.8537 (tt) REVERT: E 38 ARG cc_start: 0.8228 (tpp-160) cc_final: 0.7918 (mmp-170) REVERT: E 40 ARG cc_start: 0.7113 (ptp-110) cc_final: 0.6831 (ptp-110) REVERT: E 64 ARG cc_start: 0.7563 (mtt180) cc_final: 0.7247 (mtm180) REVERT: E 89 GLU cc_start: 0.7416 (mm-30) cc_final: 0.7188 (mm-30) REVERT: E 198 ARG cc_start: 0.8453 (mmm-85) cc_final: 0.7766 (mtt180) REVERT: E 210 MET cc_start: 0.8193 (ttm) cc_final: 0.7963 (ttm) outliers start: 44 outliers final: 34 residues processed: 339 average time/residue: 0.1099 time to fit residues: 47.9625 Evaluate side-chains 362 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 325 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain H residue 23 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN C 208 ASN E 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.142146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.118840 restraints weight = 14144.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.123120 restraints weight = 6257.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.126059 restraints weight = 3694.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.127893 restraints weight = 2669.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.128956 restraints weight = 2181.494| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9751 Z= 0.161 Angle : 0.533 9.145 13193 Z= 0.279 Chirality : 0.037 0.134 1536 Planarity : 0.003 0.050 1664 Dihedral : 3.493 16.456 1303 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 4.33 % Allowed : 20.82 % Favored : 74.85 % 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: 4.52 (0.24), residues: 1200 helix: 3.48 (0.15), residues: 1031 sheet: None (None), residues: 0 loop : -0.66 (0.49), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 219 TYR 0.024 0.001 TYR E 84 PHE 0.026 0.001 PHE E 90 TRP 0.013 0.001 TRP C 147 HIS 0.003 0.000 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 9751) covalent geometry : angle 0.53291 (13193) hydrogen bonds : bond 0.07223 ( 784) hydrogen bonds : angle 3.22866 ( 2343) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 336 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO G 37 " (corrupted residue). Skipping it. Corrupt residue: chain: G residue: PRO 37 >>> skipping TARDY: cannot create tardy model for: "ASP H 35 " (corrupted residue). Skipping it. REVERT: A 21 MET cc_start: 0.7103 (mtm) cc_final: 0.6875 (mtm) REVERT: A 37 GLN cc_start: 0.7833 (tp40) cc_final: 0.7435 (tp40) REVERT: A 80 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6835 (mm-30) REVERT: A 87 PHE cc_start: 0.8026 (t80) cc_final: 0.7442 (t80) REVERT: A 88 LYS cc_start: 0.8147 (tttp) cc_final: 0.7931 (tttp) REVERT: A 121 GLU cc_start: 0.7315 (mt-10) cc_final: 0.7019 (mt-10) REVERT: A 124 GLU cc_start: 0.7053 (mt-10) cc_final: 0.6786 (mt-10) REVERT: A 151 HIS cc_start: 0.7433 (t70) cc_final: 0.7004 (t70) REVERT: A 201 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8077 (tttm) REVERT: B 37 GLN cc_start: 0.8420 (tm-30) cc_final: 0.8116 (tm-30) REVERT: B 38 ARG cc_start: 0.8544 (tpp-160) cc_final: 0.8102 (mmt-90) REVERT: B 63 SER cc_start: 0.8249 (m) cc_final: 0.7999 (p) REVERT: B 64 ARG cc_start: 0.7683 (mmt180) cc_final: 0.7452 (mmt180) REVERT: B 85 SER cc_start: 0.8133 (m) cc_final: 0.7830 (t) REVERT: B 89 GLU cc_start: 0.7463 (tp30) cc_final: 0.6878 (tp30) REVERT: B 110 ARG cc_start: 0.7310 (mtt90) cc_final: 0.7000 (mtt90) REVERT: B 135 SER cc_start: 0.8609 (t) cc_final: 0.8372 (t) REVERT: B 156 LEU cc_start: 0.8739 (tt) cc_final: 0.8491 (tp) REVERT: B 196 ASN cc_start: 0.8304 (m-40) cc_final: 0.8099 (m-40) REVERT: C 21 MET cc_start: 0.7099 (mtp) cc_final: 0.6832 (mtt) REVERT: C 132 THR cc_start: 0.8574 (p) cc_final: 0.8372 (t) REVERT: D 89 GLU cc_start: 0.7427 (tt0) cc_final: 0.7006 (tt0) REVERT: D 135 SER cc_start: 0.8457 (t) cc_final: 0.8093 (p) REVERT: D 164 LEU cc_start: 0.8648 (tp) cc_final: 0.8208 (mp) REVERT: D 198 ARG cc_start: 0.7467 (mtt180) cc_final: 0.7116 (mtt180) REVERT: D 201 LYS cc_start: 0.7846 (mtpt) cc_final: 0.7438 (mtpt) REVERT: E 38 ARG cc_start: 0.8243 (tpp-160) cc_final: 0.7929 (mmp-170) REVERT: E 40 ARG cc_start: 0.7098 (ptp-110) cc_final: 0.6841 (ptp-110) REVERT: E 64 ARG cc_start: 0.7585 (mtt180) cc_final: 0.7262 (mtm180) REVERT: E 89 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7162 (mm-30) REVERT: E 121 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7182 (mm-30) REVERT: E 198 ARG cc_start: 0.8475 (mmm-85) cc_final: 0.7782 (mtt180) REVERT: E 210 MET cc_start: 0.8192 (ttm) cc_final: 0.7962 (ttm) outliers start: 43 outliers final: 33 residues processed: 349 average time/residue: 0.1120 time to fit residues: 50.3331 Evaluate side-chains 375 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 341 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain H residue 23 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 113 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 208 ASN E 37 GLN J 22 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.141272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.117819 restraints weight = 14207.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.122127 restraints weight = 6271.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.125064 restraints weight = 3699.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.126901 restraints weight = 2654.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.128040 restraints weight = 2167.103| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9751 Z= 0.173 Angle : 0.544 8.901 13193 Z= 0.286 Chirality : 0.037 0.140 1536 Planarity : 0.003 0.054 1664 Dihedral : 3.528 16.606 1303 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.53 % Allowed : 21.43 % Favored : 74.04 % 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: 4.42 (0.24), residues: 1200 helix: 3.41 (0.15), residues: 1030 sheet: None (None), residues: 0 loop : -0.59 (0.50), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 219 TYR 0.024 0.002 TYR E 84 PHE 0.025 0.001 PHE E 90 TRP 0.012 0.001 TRP C 147 HIS 0.003 0.000 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 9751) covalent geometry : angle 0.54409 (13193) hydrogen bonds : bond 0.07504 ( 784) hydrogen bonds : angle 3.29000 ( 2343) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 336 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO G 37 " (corrupted residue). Skipping it. Corrupt residue: chain: G residue: PRO 37 >>> skipping TARDY: cannot create tardy model for: "ASP H 35 " (corrupted residue). Skipping it. REVERT: A 37 GLN cc_start: 0.7847 (tp40) cc_final: 0.7456 (tp40) REVERT: A 80 GLU cc_start: 0.7206 (mt-10) cc_final: 0.6850 (mm-30) REVERT: A 88 LYS cc_start: 0.8147 (tttp) cc_final: 0.7931 (tttp) REVERT: A 121 GLU cc_start: 0.7335 (mt-10) cc_final: 0.6987 (mt-10) REVERT: A 124 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6810 (mt-10) REVERT: A 151 HIS cc_start: 0.7424 (t70) cc_final: 0.7004 (t70) REVERT: A 201 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.8087 (tttm) REVERT: B 37 GLN cc_start: 0.8442 (tm-30) cc_final: 0.8195 (tm-30) REVERT: B 38 ARG cc_start: 0.8552 (tpp-160) cc_final: 0.8344 (tpp-160) REVERT: B 63 SER cc_start: 0.8246 (m) cc_final: 0.7996 (p) REVERT: B 64 ARG cc_start: 0.7682 (mmt180) cc_final: 0.7449 (mmt180) REVERT: B 85 SER cc_start: 0.8148 (m) cc_final: 0.7831 (t) REVERT: B 110 ARG cc_start: 0.7303 (mtt90) cc_final: 0.6976 (mtt90) REVERT: B 135 SER cc_start: 0.8670 (t) cc_final: 0.8417 (t) REVERT: B 136 ILE cc_start: 0.8398 (mm) cc_final: 0.8179 (mm) REVERT: B 156 LEU cc_start: 0.8750 (tt) cc_final: 0.8517 (tp) REVERT: B 196 ASN cc_start: 0.8308 (m-40) cc_final: 0.8105 (m-40) REVERT: C 21 MET cc_start: 0.7129 (mtp) cc_final: 0.6849 (mtt) REVERT: C 132 THR cc_start: 0.8591 (p) cc_final: 0.8220 (t) REVERT: C 136 ILE cc_start: 0.8458 (tp) cc_final: 0.7911 (tt) REVERT: D 89 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7023 (tt0) REVERT: D 135 SER cc_start: 0.8460 (t) cc_final: 0.8101 (p) REVERT: D 164 LEU cc_start: 0.8667 (tp) cc_final: 0.8236 (mp) REVERT: D 198 ARG cc_start: 0.7412 (mtt180) cc_final: 0.7053 (mtt180) REVERT: D 201 LYS cc_start: 0.7832 (mtpt) cc_final: 0.7447 (mtpt) REVERT: E 38 ARG cc_start: 0.8274 (tpp-160) cc_final: 0.7918 (mmp-170) REVERT: E 40 ARG cc_start: 0.7081 (ptp-110) cc_final: 0.6815 (ptp-110) REVERT: E 64 ARG cc_start: 0.7575 (mtt180) cc_final: 0.7248 (mtm110) REVERT: E 89 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7166 (mm-30) REVERT: E 121 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7192 (mm-30) REVERT: E 198 ARG cc_start: 0.8500 (mmm-85) cc_final: 0.7816 (mtt180) REVERT: E 210 MET cc_start: 0.8190 (ttm) cc_final: 0.7959 (ttm) outliers start: 45 outliers final: 36 residues processed: 349 average time/residue: 0.1152 time to fit residues: 51.8326 Evaluate side-chains 373 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 335 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain H residue 23 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 53 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 104 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 66 optimal weight: 0.4980 chunk 95 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 208 ASN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.142196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.119083 restraints weight = 14070.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.123316 restraints weight = 6300.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.126180 restraints weight = 3731.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.127960 restraints weight = 2704.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.129164 restraints weight = 2216.306| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9751 Z= 0.161 Angle : 0.550 9.131 13193 Z= 0.290 Chirality : 0.037 0.137 1536 Planarity : 0.003 0.058 1664 Dihedral : 3.546 17.306 1303 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.72 % Allowed : 22.13 % Favored : 74.14 % 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: 4.38 (0.24), residues: 1200 helix: 3.38 (0.15), residues: 1033 sheet: None (None), residues: 0 loop : -0.71 (0.50), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 219 TYR 0.024 0.001 TYR E 84 PHE 0.024 0.001 PHE E 90 TRP 0.013 0.001 TRP C 147 HIS 0.003 0.000 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 9751) covalent geometry : angle 0.55020 (13193) hydrogen bonds : bond 0.07143 ( 784) hydrogen bonds : angle 3.29552 ( 2343) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 337 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO G 37 " (corrupted residue). Skipping it. Corrupt residue: chain: G residue: PRO 37 >>> skipping TARDY: cannot create tardy model for: "ASP H 35 " (corrupted residue). Skipping it. REVERT: A 37 GLN cc_start: 0.7816 (tp40) cc_final: 0.7430 (tp40) REVERT: A 80 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6813 (mm-30) REVERT: A 88 LYS cc_start: 0.8140 (tttp) cc_final: 0.7915 (tttp) REVERT: A 120 LEU cc_start: 0.8417 (mt) cc_final: 0.7510 (mt) REVERT: A 121 GLU cc_start: 0.7340 (mt-10) cc_final: 0.6998 (mt-10) REVERT: A 124 GLU cc_start: 0.7011 (mt-10) cc_final: 0.6772 (mt-10) REVERT: A 151 HIS cc_start: 0.7510 (t70) cc_final: 0.7073 (t70) REVERT: A 201 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.8097 (tttm) REVERT: B 37 GLN cc_start: 0.8449 (tm-30) cc_final: 0.8121 (tm-30) REVERT: B 38 ARG cc_start: 0.8538 (tpp-160) cc_final: 0.8085 (mmt-90) REVERT: B 63 SER cc_start: 0.8209 (m) cc_final: 0.7971 (p) REVERT: B 64 ARG cc_start: 0.7623 (mmt180) cc_final: 0.7383 (mmt180) REVERT: B 85 SER cc_start: 0.8126 (m) cc_final: 0.7779 (t) REVERT: B 110 ARG cc_start: 0.7280 (mtt90) cc_final: 0.6987 (mtt90) REVERT: B 135 SER cc_start: 0.8670 (t) cc_final: 0.8414 (t) REVERT: B 136 ILE cc_start: 0.8376 (mm) cc_final: 0.8169 (mm) REVERT: B 156 LEU cc_start: 0.8697 (tt) cc_final: 0.8455 (tp) REVERT: C 21 MET cc_start: 0.7104 (mtp) cc_final: 0.6829 (mtt) REVERT: C 132 THR cc_start: 0.8583 (p) cc_final: 0.8203 (t) REVERT: C 136 ILE cc_start: 0.8439 (tp) cc_final: 0.7885 (tt) REVERT: C 211 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7455 (tt0) REVERT: D 89 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6999 (tt0) REVERT: D 135 SER cc_start: 0.8440 (t) cc_final: 0.8082 (p) REVERT: D 164 LEU cc_start: 0.8668 (tp) cc_final: 0.8272 (mp) REVERT: D 198 ARG cc_start: 0.7460 (mtt180) cc_final: 0.7096 (mtt180) REVERT: D 201 LYS cc_start: 0.7822 (mtpt) cc_final: 0.7474 (mtpt) REVERT: E 37 GLN cc_start: 0.8385 (tm130) cc_final: 0.8148 (tm-30) REVERT: E 38 ARG cc_start: 0.8217 (tpp-160) cc_final: 0.7914 (mmp-170) REVERT: E 40 ARG cc_start: 0.7019 (ptp-110) cc_final: 0.6748 (ptp-110) REVERT: E 64 ARG cc_start: 0.7551 (mtt180) cc_final: 0.7218 (mtm110) REVERT: E 89 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7149 (mm-30) REVERT: E 121 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7196 (mm-30) REVERT: E 198 ARG cc_start: 0.8497 (mmm-85) cc_final: 0.7815 (mtt180) REVERT: E 210 MET cc_start: 0.8133 (ttm) cc_final: 0.7914 (ttm) outliers start: 37 outliers final: 33 residues processed: 348 average time/residue: 0.1104 time to fit residues: 49.8648 Evaluate side-chains 369 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 333 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain H residue 23 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 15 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 84 optimal weight: 6.9990 chunk 83 optimal weight: 0.5980 chunk 56 optimal weight: 0.1980 chunk 29 optimal weight: 0.9980 chunk 37 optimal weight: 0.0370 chunk 73 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 208 ASN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.144640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.121499 restraints weight = 14078.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.125722 restraints weight = 6268.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.128628 restraints weight = 3692.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.130491 restraints weight = 2669.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.131624 restraints weight = 2173.278| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9751 Z= 0.147 Angle : 0.568 14.711 13193 Z= 0.290 Chirality : 0.036 0.173 1536 Planarity : 0.003 0.059 1664 Dihedral : 3.533 16.035 1303 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.42 % Allowed : 24.04 % Favored : 72.54 % 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: 4.48 (0.24), residues: 1200 helix: 3.44 (0.15), residues: 1036 sheet: None (None), residues: 0 loop : -0.68 (0.50), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 219 TYR 0.023 0.001 TYR E 84 PHE 0.023 0.001 PHE D 90 TRP 0.013 0.001 TRP C 147 HIS 0.003 0.000 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9751) covalent geometry : angle 0.56793 (13193) hydrogen bonds : bond 0.06511 ( 784) hydrogen bonds : angle 3.22955 ( 2343) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1594.36 seconds wall clock time: 28 minutes 1.67 seconds (1681.67 seconds total)