Starting phenix.real_space_refine on Wed Aug 5 23:55:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i91_52748/08_2026/9i91_52748.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i91_52748/08_2026/9i91_52748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9i91_52748/08_2026/9i91_52748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i91_52748/08_2026/9i91_52748.map" model { file = "/net/cci-nas-00/data/ceres_data/9i91_52748/08_2026/9i91_52748.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i91_52748/08_2026/9i91_52748.cif" } resolution = 2.96 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= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 88 5.49 5 S 55 5.16 5 C 7332 2.51 5 N 2072 2.21 5 O 2462 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12009 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1777 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 10, 'TRANS': 218} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1794 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 10, 'TRANS': 219} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1571 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 10, 'TRANS': 218} Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 228 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 12, 'PHE:plan': 1, 'GLN:plan1': 3, 'ASN:plan1': 1, 'TYR:plan': 3, 'GLU:plan': 12, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 180 Chain: "D" Number of atoms: 1596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1596 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 10, 'TRANS': 216} Unresolved non-hydrogen bonds: 233 Unresolved non-hydrogen angles: 283 Unresolved non-hydrogen dihedrals: 188 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 10, 'ASP:plan': 11, 'GLN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 154 Chain: "E" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1748 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 10, 'TRANS': 218} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 3, 'GLN:plan1': 2, 'GLU:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 51 Chain: "F" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1720 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 10, 'TRANS': 219} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 10, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 85 Chain: "G" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 579 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "H" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 607 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "I" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 308 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "J" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 305 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.77, per 1000 atoms: 0.23 Number of scatterers: 12009 At special positions: 0 Unit cell: (85.696, 98.88, 193.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 55 16.00 P 88 15.00 O 2462 8.00 N 2072 7.00 C 7332 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 502.3 milliseconds 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2638 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 14 sheets defined 32.0% alpha, 29.3% beta 21 base pairs and 49 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 75 through 82 removed outlier: 3.689A pdb=" N ILE A 79 " --> pdb=" O THR A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 101 No H-bonds generated for 'chain 'A' and resid 99 through 101' Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 119 through 133 Processing helix chain 'A' and resid 169 through 173 removed outlier: 3.686A pdb=" N ILE A 173 " --> pdb=" O PRO A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 182 removed outlier: 3.786A pdb=" N LEU A 181 " --> pdb=" O PHE A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 203 removed outlier: 4.085A pdb=" N GLN A 197 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 198 " --> pdb=" O MET A 194 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 213 through 229 Processing helix chain 'B' and resid 56 through 58 No H-bonds generated for 'chain 'B' and resid 56 through 58' Processing helix chain 'B' and resid 75 through 82 removed outlier: 3.852A pdb=" N ILE B 79 " --> pdb=" O THR B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.898A pdb=" N VAL B 101 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 133 Processing helix chain 'B' and resid 169 through 173 removed outlier: 3.729A pdb=" N ILE B 173 " --> pdb=" O PRO B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'B' and resid 188 through 202 removed outlier: 3.991A pdb=" N GLY B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLN B 197 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL B 198 " --> pdb=" O MET B 194 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET B 202 " --> pdb=" O VAL B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 211 removed outlier: 3.547A pdb=" N ARG B 210 " --> pdb=" O ASN B 207 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR B 211 " --> pdb=" O PRO B 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 207 through 211' Processing helix chain 'B' and resid 213 through 230 removed outlier: 3.509A pdb=" N GLY B 229 " --> pdb=" O THR B 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 82 removed outlier: 4.059A pdb=" N ILE C 79 " --> pdb=" O THR C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 133 removed outlier: 3.516A pdb=" N LEU C 129 " --> pdb=" O LEU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 173 Processing helix chain 'C' and resid 178 through 183 Processing helix chain 'C' and resid 189 through 203 removed outlier: 3.890A pdb=" N LYS C 193 " --> pdb=" O PRO C 189 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET C 194 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET C 202 " --> pdb=" O VAL C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 211 removed outlier: 3.626A pdb=" N TYR C 211 " --> pdb=" O PRO C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 229 removed outlier: 3.507A pdb=" N GLU C 221 " --> pdb=" O GLU C 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 133 removed outlier: 3.612A pdb=" N VAL D 123 " --> pdb=" O SER D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 173 removed outlier: 3.852A pdb=" N ILE D 173 " --> pdb=" O PRO D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 182 Processing helix chain 'D' and resid 188 through 200 removed outlier: 3.909A pdb=" N ASP D 200 " --> pdb=" O GLY D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 227 removed outlier: 3.742A pdb=" N GLU D 221 " --> pdb=" O GLU D 217 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU D 222 " --> pdb=" O GLN D 218 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE D 223 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR D 225 " --> pdb=" O GLU D 221 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 58 No H-bonds generated for 'chain 'E' and resid 56 through 58' Processing helix chain 'E' and resid 75 through 82 removed outlier: 3.521A pdb=" N ILE E 79 " --> pdb=" O THR E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 101 No H-bonds generated for 'chain 'E' and resid 99 through 101' Processing helix chain 'E' and resid 102 through 104 No H-bonds generated for 'chain 'E' and resid 102 through 104' Processing helix chain 'E' and resid 119 through 133 Processing helix chain 'E' and resid 169 through 173 removed outlier: 3.790A pdb=" N ILE E 173 " --> pdb=" O PRO E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 183 removed outlier: 3.742A pdb=" N ASP E 182 " --> pdb=" O PHE E 178 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN E 183 " --> pdb=" O PRO E 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 178 through 183' Processing helix chain 'E' and resid 188 through 202 removed outlier: 4.173A pdb=" N MET E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET E 202 " --> pdb=" O VAL E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 211 Processing helix chain 'E' and resid 213 through 229 removed outlier: 3.516A pdb=" N ILE E 223 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP E 224 " --> pdb=" O GLN E 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 58 No H-bonds generated for 'chain 'F' and resid 56 through 58' Processing helix chain 'F' and resid 75 through 81 removed outlier: 3.906A pdb=" N ILE F 79 " --> pdb=" O THR F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 104 No H-bonds generated for 'chain 'F' and resid 102 through 104' Processing helix chain 'F' and resid 119 through 132 Processing helix chain 'F' and resid 169 through 173 removed outlier: 3.595A pdb=" N ILE F 173 " --> pdb=" O PRO F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 183 removed outlier: 3.815A pdb=" N ASP F 182 " --> pdb=" O PHE F 178 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN F 183 " --> pdb=" O PRO F 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 178 through 183' Processing helix chain 'F' and resid 188 through 203 removed outlier: 4.013A pdb=" N GLN F 197 " --> pdb=" O LYS F 193 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL F 198 " --> pdb=" O MET F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 211 removed outlier: 3.587A pdb=" N TYR F 211 " --> pdb=" O PRO F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 229 removed outlier: 3.574A pdb=" N LEU F 222 " --> pdb=" O GLN F 218 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE F 223 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP F 224 " --> pdb=" O GLN F 220 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 11 removed outlier: 3.873A pdb=" N TRP A 5 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N THR A 166 " --> pdb=" O ASP A 107 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER A 109 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL A 164 " --> pdb=" O SER A 109 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N PHE A 111 " --> pdb=" O MET A 162 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N MET A 162 " --> pdb=" O PHE A 111 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N GLU A 113 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 12.488A pdb=" N GLU A 160 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG A 159 " --> pdb=" O PHE A 156 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU A 148 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N VAL A 153 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ARG A 134 " --> pdb=" O VAL A 153 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU A 94 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N HIS A 139 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL A 92 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N THR A 141 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ILE A 90 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N ILE A 90 " --> pdb=" O THR A 6 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N SER A 8 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N VAL A 92 " --> pdb=" O SER A 8 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ALA A 10 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N GLU A 94 " --> pdb=" O ALA A 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 35 removed outlier: 3.925A pdb=" N ARG B 62 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL B 72 " --> pdb=" O TYR B 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 48 Processing sheet with id=AA4, first strand: chain 'A' and resid 60 through 63 Processing sheet with id=AA5, first strand: chain 'B' and resid 5 through 10 removed outlier: 3.741A pdb=" N TRP B 5 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG B 108 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N MET B 162 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 12.828A pdb=" N GLU B 160 " --> pdb=" O PRO B 114 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU B 148 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE B 137 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N THR B 141 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLU B 89 " --> pdb=" O THR B 141 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N ILE B 90 " --> pdb=" O THR B 6 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER B 8 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL B 92 " --> pdb=" O SER B 8 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ALA B 10 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 9.108A pdb=" N GLU B 94 " --> pdb=" O ALA B 10 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 153 through 156 removed outlier: 4.333A pdb=" N LEU C 148 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU C 94 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N HIS C 139 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL C 92 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N THR C 141 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ILE C 90 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TRP C 5 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N MET C 162 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 12.598A pdb=" N GLU C 160 " --> pdb=" O PRO C 114 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 33 removed outlier: 7.336A pdb=" N ARG D 62 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ALA D 73 " --> pdb=" O ARG D 62 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR D 64 " --> pdb=" O MET D 71 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N MET D 71 " --> pdb=" O TYR D 64 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 61 through 63 removed outlier: 3.546A pdb=" N ALA C 61 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL D 34 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA C 63 " --> pdb=" O HIS D 32 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N HIS D 32 " --> pdb=" O ALA C 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 5 through 10 removed outlier: 4.414A pdb=" N TRP D 5 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N MET D 162 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 12.937A pdb=" N GLU D 160 " --> pdb=" O PRO D 114 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL D 161 " --> pdb=" O LYS D 154 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N VAL D 153 " --> pdb=" O ARG D 134 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ARG D 134 " --> pdb=" O VAL D 153 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N MET D 135 " --> pdb=" O PHE D 95 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N PHE D 95 " --> pdb=" O MET D 135 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE D 137 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N THR D 141 " --> pdb=" O GLU D 89 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLU D 89 " --> pdb=" O THR D 141 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N ILE D 90 " --> pdb=" O THR D 6 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N SER D 8 " --> pdb=" O ILE D 90 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N VAL D 92 " --> pdb=" O SER D 8 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ALA D 10 " --> pdb=" O VAL D 92 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N GLU D 94 " --> pdb=" O ALA D 10 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 5 through 10 removed outlier: 3.831A pdb=" N TRP E 5 " --> pdb=" O VAL E 20 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR E 166 " --> pdb=" O ASP E 107 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N SER E 109 " --> pdb=" O VAL E 164 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL E 164 " --> pdb=" O SER E 109 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N PHE E 111 " --> pdb=" O MET E 162 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N MET E 162 " --> pdb=" O PHE E 111 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU E 113 " --> pdb=" O GLU E 160 " (cutoff:3.500A) removed outlier: 12.412A pdb=" N GLU E 160 " --> pdb=" O GLU E 113 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU E 148 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N VAL E 153 " --> pdb=" O ARG E 134 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N ARG E 134 " --> pdb=" O VAL E 153 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU E 94 " --> pdb=" O ILE E 137 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N HIS E 139 " --> pdb=" O VAL E 92 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL E 92 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N THR E 141 " --> pdb=" O ILE E 90 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILE E 90 " --> pdb=" O THR E 141 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N ILE E 90 " --> pdb=" O THR E 6 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N SER E 8 " --> pdb=" O ILE E 90 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL E 92 " --> pdb=" O SER E 8 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ALA E 10 " --> pdb=" O VAL E 92 " (cutoff:3.500A) removed outlier: 9.442A pdb=" N GLU E 94 " --> pdb=" O ALA E 10 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 32 through 35 Processing sheet with id=AB3, first strand: chain 'E' and resid 42 through 48 removed outlier: 3.904A pdb=" N VAL F 47 " --> pdb=" O ARG E 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 72 through 74 removed outlier: 3.615A pdb=" N ARG E 62 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 5 through 10 removed outlier: 3.785A pdb=" N TRP F 5 " --> pdb=" O VAL F 20 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL F 16 " --> pdb=" O ILE F 9 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR F 166 " --> pdb=" O ASP F 107 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N SER F 109 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL F 164 " --> pdb=" O SER F 109 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N PHE F 111 " --> pdb=" O MET F 162 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N MET F 162 " --> pdb=" O PHE F 111 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N GLU F 113 " --> pdb=" O GLU F 160 " (cutoff:3.500A) removed outlier: 11.842A pdb=" N GLU F 160 " --> pdb=" O GLU F 113 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU F 148 " --> pdb=" O LEU F 167 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N VAL F 153 " --> pdb=" O ARG F 134 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N ARG F 134 " --> pdb=" O VAL F 153 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU F 94 " --> pdb=" O ILE F 137 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N HIS F 139 " --> pdb=" O VAL F 92 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N VAL F 92 " --> pdb=" O HIS F 139 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N THR F 141 " --> pdb=" O ILE F 90 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ILE F 90 " --> pdb=" O THR F 141 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1158 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 49 stacking parallelities Total time for adding SS restraints: 1.90 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1915 1.32 - 1.44: 3643 1.44 - 1.57: 6600 1.57 - 1.70: 172 1.70 - 1.82: 99 Bond restraints: 12429 Sorted by residual: bond pdb=" CA ALA C 150 " pdb=" CB ALA C 150 " ideal model delta sigma weight residual 1.529 1.470 0.059 1.54e-02 4.22e+03 1.48e+01 bond pdb=" C ALA C 150 " pdb=" O ALA C 150 " ideal model delta sigma weight residual 1.235 1.190 0.045 1.19e-02 7.06e+03 1.41e+01 bond pdb=" C3' DT I 5 " pdb=" C2' DT I 5 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DG H 36 " pdb=" C2' DG H 36 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.40e+00 bond pdb=" C3' DA J 39 " pdb=" C2' DA J 39 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.05e+00 ... (remaining 12424 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 17055 2.53 - 5.05: 216 5.05 - 7.58: 34 7.58 - 10.11: 7 10.11 - 12.64: 1 Bond angle restraints: 17313 Sorted by residual: angle pdb=" N GLY E 69 " pdb=" CA GLY E 69 " pdb=" C GLY E 69 " ideal model delta sigma weight residual 112.51 105.24 7.27 1.53e+00 4.27e-01 2.26e+01 angle pdb=" N ALA C 150 " pdb=" CA ALA C 150 " pdb=" CB ALA C 150 " ideal model delta sigma weight residual 110.90 104.07 6.83 1.56e+00 4.11e-01 1.92e+01 angle pdb=" C ARG C 152 " pdb=" N VAL C 153 " pdb=" CA VAL C 153 " ideal model delta sigma weight residual 122.67 115.34 7.33 1.68e+00 3.54e-01 1.90e+01 angle pdb=" CB MET B 194 " pdb=" CG MET B 194 " pdb=" SD MET B 194 " ideal model delta sigma weight residual 112.70 125.34 -12.64 3.00e+00 1.11e-01 1.77e+01 angle pdb=" CB LYS A 188 " pdb=" CG LYS A 188 " pdb=" CD LYS A 188 " ideal model delta sigma weight residual 111.30 120.95 -9.65 2.30e+00 1.89e-01 1.76e+01 ... (remaining 17308 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 5849 17.79 - 35.58: 868 35.58 - 53.37: 379 53.37 - 71.16: 86 71.16 - 88.95: 18 Dihedral angle restraints: 7200 sinusoidal: 3150 harmonic: 4050 Sorted by residual: dihedral pdb=" N ALA C 150 " pdb=" C ALA C 150 " pdb=" CA ALA C 150 " pdb=" CB ALA C 150 " ideal model delta harmonic sigma weight residual 122.90 113.19 9.71 0 2.50e+00 1.60e-01 1.51e+01 dihedral pdb=" CA VAL C 18 " pdb=" C VAL C 18 " pdb=" N LYS C 19 " pdb=" CA LYS C 19 " ideal model delta harmonic sigma weight residual 180.00 162.26 17.74 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" C ALA C 150 " pdb=" N ALA C 150 " pdb=" CA ALA C 150 " pdb=" CB ALA C 150 " ideal model delta harmonic sigma weight residual -122.60 -113.83 -8.77 0 2.50e+00 1.60e-01 1.23e+01 ... (remaining 7197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1349 0.039 - 0.078: 398 0.078 - 0.117: 235 0.117 - 0.156: 21 0.156 - 0.195: 4 Chirality restraints: 2007 Sorted by residual: chirality pdb=" CA ARG C 152 " pdb=" N ARG C 152 " pdb=" C ARG C 152 " pdb=" CB ARG C 152 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.52e-01 chirality pdb=" CA VAL C 153 " pdb=" N VAL C 153 " pdb=" C VAL C 153 " pdb=" CB VAL C 153 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.97e-01 chirality pdb=" CA ALA C 150 " pdb=" N ALA C 150 " pdb=" C ALA C 150 " pdb=" CB ALA C 150 " both_signs ideal model delta sigma weight residual False 2.48 2.65 -0.17 2.00e-01 2.50e+01 6.82e-01 ... (remaining 2004 not shown) Planarity restraints: 1956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP E 68 " 0.013 2.00e-02 2.50e+03 2.76e-02 7.61e+00 pdb=" C ASP E 68 " -0.048 2.00e-02 2.50e+03 pdb=" O ASP E 68 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY E 69 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS E 188 " 0.044 5.00e-02 4.00e+02 6.79e-02 7.38e+00 pdb=" N PRO E 189 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO E 189 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 189 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 150 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.77e+00 pdb=" C ALA C 150 " -0.045 2.00e-02 2.50e+03 pdb=" O ALA C 150 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU C 151 " 0.016 2.00e-02 2.50e+03 ... (remaining 1953 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 507 2.71 - 3.25: 11482 3.25 - 3.80: 19012 3.80 - 4.35: 23671 4.35 - 4.90: 38440 Nonbonded interactions: 93112 Sorted by model distance: nonbonded pdb=" N GLN E 33 " pdb=" OE1 GLN E 33 " model vdw 2.157 3.120 nonbonded pdb=" N GLN B 197 " pdb=" OE1 GLN B 197 " model vdw 2.175 3.120 nonbonded pdb=" O ASP F 78 " pdb=" OG SER F 81 " model vdw 2.210 3.040 nonbonded pdb=" NH1 ARG D 143 " pdb=" O4' DC H 27 " model vdw 2.211 3.120 nonbonded pdb=" NZ LYS C 154 " pdb=" SD MET D 104 " model vdw 2.215 3.480 ... (remaining 93107 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 1 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 or (resid 13 through 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 25 or (resid 26 and (na \ me N or name CA or name C or name O or name CB )) or resid 27 or (resid 28 throu \ gh 30 and (name N or name CA or name C or name O or name CB )) or resid 31 throu \ gh 32 or (resid 33 through 39 and (name N or name CA or name C or name O or name \ CB )) or resid 40 or (resid 41 and (name N or name CA or name C or name O or na \ me CB )) or resid 42 or (resid 43 through 46 and (name N or name CA or name C or \ name O or name CB )) or resid 47 or (resid 48 through 50 and (name N or name CA \ or name C or name O or name CB )) or resid 51 through 52 or (resid 53 and (name \ N or name CA or name C or name O or name CB )) or resid 54 or (resid 55 through \ 59 and (name N or name CA or name C or name O or name CB )) or resid 60 through \ 61 or (resid 62 through 66 and (name N or name CA or name C or name O or name C \ B )) or resid 67 through 77 or (resid 78 and (name N or name CA or name C or nam \ e O or name CB )) or resid 79 through 80 or (resid 81 through 82 and (name N or \ name CA or name C or name O or name CB )) or resid 83 through 86 or (resid 87 th \ rough 89 and (name N or name CA or name C or name O or name CB )) or resid 90 or \ (resid 91 and (name N or name CA or name C or name O or name CB )) or resid 92 \ through 93 or (resid 94 and (name N or name CA or name C or name O or name CB )) \ or resid 95 through 101 or (resid 102 and (name N or name CA or name C or name \ O or name CB )) or resid 103 through 106 or (resid 107 and (name N or name CA or \ name C or name O or name CB )) or resid 108 through 112 or (resid 113 and (name \ N or name CA or name C or name O or name CB )) or resid 114 through 118 or (res \ id 119 through 120 and (name N or name CA or name C or name O or name CB )) or r \ esid 121 through 123 or (resid 124 and (name N or name CA or name C or name O or \ name CB )) or resid 125 through 126 or (resid 127 and (name N or name CA or nam \ e C or name O or name CB )) or resid 128 through 130 or (resid 131 through 136 a \ nd (name N or name CA or name C or name O or name CB )) or resid 137 through 142 \ or (resid 143 and (name N or name CA or name C or name O or name CB )) or resid \ 144 or (resid 145 and (name N or name CA or name C or name O or name CB )) or r \ esid 146 through 158 or (resid 159 and (name N or name CA or name C or name O or \ name CB )) or resid 160 through 161 or (resid 162 and (name N or name CA or nam \ e C or name O or name CB )) or resid 163 through 165 or (resid 166 and (name N o \ r name CA or name C or name O or name CB )) or resid 167 through 170 or (resid 1 \ 71 through 172 and (name N or name CA or name C or name O or name CB )) or resid \ 173 through 174 or (resid 175 and (name N or name CA or name C or name O or nam \ e CB )) or resid 176 or (resid 177 and (name N or name CA or name C or name O or \ name CB )) or resid 178 through 181 or (resid 182 through 188 and (name N or na \ me CA or name C or name O or name CB )) or resid 189 through 190 or (resid 191 t \ hrough 195 and (name N or name CA or name C or name O or name CB )) or resid 196 \ or (resid 197 and (name N or name CA or name C or name O or name CB )) or resid \ 198 through 200 or (resid 201 through 204 and (name N or name CA or name C or n \ ame O or name CB )) or resid 205 through 206 or (resid 207 and (name N or name C \ A or name C or name O or name CB )) or resid 208 or (resid 209 through 210 and ( \ name N or name CA or name C or name O or name CB )) or resid 211 through 216 or \ (resid 217 and (name N or name CA or name C or name O or name CB )) or resid 218 \ through 220 or (resid 221 through 227 and (name N or name CA or name C or name \ O or name CB )))) selection = (chain 'B' and ((resid 1 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 5 or (resid 6 and (name N or name CA or name C or \ name O or name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 or (resid 13 through 14 and (name \ N or name CA or name C or name O or name CB )) or resid 15 through 25 or (resid \ 26 and (name N or name CA or name C or name O or name CB )) or resid 27 or (resi \ d 28 through 30 and (name N or name CA or name C or name O or name CB )) or resi \ d 31 through 32 or (resid 33 through 39 and (name N or name CA or name C or name \ O or name CB )) or resid 40 or (resid 41 and (name N or name CA or name C or na \ me O or name CB )) or resid 42 or (resid 43 through 46 and (name N or name CA or \ name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (name N \ or name CA or name C or name O or name CB )) or resid 51 through 52 or (resid 53 \ and (name N or name CA or name C or name O or name CB )) or resid 54 or (resid \ 55 through 59 and (name N or name CA or name C or name O or name CB )) or resid \ 60 through 61 or (resid 62 through 66 and (name N or name CA or name C or name O \ or name CB )) or resid 67 or (resid 68 and (name N or name CA or name C or name \ O or name CB )) or resid 69 or (resid 70 through 73 and (name N or name CA or n \ ame C or name O or name CB )) or resid 74 or (resid 75 through 78 and (name N or \ name CA or name C or name O or name CB )) or resid 79 through 81 or (resid 82 a \ nd (name N or name CA or name C or name O or name CB )) or resid 83 or (resid 84 \ through 89 and (name N or name CA or name C or name O or name CB )) or resid 90 \ or (resid 91 and (name N or name CA or name C or name O or name CB )) or resid \ 92 through 93 or (resid 94 and (name N or name CA or name C or name O or name CB \ )) or resid 95 through 101 or (resid 102 and (name N or name CA or name C or na \ me O or name CB )) or resid 103 through 106 or (resid 107 and (name N or name CA \ or name C or name O or name CB )) or resid 108 through 112 or (resid 113 and (n \ ame N or name CA or name C or name O or name CB )) or resid 114 or (resid 115 th \ rough 120 and (name N or name CA or name C or name O or name CB )) or resid 121 \ through 123 or (resid 124 and (name N or name CA or name C or name O or name CB \ )) or resid 125 through 126 or (resid 127 and (name N or name CA or name C or na \ me O or name CB )) or resid 128 through 131 or (resid 132 through 136 and (name \ N or name CA or name C or name O or name CB )) or resid 137 through 142 or (resi \ d 143 and (name N or name CA or name C or name O or name CB )) or resid 144 or ( \ resid 145 and (name N or name CA or name C or name O or name CB )) or resid 146 \ through 158 or (resid 159 and (name N or name CA or name C or name O or name CB \ )) or resid 160 through 161 or (resid 162 and (name N or name CA or name C or na \ me O or name CB )) or resid 163 through 165 or (resid 166 and (name N or name CA \ or name C or name O or name CB )) or resid 167 through 170 or (resid 171 throug \ h 172 and (name N or name CA or name C or name O or name CB )) or resid 173 thro \ ugh 174 or (resid 175 and (name N or name CA or name C or name O or name CB )) o \ r resid 176 or (resid 177 and (name N or name CA or name C or name O or name CB \ )) or resid 178 through 181 or (resid 182 through 188 and (name N or name CA or \ name C or name O or name CB )) or resid 189 through 190 or (resid 191 through 19 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 196 or (resi \ d 197 and (name N or name CA or name C or name O or name CB )) or resid 198 thro \ ugh 201 or (resid 202 through 204 and (name N or name CA or name C or name O or \ name CB )) or resid 205 through 206 or (resid 207 and (name N or name CA or name \ C or name O or name CB )) or resid 208 or (resid 209 through 210 and (name N or \ name CA or name C or name O or name CB )) or resid 211 through 216 or (resid 21 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 218 through \ 220 or (resid 221 through 227 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain 'C' and (resid 1 through 5 or (resid 6 and (name N or name CA or name C o \ r name O or name CB )) or resid 7 through 25 or (resid 26 and (name N or name CA \ or name C or name O or name CB )) or resid 27 or (resid 28 through 30 and (name \ N or name CA or name C or name O or name CB )) or resid 31 through 33 or (resid \ 34 through 39 and (name N or name CA or name C or name O or name CB )) or resid \ 40 through 58 or (resid 59 and (name N or name CA or name C or name O or name C \ B )) or resid 60 through 71 or (resid 72 through 73 and (name N or name CA or na \ me C or name O or name CB )) or resid 74 or (resid 75 through 78 and (name N or \ name CA or name C or name O or name CB )) or resid 79 through 81 or (resid 82 an \ d (name N or name CA or name C or name O or name CB )) or resid 83 through 84 or \ (resid 85 through 89 and (name N or name CA or name C or name O or name CB )) o \ r resid 90 or (resid 91 and (name N or name CA or name C or name O or name CB )) \ or resid 92 through 106 or (resid 107 and (name N or name CA or name C or name \ O or name CB )) or resid 108 through 115 or (resid 116 through 120 and (name N o \ r name CA or name C or name O or name CB )) or resid 121 through 132 or (resid 1 \ 33 through 136 and (name N or name CA or name C or name O or name CB )) or resid \ 137 through 158 or (resid 159 and (name N or name CA or name C or name O or nam \ e CB )) or resid 160 through 165 or (resid 166 and (name N or name CA or name C \ or name O or name CB )) or resid 167 through 174 or (resid 175 and (name N or na \ me CA or name C or name O or name CB )) or resid 176 through 182 or (resid 183 t \ hrough 188 and (name N or name CA or name C or name O or name CB )) or resid 189 \ through 190 or (resid 191 through 195 and (name N or name CA or name C or name \ O or name CB )) or resid 196 through 200 or (resid 201 through 204 and (name N o \ r name CA or name C or name O or name CB )) or resid 205 through 206 or (resid 2 \ 07 and (name N or name CA or name C or name O or name CB )) or resid 208 or (res \ id 209 through 210 and (name N or name CA or name C or name O or name CB )) or r \ esid 211 through 220 or (resid 221 through 227 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'D' and ((resid 1 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 5 or (resid 6 and (name N or name CA or name C or \ name O or name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 or (resid 13 through 14 and (name \ N or name CA or name C or name O or name CB )) or resid 15 through 38 or (resid \ 39 and (name N or name CA or name C or name O or name CB )) or resid 40 through \ 43 or (resid 44 through 46 and (name N or name CA or name C or name O or name CB \ )) or resid 47 or (resid 48 through 50 and (name N or name CA or name C or name \ O or name CB )) or resid 51 through 54 or (resid 55 through 59 and (name N or n \ ame CA or name C or name O or name CB )) or resid 60 through 63 or (resid 64 thr \ ough 66 and (name N or name CA or name C or name O or name CB )) or resid 67 or \ (resid 68 and (name N or name CA or name C or name O or name CB )) or resid 69 o \ r (resid 70 through 73 and (name N or name CA or name C or name O or name CB )) \ or resid 74 through 76 or (resid 77 through 78 and (name N or name CA or name C \ or name O or name CB )) or resid 79 through 80 or (resid 81 through 82 and (name \ N or name CA or name C or name O or name CB )) or resid 83 through 86 or (resid \ 87 through 89 and (name N or name CA or name C or name O or name CB )) or resid \ 90 through 101 or (resid 102 and (name N or name CA or name C or name O or name \ CB )) or resid 103 through 106 or (resid 107 and (name N or name CA or name C o \ r name O or name CB )) or resid 108 through 112 or (resid 113 and (name N or nam \ e CA or name C or name O or name CB )) or resid 114 through 119 or (resid 120 an \ d (name N or name CA or name C or name O or name CB )) or resid 121 through 123 \ or (resid 124 and (name N or name CA or name C or name O or name CB )) or resid \ 125 through 126 or (resid 127 and (name N or name CA or name C or name O or name \ CB )) or resid 128 through 130 or (resid 131 through 136 and (name N or name CA \ or name C or name O or name CB )) or resid 137 through 142 or (resid 143 and (n \ ame N or name CA or name C or name O or name CB )) or resid 144 or (resid 145 an \ d (name N or name CA or name C or name O or name CB )) or resid 146 through 161 \ or (resid 162 and (name N or name CA or name C or name O or name CB )) or resid \ 163 through 165 or (resid 166 and (name N or name CA or name C or name O or name \ CB )) or resid 167 through 170 or (resid 171 through 172 and (name N or name CA \ or name C or name O or name CB )) or resid 173 through 176 or (resid 177 and (n \ ame N or name CA or name C or name O or name CB )) or resid 178 through 200 or ( \ resid 201 through 204 and (name N or name CA or name C or name O or name CB )) o \ r resid 205 through 208 or (resid 209 through 210 and (name N or name CA or name \ C or name O or name CB )) or resid 211 through 221 or (resid 222 through 227 an \ d (name N or name CA or name C or name O or name CB )))) selection = (chain 'E' and ((resid 1 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 5 or (resid 6 and (name N or name CA or name C or \ name O or name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 or (resid 13 through 14 and (name \ N or name CA or name C or name O or name CB )) or resid 15 through 25 or (resid \ 26 and (name N or name CA or name C or name O or name CB )) or resid 27 or (resi \ d 28 through 30 and (name N or name CA or name C or name O or name CB )) or resi \ d 31 through 32 or (resid 33 through 39 and (name N or name CA or name C or name \ O or name CB )) or resid 40 through 43 or (resid 44 through 46 and (name N or n \ ame CA or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and \ (name N or name CA or name C or name O or name CB )) or resid 51 through 52 or \ (resid 53 and (name N or name CA or name C or name O or name CB )) or resid 54 o \ r (resid 55 through 59 and (name N or name CA or name C or name O or name CB )) \ or resid 60 through 61 or (resid 62 through 66 and (name N or name CA or name C \ or name O or name CB )) or (resid 67 through 73 and (name N or name CA or name C \ or name O or name CB )) or resid 74 or (resid 75 through 78 and (name N or name \ CA or name C or name O or name CB )) or resid 79 through 87 or (resid 88 throug \ h 89 and (name N or name CA or name C or name O or name CB )) or resid 90 or (re \ sid 91 and (name N or name CA or name C or name O or name CB )) or resid 92 thro \ ugh 93 or (resid 94 and (name N or name CA or name C or name O or name CB )) or \ resid 95 through 101 or (resid 102 and (name N or name CA or name C or name O or \ name CB )) or resid 103 through 112 or (resid 113 and (name N or name CA or nam \ e C or name O or name CB )) or resid 114 or (resid 115 through 120 and (name N o \ r name CA or name C or name O or name CB )) or resid 121 through 123 or (resid 1 \ 24 and (name N or name CA or name C or name O or name CB )) or resid 125 through \ 126 or (resid 127 and (name N or name CA or name C or name O or name CB )) or r \ esid 128 through 130 or (resid 131 through 136 and (name N or name CA or name C \ or name O or name CB )) or resid 137 through 142 or (resid 143 and (name N or na \ me CA or name C or name O or name CB )) or resid 144 or (resid 145 and (name N o \ r name CA or name C or name O or name CB )) or resid 146 through 158 or (resid 1 \ 59 and (name N or name CA or name C or name O or name CB )) or resid 160 through \ 161 or (resid 162 and (name N or name CA or name C or name O or name CB )) or r \ esid 163 through 170 or (resid 171 through 172 and (name N or name CA or name C \ or name O or name CB )) or resid 173 through 174 or (resid 175 and (name N or na \ me CA or name C or name O or name CB )) or resid 176 or (resid 177 and (name N o \ r name CA or name C or name O or name CB )) or resid 178 through 181 or (resid 1 \ 82 through 188 and (name N or name CA or name C or name O or name CB )) or resid \ 189 through 190 or (resid 191 through 195 and (name N or name CA or name C or n \ ame O or name CB )) or resid 196 through 200 or (resid 201 through 204 and (name \ N or name CA or name C or name O or name CB )) or resid 205 through 208 or (res \ id 209 through 210 and (name N or name CA or name C or name O or name CB )) or r \ esid 211 through 216 or (resid 217 and (name N or name CA or name C or name O or \ name CB )) or resid 218 through 220 or (resid 221 through 227 and (name N or na \ me CA or name C or name O or name CB )))) selection = (chain 'F' and ((resid 1 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 5 or (resid 6 and (name N or name CA or name C or \ name O or name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA \ or name C or name O or name CB )) or (resid 12 through 14 and (name N or name CA \ or name C or name O or name CB )) or resid 15 through 25 or (resid 26 and (name \ N or name CA or name C or name O or name CB )) or resid 27 or (resid 28 through \ 30 and (name N or name CA or name C or name O or name CB )) or resid 31 through \ 32 or (resid 33 through 39 and (name N or name CA or name C or name O or name C \ B )) or resid 40 through 42 or (resid 43 through 46 and (name N or name CA or na \ me C or name O or name CB )) or resid 47 or (resid 48 through 50 and (name N or \ name CA or name C or name O or name CB )) or resid 51 through 54 or (resid 55 th \ rough 59 and (name N or name CA or name C or name O or name CB )) or resid 60 th \ rough 63 or (resid 64 through 66 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 67 through 73 and (name N or name CA or name C or name O or \ name CB )) or resid 74 or (resid 75 through 78 and (name N or name CA or name C \ or name O or name CB )) or resid 79 through 80 or (resid 81 through 82 and (name \ N or name CA or name C or name O or name CB )) or resid 83 through 86 or (resid \ 87 through 89 and (name N or name CA or name C or name O or name CB )) or resid \ 90 through 101 or (resid 102 and (name N or name CA or name C or name O or name \ CB )) or resid 103 through 106 or (resid 107 and (name N or name CA or name C o \ r name O or name CB )) or resid 108 through 112 or (resid 113 and (name N or nam \ e CA or name C or name O or name CB )) or resid 114 through 115 or (resid 116 th \ rough 120 and (name N or name CA or name C or name O or name CB )) or resid 121 \ through 123 or (resid 124 and (name N or name CA or name C or name O or name CB \ )) or resid 125 through 126 or (resid 127 and (name N or name CA or name C or na \ me O or name CB )) or resid 128 through 130 or (resid 131 through 136 and (name \ N or name CA or name C or name O or name CB )) or resid 137 through 144 or (resi \ d 145 and (name N or name CA or name C or name O or name CB )) or resid 146 thro \ ugh 158 or (resid 159 and (name N or name CA or name C or name O or name CB )) o \ r resid 160 through 161 or (resid 162 and (name N or name CA or name C or name O \ or name CB )) or resid 163 through 165 or (resid 166 and (name N or name CA or \ name C or name O or name CB )) or resid 167 through 170 or (resid 171 through 17 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 173 through \ 174 or (resid 175 and (name N or name CA or name C or name O or name CB )) or re \ sid 176 or (resid 177 and (name N or name CA or name C or name O or name CB )) o \ r resid 178 through 181 or (resid 182 through 188 and (name N or name CA or name \ C or name O or name CB )) or resid 189 through 191 or (resid 192 through 195 an \ d (name N or name CA or name C or name O or name CB )) or resid 196 or (resid 19 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 198 through \ 200 or (resid 201 through 204 and (name N or name CA or name C or name O or name \ CB )) or resid 205 through 206 or (resid 207 and (name N or name CA or name C o \ r name O or name CB )) or resid 208 through 209 or (resid 210 and (name N or nam \ e CA or name C or name O or name CB )) or resid 211 through 216 or (resid 217 an \ d (name N or name CA or name C or name O or name CB )) or resid 218 through 220 \ or (resid 221 through 227 and (name N or name CA or name C or name O or name CB \ )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.010 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.590 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 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:7.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 12429 Z= 0.328 Angle : 0.720 12.636 17313 Z= 0.469 Chirality : 0.047 0.195 2007 Planarity : 0.005 0.068 1956 Dihedral : 20.424 88.951 4562 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.77 % Favored : 95.15 % Rotamer: Outliers : 3.26 % Allowed : 39.31 % Favored : 57.43 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.23), residues: 1362 helix: 0.83 (0.29), residues: 301 sheet: -0.31 (0.33), residues: 281 loop : -0.27 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 174 TYR 0.010 0.001 TYR C 110 PHE 0.013 0.001 PHE B 11 TRP 0.037 0.002 TRP C 5 HIS 0.012 0.001 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.33 (12429) covalent geometry : angle 0.72015 / 0.47 (17313) hydrogen bonds : bond 0.25952 / 17.40 ( 469) hydrogen bonds : angle 9.23933 / 6.29 ( 1246) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 301 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8646 (pt0) REVERT: A 144 ASN cc_start: 0.9245 (t0) cc_final: 0.8928 (t0) REVERT: A 146 THR cc_start: 0.9368 (t) cc_final: 0.9119 (m) REVERT: B 147 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8027 (mtp85) REVERT: C 159 ARG cc_start: 0.7894 (mtp180) cc_final: 0.7197 (mtp85) REVERT: C 174 ARG cc_start: 0.7329 (ttm110) cc_final: 0.6973 (mtp85) REVERT: C 221 GLU cc_start: 0.9050 (tt0) cc_final: 0.8807 (tp30) REVERT: D 8 SER cc_start: 0.8893 (p) cc_final: 0.8584 (p) REVERT: D 15 ASN cc_start: 0.8630 (t0) cc_final: 0.8401 (t0) REVERT: D 113 GLU cc_start: 0.7819 (tt0) cc_final: 0.7594 (pt0) REVERT: D 131 GLU cc_start: 0.8769 (tt0) cc_final: 0.8541 (tt0) REVERT: D 154 LYS cc_start: 0.8229 (ptmt) cc_final: 0.7980 (pttt) REVERT: E 177 ASP cc_start: 0.9100 (t0) cc_final: 0.8586 (p0) REVERT: F 105 MET cc_start: 0.9068 (mmm) cc_final: 0.8820 (mmm) REVERT: F 160 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7797 (mt-10) outliers start: 32 outliers final: 19 residues processed: 323 average time/residue: 0.5760 time to fit residues: 201.7652 Evaluate side-chains 302 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 281 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain E residue 71 MET Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 198 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 HIS ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN D 27 HIS ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.128026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.083162 restraints weight = 21449.818| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.13 r_work: 0.2900 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12429 Z= 0.177 Angle : 0.660 7.814 17313 Z= 0.363 Chirality : 0.046 0.230 2007 Planarity : 0.005 0.046 1956 Dihedral : 20.260 86.689 2467 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 6.92 % Allowed : 34.01 % Favored : 59.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.22), residues: 1362 helix: 0.88 (0.28), residues: 337 sheet: -0.31 (0.33), residues: 252 loop : -0.62 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 58 TYR 0.021 0.001 TYR E 64 PHE 0.015 0.001 PHE B 11 TRP 0.023 0.002 TRP C 5 HIS 0.006 0.001 HIS D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.18 (12429) covalent geometry : angle 0.65982 / 0.36 (17313) hydrogen bonds : bond 0.06956 / 4.57 ( 469) hydrogen bonds : angle 6.25730 / 4.35 ( 1246) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 299 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9173 (OUTLIER) cc_final: 0.8906 (pt0) REVERT: A 102 ASP cc_start: 0.8786 (OUTLIER) cc_final: 0.8552 (p0) REVERT: A 144 ASN cc_start: 0.9264 (t0) cc_final: 0.8993 (t0) REVERT: A 183 GLN cc_start: 0.9026 (pt0) cc_final: 0.8819 (pp30) REVERT: B 185 VAL cc_start: 0.9058 (OUTLIER) cc_final: 0.8755 (m) REVERT: C 8 SER cc_start: 0.8807 (m) cc_final: 0.8282 (t) REVERT: C 154 LYS cc_start: 0.7538 (tttt) cc_final: 0.7057 (tttt) REVERT: C 221 GLU cc_start: 0.9109 (tt0) cc_final: 0.8836 (tp30) REVERT: D 8 SER cc_start: 0.9114 (p) cc_final: 0.8824 (p) REVERT: D 88 ARG cc_start: 0.8519 (tpt-90) cc_final: 0.7775 (tpp-160) REVERT: D 113 GLU cc_start: 0.8056 (tt0) cc_final: 0.7771 (pt0) REVERT: D 120 LYS cc_start: 0.9441 (OUTLIER) cc_final: 0.8835 (ttpt) REVERT: E 172 GLU cc_start: 0.9185 (OUTLIER) cc_final: 0.8897 (tt0) REVERT: E 177 ASP cc_start: 0.9161 (t0) cc_final: 0.8599 (p0) REVERT: E 194 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8225 (tpt) REVERT: F 2 ARG cc_start: 0.9108 (mtp-110) cc_final: 0.8833 (mtp-110) REVERT: F 160 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7846 (mt-10) REVERT: F 182 ASP cc_start: 0.8954 (m-30) cc_final: 0.8668 (m-30) outliers start: 68 outliers final: 34 residues processed: 338 average time/residue: 0.5630 time to fit residues: 206.8374 Evaluate side-chains 320 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 280 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 211 TYR Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain D residue 27 HIS Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 71 MET Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 194 MET Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 11 PHE Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 227 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 6 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN D 27 HIS ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.126127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.081108 restraints weight = 21513.073| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 3.04 r_work: 0.2866 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12429 Z= 0.230 Angle : 0.634 7.618 17313 Z= 0.350 Chirality : 0.045 0.171 2007 Planarity : 0.005 0.047 1956 Dihedral : 20.557 86.034 2452 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 7.54 % Allowed : 33.60 % Favored : 58.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.22), residues: 1362 helix: 1.01 (0.28), residues: 342 sheet: -0.26 (0.34), residues: 233 loop : -0.76 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 58 TYR 0.016 0.002 TYR D 211 PHE 0.019 0.001 PHE B 11 TRP 0.025 0.002 TRP C 5 HIS 0.013 0.001 HIS D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.23 (12429) covalent geometry : angle 0.63411 / 0.35 (17313) hydrogen bonds : bond 0.05561 / 3.65 ( 469) hydrogen bonds : angle 5.86005 / 4.08 ( 1246) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 291 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 144 ASN cc_start: 0.9237 (t0) cc_final: 0.8942 (t0) REVERT: A 183 GLN cc_start: 0.9086 (pt0) cc_final: 0.8755 (pp30) REVERT: B 183 GLN cc_start: 0.8741 (pp30) cc_final: 0.8457 (pp30) REVERT: B 185 VAL cc_start: 0.9100 (OUTLIER) cc_final: 0.8789 (m) REVERT: C 8 SER cc_start: 0.8902 (OUTLIER) cc_final: 0.8439 (t) REVERT: C 60 LEU cc_start: 0.7223 (mm) cc_final: 0.6730 (tm) REVERT: C 159 ARG cc_start: 0.7957 (mtp180) cc_final: 0.7353 (mtp85) REVERT: C 221 GLU cc_start: 0.9092 (tt0) cc_final: 0.8846 (tp30) REVERT: D 8 SER cc_start: 0.9192 (p) cc_final: 0.8929 (p) REVERT: D 88 ARG cc_start: 0.8405 (tpt-90) cc_final: 0.7756 (tpp-160) REVERT: D 113 GLU cc_start: 0.8067 (tt0) cc_final: 0.7780 (pt0) REVERT: D 120 LYS cc_start: 0.9470 (OUTLIER) cc_final: 0.8888 (ttpt) REVERT: D 174 ARG cc_start: 0.8624 (ttm110) cc_final: 0.8389 (mtt-85) REVERT: E 172 GLU cc_start: 0.9161 (OUTLIER) cc_final: 0.8897 (tt0) REVERT: E 177 ASP cc_start: 0.9180 (t0) cc_final: 0.8554 (p0) REVERT: E 182 ASP cc_start: 0.8588 (m-30) cc_final: 0.8160 (m-30) REVERT: F 1 MET cc_start: 0.6654 (OUTLIER) cc_final: 0.6283 (mtm) REVERT: F 2 ARG cc_start: 0.9086 (mtp-110) cc_final: 0.8842 (mtp-110) REVERT: F 160 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7919 (mt-10) REVERT: F 182 ASP cc_start: 0.8958 (m-30) cc_final: 0.8715 (m-30) outliers start: 74 outliers final: 44 residues processed: 323 average time/residue: 0.5387 time to fit residues: 189.6229 Evaluate side-chains 326 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 277 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 211 TYR Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 27 HIS Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 71 MET Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 11 PHE Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 227 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 100 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 30 optimal weight: 0.2980 chunk 82 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 75 optimal weight: 0.0020 chunk 2 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 216 GLN C 218 GLN D 27 HIS ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.128199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.083747 restraints weight = 21386.348| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.05 r_work: 0.2913 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12429 Z= 0.131 Angle : 0.599 10.786 17313 Z= 0.328 Chirality : 0.044 0.172 2007 Planarity : 0.004 0.049 1956 Dihedral : 20.614 86.895 2445 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 6.62 % Allowed : 34.93 % Favored : 58.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.22), residues: 1362 helix: 1.19 (0.28), residues: 342 sheet: -0.06 (0.35), residues: 224 loop : -0.74 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 58 TYR 0.018 0.001 TYR C 215 PHE 0.013 0.001 PHE D 11 TRP 0.027 0.002 TRP C 5 HIS 0.004 0.001 HIS C 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 (12429) covalent geometry : angle 0.59948 / 0.33 (17313) hydrogen bonds : bond 0.04710 / 3.07 ( 469) hydrogen bonds : angle 5.61092 / 3.90 ( 1246) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 298 time to evaluate : 0.276 Fit side-chains REVERT: A 94 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8752 (pt0) REVERT: A 102 ASP cc_start: 0.8856 (OUTLIER) cc_final: 0.8634 (p0) REVERT: A 144 ASN cc_start: 0.9235 (t0) cc_final: 0.8964 (t0) REVERT: A 183 GLN cc_start: 0.9046 (pt0) cc_final: 0.8770 (pp30) REVERT: B 183 GLN cc_start: 0.8694 (pp30) cc_final: 0.8354 (pp30) REVERT: B 185 VAL cc_start: 0.9096 (OUTLIER) cc_final: 0.8746 (m) REVERT: C 8 SER cc_start: 0.8879 (OUTLIER) cc_final: 0.8413 (t) REVERT: C 154 LYS cc_start: 0.7523 (OUTLIER) cc_final: 0.7259 (tttt) REVERT: C 155 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.8517 (p0) REVERT: C 159 ARG cc_start: 0.8013 (mtp180) cc_final: 0.7426 (mtp85) REVERT: C 160 GLU cc_start: 0.7313 (tp30) cc_final: 0.6794 (tp30) REVERT: C 221 GLU cc_start: 0.9083 (tt0) cc_final: 0.8831 (tp30) REVERT: D 6 THR cc_start: 0.8714 (t) cc_final: 0.8513 (m) REVERT: D 8 SER cc_start: 0.9134 (p) cc_final: 0.8834 (p) REVERT: D 88 ARG cc_start: 0.8345 (tpt-90) cc_final: 0.7735 (tpp-160) REVERT: D 113 GLU cc_start: 0.8013 (tt0) cc_final: 0.7722 (pt0) REVERT: D 154 LYS cc_start: 0.8184 (ptmt) cc_final: 0.7807 (pttp) REVERT: E 172 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8819 (tt0) REVERT: E 177 ASP cc_start: 0.9177 (t0) cc_final: 0.8593 (p0) REVERT: E 194 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.7823 (tmm) REVERT: F 2 ARG cc_start: 0.9087 (mtp-110) cc_final: 0.8852 (mtp-110) REVERT: F 160 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7866 (mt-10) REVERT: F 182 ASP cc_start: 0.8937 (m-30) cc_final: 0.8711 (m-30) outliers start: 65 outliers final: 33 residues processed: 327 average time/residue: 0.4759 time to fit residues: 169.1296 Evaluate side-chains 323 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 282 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 154 LYS Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 211 TYR Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 71 MET Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 194 MET Chi-restraints excluded: chain F residue 11 PHE Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 198 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 21 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 52 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 16 optimal weight: 0.0570 chunk 99 optimal weight: 0.4980 overall best weight: 1.7104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 HIS ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN D 27 HIS ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.125631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.080855 restraints weight = 21678.228| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.05 r_work: 0.2862 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 12429 Z= 0.245 Angle : 0.629 8.628 17313 Z= 0.344 Chirality : 0.045 0.177 2007 Planarity : 0.005 0.049 1956 Dihedral : 20.736 86.311 2445 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 7.54 % Allowed : 34.62 % Favored : 57.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.22), residues: 1362 helix: 1.19 (0.28), residues: 342 sheet: -0.29 (0.34), residues: 226 loop : -0.76 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 58 TYR 0.018 0.001 TYR C 215 PHE 0.019 0.001 PHE E 11 TRP 0.028 0.002 TRP C 5 HIS 0.006 0.001 HIS D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.25 (12429) covalent geometry : angle 0.62889 / 0.34 (17313) hydrogen bonds : bond 0.04779 / 3.10 ( 469) hydrogen bonds : angle 5.54461 / 3.89 ( 1246) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 276 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9097 (OUTLIER) cc_final: 0.8526 (pt0) REVERT: A 144 ASN cc_start: 0.9241 (t0) cc_final: 0.8947 (t0) REVERT: A 183 GLN cc_start: 0.9102 (pt0) cc_final: 0.8725 (pp30) REVERT: B 183 GLN cc_start: 0.8703 (pp30) cc_final: 0.8437 (pp30) REVERT: B 185 VAL cc_start: 0.9133 (OUTLIER) cc_final: 0.8782 (m) REVERT: C 8 SER cc_start: 0.8902 (m) cc_final: 0.8446 (t) REVERT: C 159 ARG cc_start: 0.8037 (mtp180) cc_final: 0.7436 (mtp85) REVERT: C 221 GLU cc_start: 0.9095 (tt0) cc_final: 0.8833 (tp30) REVERT: D 8 SER cc_start: 0.9191 (p) cc_final: 0.8915 (p) REVERT: D 88 ARG cc_start: 0.8372 (tpt-90) cc_final: 0.7753 (tpp-160) REVERT: D 113 GLU cc_start: 0.8081 (tt0) cc_final: 0.7783 (pt0) REVERT: D 120 LYS cc_start: 0.9465 (OUTLIER) cc_final: 0.8905 (ttpt) REVERT: D 132 THR cc_start: 0.8885 (t) cc_final: 0.8607 (p) REVERT: E 172 GLU cc_start: 0.9164 (OUTLIER) cc_final: 0.8826 (tt0) REVERT: E 177 ASP cc_start: 0.9191 (t0) cc_final: 0.8537 (p0) REVERT: E 182 ASP cc_start: 0.8630 (m-30) cc_final: 0.8179 (m-30) REVERT: E 194 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.7849 (tmm) REVERT: F 1 MET cc_start: 0.6647 (OUTLIER) cc_final: 0.6269 (mtm) REVERT: F 160 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7918 (mt-10) REVERT: F 182 ASP cc_start: 0.8976 (m-30) cc_final: 0.8725 (m-30) REVERT: F 197 GLN cc_start: 0.9311 (mp10) cc_final: 0.8611 (mp10) outliers start: 74 outliers final: 48 residues processed: 315 average time/residue: 0.4778 time to fit residues: 163.9751 Evaluate side-chains 324 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 270 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 154 LYS Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 27 HIS Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 71 MET Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 194 MET Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 11 PHE Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 223 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 40 optimal weight: 3.9990 chunk 6 optimal weight: 0.0970 chunk 84 optimal weight: 0.7980 chunk 125 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 chunk 137 optimal weight: 9.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 ASN C 216 GLN C 218 GLN D 27 HIS ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.127263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.082647 restraints weight = 21604.143| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 3.10 r_work: 0.2895 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12429 Z= 0.142 Angle : 0.604 9.779 17313 Z= 0.333 Chirality : 0.044 0.176 2007 Planarity : 0.004 0.051 1956 Dihedral : 20.763 87.077 2445 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 6.31 % Allowed : 35.85 % Favored : 57.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.22), residues: 1362 helix: 1.29 (0.28), residues: 342 sheet: -0.21 (0.35), residues: 220 loop : -0.75 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 2 TYR 0.027 0.001 TYR E 64 PHE 0.029 0.001 PHE D 206 TRP 0.031 0.002 TRP C 5 HIS 0.022 0.001 HIS D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (12429) covalent geometry : angle 0.60401 / 0.33 (17313) hydrogen bonds : bond 0.04315 / 2.77 ( 469) hydrogen bonds : angle 5.42185 / 3.80 ( 1246) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 293 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8746 (pt0) REVERT: A 102 ASP cc_start: 0.8872 (OUTLIER) cc_final: 0.8652 (p0) REVERT: A 144 ASN cc_start: 0.9236 (t0) cc_final: 0.8959 (t0) REVERT: A 183 GLN cc_start: 0.9042 (pt0) cc_final: 0.8666 (pp30) REVERT: A 185 VAL cc_start: 0.9574 (OUTLIER) cc_final: 0.9316 (m) REVERT: B 183 GLN cc_start: 0.8707 (pp30) cc_final: 0.8363 (pp30) REVERT: B 185 VAL cc_start: 0.9101 (OUTLIER) cc_final: 0.8741 (m) REVERT: C 8 SER cc_start: 0.8894 (m) cc_final: 0.8426 (t) REVERT: C 159 ARG cc_start: 0.7985 (mtp180) cc_final: 0.7425 (mtp85) REVERT: C 221 GLU cc_start: 0.9084 (tt0) cc_final: 0.8826 (tp30) REVERT: D 6 THR cc_start: 0.8659 (t) cc_final: 0.8384 (m) REVERT: D 8 SER cc_start: 0.9127 (p) cc_final: 0.8829 (p) REVERT: D 88 ARG cc_start: 0.8349 (tpt-90) cc_final: 0.7724 (tpp-160) REVERT: D 113 GLU cc_start: 0.8043 (tt0) cc_final: 0.7733 (pt0) REVERT: D 154 LYS cc_start: 0.8132 (ptmt) cc_final: 0.7773 (pttp) REVERT: D 174 ARG cc_start: 0.8598 (ptp90) cc_final: 0.8304 (ptp90) REVERT: E 172 GLU cc_start: 0.9188 (OUTLIER) cc_final: 0.8888 (tt0) REVERT: E 177 ASP cc_start: 0.9190 (t0) cc_final: 0.8566 (p0) REVERT: F 76 ASP cc_start: 0.8338 (m-30) cc_final: 0.7388 (p0) REVERT: F 160 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7842 (mt-10) REVERT: F 182 ASP cc_start: 0.8969 (m-30) cc_final: 0.8723 (m-30) REVERT: F 193 LYS cc_start: 0.9431 (ttmt) cc_final: 0.9115 (ttpp) REVERT: F 197 GLN cc_start: 0.9312 (OUTLIER) cc_final: 0.8730 (mp10) outliers start: 62 outliers final: 40 residues processed: 318 average time/residue: 0.4686 time to fit residues: 162.3854 Evaluate side-chains 333 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 287 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 154 LYS Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 27 HIS Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 71 MET Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 11 PHE Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 197 GLN Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 223 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 115 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN D 27 HIS ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.125881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.082034 restraints weight = 21372.825| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.97 r_work: 0.2875 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12429 Z= 0.203 Angle : 0.631 10.253 17313 Z= 0.345 Chirality : 0.045 0.175 2007 Planarity : 0.004 0.050 1956 Dihedral : 20.839 87.131 2445 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 7.13 % Allowed : 35.34 % Favored : 57.54 % 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: -0.17 (0.22), residues: 1362 helix: 1.33 (0.28), residues: 342 sheet: -0.15 (0.34), residues: 234 loop : -0.75 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 108 TYR 0.029 0.002 TYR F 122 PHE 0.019 0.001 PHE B 11 TRP 0.034 0.002 TRP C 5 HIS 0.015 0.001 HIS D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.20 (12429) covalent geometry : angle 0.63145 / 0.34 (17313) hydrogen bonds : bond 0.04356 / 2.79 ( 469) hydrogen bonds : angle 5.39317 / 3.78 ( 1246) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 288 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8499 (pt0) REVERT: A 102 ASP cc_start: 0.8834 (OUTLIER) cc_final: 0.8604 (p0) REVERT: A 144 ASN cc_start: 0.9241 (t0) cc_final: 0.8948 (t0) REVERT: A 183 GLN cc_start: 0.9052 (pt0) cc_final: 0.8662 (pp30) REVERT: A 185 VAL cc_start: 0.9578 (OUTLIER) cc_final: 0.9329 (m) REVERT: B 145 LYS cc_start: 0.9467 (OUTLIER) cc_final: 0.8948 (tttm) REVERT: B 183 GLN cc_start: 0.8708 (pp30) cc_final: 0.8373 (pp30) REVERT: B 185 VAL cc_start: 0.9140 (OUTLIER) cc_final: 0.8745 (m) REVERT: C 8 SER cc_start: 0.8960 (m) cc_final: 0.8516 (t) REVERT: C 154 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7483 (tttt) REVERT: C 159 ARG cc_start: 0.8016 (mtp180) cc_final: 0.7461 (mtp85) REVERT: C 221 GLU cc_start: 0.9089 (tt0) cc_final: 0.8825 (tp30) REVERT: D 6 THR cc_start: 0.8687 (t) cc_final: 0.8397 (m) REVERT: D 8 SER cc_start: 0.9178 (p) cc_final: 0.8877 (p) REVERT: D 88 ARG cc_start: 0.8378 (tpt-90) cc_final: 0.7780 (tpp-160) REVERT: D 113 GLU cc_start: 0.8054 (tt0) cc_final: 0.7746 (pt0) REVERT: D 132 THR cc_start: 0.8885 (t) cc_final: 0.8628 (p) REVERT: D 154 LYS cc_start: 0.8121 (ptmt) cc_final: 0.7736 (pttt) REVERT: D 174 ARG cc_start: 0.8628 (ptp90) cc_final: 0.8304 (ptp90) REVERT: D 205 ASP cc_start: 0.8250 (t0) cc_final: 0.7911 (t70) REVERT: E 172 GLU cc_start: 0.9196 (OUTLIER) cc_final: 0.8891 (tt0) REVERT: E 177 ASP cc_start: 0.9176 (t0) cc_final: 0.8514 (p0) REVERT: E 194 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.7843 (tmm) REVERT: F 1 MET cc_start: 0.6590 (mtm) cc_final: 0.6139 (mtm) REVERT: F 76 ASP cc_start: 0.8337 (m-30) cc_final: 0.7445 (p0) REVERT: F 160 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7857 (mt-10) REVERT: F 182 ASP cc_start: 0.8979 (m-30) cc_final: 0.8733 (m-30) REVERT: F 200 ASP cc_start: 0.9248 (m-30) cc_final: 0.8853 (m-30) outliers start: 70 outliers final: 43 residues processed: 320 average time/residue: 0.5079 time to fit residues: 177.3170 Evaluate side-chains 326 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 275 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 154 LYS Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 27 HIS Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 71 MET Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 194 MET Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 11 PHE Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 223 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 111 optimal weight: 0.7980 chunk 99 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 112 optimal weight: 0.3980 chunk 43 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 chunk 51 optimal weight: 20.0000 chunk 135 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN D 27 HIS ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.126994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.082415 restraints weight = 21356.144| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.08 r_work: 0.2895 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12429 Z= 0.150 Angle : 0.629 10.947 17313 Z= 0.343 Chirality : 0.044 0.193 2007 Planarity : 0.004 0.049 1956 Dihedral : 20.816 87.700 2445 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 6.11 % Allowed : 36.66 % Favored : 57.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.22), residues: 1362 helix: 1.40 (0.29), residues: 342 sheet: -0.26 (0.33), residues: 246 loop : -0.72 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 108 TYR 0.027 0.001 TYR E 64 PHE 0.018 0.001 PHE D 206 TRP 0.037 0.002 TRP C 5 HIS 0.006 0.001 HIS D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (12429) covalent geometry : angle 0.62851 / 0.34 (17313) hydrogen bonds : bond 0.04146 / 2.65 ( 469) hydrogen bonds : angle 5.33932 / 3.74 ( 1246) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 286 time to evaluate : 0.417 Fit side-chains REVERT: A 94 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8519 (pt0) REVERT: A 144 ASN cc_start: 0.9237 (t0) cc_final: 0.8961 (t0) REVERT: A 183 GLN cc_start: 0.9018 (pt0) cc_final: 0.8623 (pp30) REVERT: A 185 VAL cc_start: 0.9556 (OUTLIER) cc_final: 0.9303 (m) REVERT: B 145 LYS cc_start: 0.9477 (OUTLIER) cc_final: 0.9088 (tttm) REVERT: B 183 GLN cc_start: 0.8708 (pp30) cc_final: 0.8351 (pp30) REVERT: B 185 VAL cc_start: 0.9115 (OUTLIER) cc_final: 0.8691 (m) REVERT: C 8 SER cc_start: 0.8949 (OUTLIER) cc_final: 0.8514 (t) REVERT: C 154 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7473 (tttt) REVERT: C 159 ARG cc_start: 0.7974 (mtp180) cc_final: 0.7423 (mtp85) REVERT: C 221 GLU cc_start: 0.9087 (tt0) cc_final: 0.8825 (tp30) REVERT: D 6 THR cc_start: 0.8603 (t) cc_final: 0.8315 (m) REVERT: D 8 SER cc_start: 0.9134 (p) cc_final: 0.8830 (p) REVERT: D 88 ARG cc_start: 0.8371 (tpt-90) cc_final: 0.7754 (tpp-160) REVERT: D 113 GLU cc_start: 0.8062 (tt0) cc_final: 0.7737 (pt0) REVERT: D 132 THR cc_start: 0.8849 (t) cc_final: 0.8578 (p) REVERT: D 166 THR cc_start: 0.9196 (m) cc_final: 0.8796 (p) REVERT: D 174 ARG cc_start: 0.8641 (ptp90) cc_final: 0.8391 (ptp90) REVERT: D 205 ASP cc_start: 0.8239 (t0) cc_final: 0.7907 (t70) REVERT: E 172 GLU cc_start: 0.9182 (OUTLIER) cc_final: 0.8898 (tt0) REVERT: E 177 ASP cc_start: 0.9175 (t0) cc_final: 0.8514 (p0) REVERT: F 1 MET cc_start: 0.6570 (mtm) cc_final: 0.6105 (mtm) REVERT: F 76 ASP cc_start: 0.8362 (m-30) cc_final: 0.7461 (p0) REVERT: F 160 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7840 (mt-10) REVERT: F 182 ASP cc_start: 0.8982 (m-30) cc_final: 0.8736 (m-30) REVERT: F 200 ASP cc_start: 0.9248 (m-30) cc_final: 0.8862 (m-30) outliers start: 60 outliers final: 39 residues processed: 315 average time/residue: 0.4818 time to fit residues: 165.3509 Evaluate side-chains 323 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 277 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 154 LYS Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 27 HIS Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 11 PHE Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 223 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 76 optimal weight: 0.5980 chunk 60 optimal weight: 8.9990 chunk 88 optimal weight: 9.9990 chunk 139 optimal weight: 8.9990 chunk 140 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 71 optimal weight: 20.0000 chunk 107 optimal weight: 0.2980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 ASN C 218 GLN D 27 HIS ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.125681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.081027 restraints weight = 21459.201| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.02 r_work: 0.2870 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12429 Z= 0.214 Angle : 0.659 10.148 17313 Z= 0.358 Chirality : 0.045 0.187 2007 Planarity : 0.005 0.061 1956 Dihedral : 20.733 87.572 2438 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 6.42 % Allowed : 36.35 % Favored : 57.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.22), residues: 1362 helix: 1.39 (0.28), residues: 342 sheet: -0.24 (0.33), residues: 241 loop : -0.78 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 2 TYR 0.043 0.002 TYR F 122 PHE 0.019 0.001 PHE E 11 TRP 0.040 0.002 TRP C 5 HIS 0.014 0.001 HIS D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.21 (12429) covalent geometry : angle 0.65855 / 0.36 (17313) hydrogen bonds : bond 0.04247 / 2.72 ( 469) hydrogen bonds : angle 5.33743 / 3.74 ( 1246) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 275 time to evaluate : 0.345 Fit side-chains REVERT: A 94 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8493 (pt0) REVERT: A 144 ASN cc_start: 0.9231 (t0) cc_final: 0.8925 (t0) REVERT: A 183 GLN cc_start: 0.9038 (pt0) cc_final: 0.8623 (pp30) REVERT: A 185 VAL cc_start: 0.9573 (OUTLIER) cc_final: 0.9313 (m) REVERT: B 145 LYS cc_start: 0.9488 (OUTLIER) cc_final: 0.8986 (tttm) REVERT: B 183 GLN cc_start: 0.8720 (pp30) cc_final: 0.8370 (pp30) REVERT: B 185 VAL cc_start: 0.9138 (OUTLIER) cc_final: 0.8712 (m) REVERT: C 8 SER cc_start: 0.8961 (m) cc_final: 0.8527 (t) REVERT: C 154 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.7489 (tttt) REVERT: C 159 ARG cc_start: 0.7983 (mtp180) cc_final: 0.7423 (mtp85) REVERT: C 221 GLU cc_start: 0.9095 (tt0) cc_final: 0.8837 (tp30) REVERT: D 6 THR cc_start: 0.8646 (t) cc_final: 0.8346 (m) REVERT: D 8 SER cc_start: 0.9192 (p) cc_final: 0.8897 (p) REVERT: D 88 ARG cc_start: 0.8374 (tpt-90) cc_final: 0.7781 (tpp-160) REVERT: D 113 GLU cc_start: 0.8106 (tt0) cc_final: 0.7786 (pt0) REVERT: D 154 LYS cc_start: 0.8182 (ptmt) cc_final: 0.7839 (pttt) REVERT: D 166 THR cc_start: 0.9217 (m) cc_final: 0.8802 (p) REVERT: D 172 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8152 (mt-10) REVERT: D 174 ARG cc_start: 0.8663 (ptp90) cc_final: 0.8409 (ptp90) REVERT: D 205 ASP cc_start: 0.8250 (t0) cc_final: 0.7933 (t70) REVERT: E 172 GLU cc_start: 0.9195 (OUTLIER) cc_final: 0.8897 (tt0) REVERT: E 177 ASP cc_start: 0.9180 (t0) cc_final: 0.8515 (p0) REVERT: E 194 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.7863 (tmm) REVERT: F 1 MET cc_start: 0.6575 (OUTLIER) cc_final: 0.6150 (mtm) REVERT: F 76 ASP cc_start: 0.8447 (m-30) cc_final: 0.7522 (p0) REVERT: F 82 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8661 (mm) REVERT: F 160 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7843 (mt-10) REVERT: F 182 ASP cc_start: 0.8984 (m-30) cc_final: 0.8743 (m-30) REVERT: F 200 ASP cc_start: 0.9246 (m-30) cc_final: 0.8845 (m-30) outliers start: 63 outliers final: 40 residues processed: 304 average time/residue: 0.4677 time to fit residues: 155.0237 Evaluate side-chains 319 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 270 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 154 LYS Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 194 MET Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 11 PHE Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 223 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 89 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 70 optimal weight: 8.9990 chunk 84 optimal weight: 0.3980 chunk 88 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 50 optimal weight: 20.0000 chunk 124 optimal weight: 3.9990 chunk 140 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.126049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.081584 restraints weight = 21476.085| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.04 r_work: 0.2873 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12429 Z= 0.183 Angle : 0.659 12.442 17313 Z= 0.357 Chirality : 0.044 0.192 2007 Planarity : 0.005 0.055 1956 Dihedral : 20.693 87.776 2438 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 5.09 % Allowed : 38.09 % Favored : 56.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.22), residues: 1362 helix: 1.43 (0.29), residues: 342 sheet: -0.20 (0.34), residues: 223 loop : -0.80 (0.21), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 2 TYR 0.044 0.002 TYR F 122 PHE 0.018 0.001 PHE C 178 TRP 0.044 0.002 TRP C 5 HIS 0.005 0.001 HIS D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (12429) covalent geometry : angle 0.65930 / 0.36 (17313) hydrogen bonds : bond 0.04103 / 2.63 ( 469) hydrogen bonds : angle 5.29968 / 3.71 ( 1246) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 283 time to evaluate : 0.450 Fit side-chains REVERT: A 94 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8494 (pt0) REVERT: A 144 ASN cc_start: 0.9251 (t0) cc_final: 0.8991 (t0) REVERT: A 183 GLN cc_start: 0.9025 (pt0) cc_final: 0.8663 (pp30) REVERT: A 185 VAL cc_start: 0.9572 (OUTLIER) cc_final: 0.9306 (m) REVERT: B 145 LYS cc_start: 0.9469 (OUTLIER) cc_final: 0.8964 (tttm) REVERT: B 183 GLN cc_start: 0.8728 (pp30) cc_final: 0.8386 (pp30) REVERT: B 185 VAL cc_start: 0.9128 (OUTLIER) cc_final: 0.8703 (m) REVERT: C 8 SER cc_start: 0.8968 (OUTLIER) cc_final: 0.8531 (t) REVERT: C 154 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7383 (tttt) REVERT: C 159 ARG cc_start: 0.8019 (mtp180) cc_final: 0.7433 (mtp85) REVERT: C 221 GLU cc_start: 0.9102 (tt0) cc_final: 0.8841 (tp30) REVERT: D 6 THR cc_start: 0.8580 (t) cc_final: 0.8292 (m) REVERT: D 8 SER cc_start: 0.9169 (p) cc_final: 0.8873 (p) REVERT: D 88 ARG cc_start: 0.8345 (tpt-90) cc_final: 0.7771 (tpp-160) REVERT: D 113 GLU cc_start: 0.8121 (tt0) cc_final: 0.7795 (pt0) REVERT: D 120 LYS cc_start: 0.9447 (OUTLIER) cc_final: 0.8849 (ttpt) REVERT: D 132 THR cc_start: 0.8910 (t) cc_final: 0.8699 (p) REVERT: D 154 LYS cc_start: 0.8167 (ptmt) cc_final: 0.7799 (pttt) REVERT: D 166 THR cc_start: 0.9222 (m) cc_final: 0.8801 (p) REVERT: D 172 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8232 (mt-10) REVERT: D 174 ARG cc_start: 0.8659 (ptp90) cc_final: 0.8418 (ptp90) REVERT: D 205 ASP cc_start: 0.8245 (t0) cc_final: 0.7943 (t70) REVERT: E 58 ARG cc_start: 0.8803 (mmp80) cc_final: 0.8430 (mmp80) REVERT: E 71 MET cc_start: 0.7705 (pmt) cc_final: 0.7312 (pmm) REVERT: E 172 GLU cc_start: 0.9188 (OUTLIER) cc_final: 0.8905 (tt0) REVERT: E 177 ASP cc_start: 0.9184 (t0) cc_final: 0.8515 (p0) REVERT: F 1 MET cc_start: 0.6712 (mtm) cc_final: 0.6271 (mtm) REVERT: F 76 ASP cc_start: 0.8454 (m-30) cc_final: 0.7520 (p0) REVERT: F 82 LEU cc_start: 0.8895 (mm) cc_final: 0.8681 (mm) REVERT: F 160 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7861 (mt-10) REVERT: F 182 ASP cc_start: 0.8977 (m-30) cc_final: 0.8724 (m-30) REVERT: F 200 ASP cc_start: 0.9252 (m-30) cc_final: 0.8876 (m-30) outliers start: 50 outliers final: 38 residues processed: 307 average time/residue: 0.5404 time to fit residues: 180.4212 Evaluate side-chains 327 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 281 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 154 LYS Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 11 PHE Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 227 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 56 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 133 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 ASN ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.126142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.082002 restraints weight = 21311.160| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.01 r_work: 0.2882 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12429 Z= 0.167 Angle : 0.655 10.203 17313 Z= 0.354 Chirality : 0.044 0.200 2007 Planarity : 0.005 0.060 1956 Dihedral : 20.700 88.205 2438 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 5.09 % Allowed : 37.98 % Favored : 56.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.22), residues: 1362 helix: 1.41 (0.29), residues: 342 sheet: -0.39 (0.33), residues: 232 loop : -0.76 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 2 TYR 0.027 0.001 TYR F 122 PHE 0.016 0.001 PHE C 178 TRP 0.048 0.002 TRP C 5 HIS 0.004 0.001 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (12429) covalent geometry : angle 0.65511 / 0.35 (17313) hydrogen bonds : bond 0.04060 / 2.59 ( 469) hydrogen bonds : angle 5.30214 / 3.71 ( 1246) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4768.46 seconds wall clock time: 81 minutes 34.23 seconds (4894.23 seconds total)