Starting phenix.real_space_refine on Fri Jul 3 05:44:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i91_52748/07_2026/9i91_52748.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i91_52748/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9i91_52748/07_2026/9i91_52748.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i91_52748/07_2026/9i91_52748.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9i91_52748/07_2026/9i91_52748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i91_52748/07_2026/9i91_52748.map" } 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-dev-6108/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: 2.14, per 1000 atoms: 0.18 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: 0.93 Conformation dependent library (CDL) restraints added in 476.5 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: 0.98 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: 1.35 Time building geometry restraints manager: 1.28 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: 6.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 10.140 Find NCS groups from input model: 0.250 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:7.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.670 ------------------------------------------------------------------------------- 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 : 0.719 12.636 17313 Z= 0.468 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 0.71940 / 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 : 0.364 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: 0.4741 time to fit residues: 166.0589 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 : 0.321 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3786 r_free = 0.3786 target = 0.127957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.083102 restraints weight = 21457.174| |-----------------------------------------------------------------------------| 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: 0.8646 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12429 Z= 0.176 Angle : 0.652 7.987 17313 Z= 0.362 Chirality : 0.046 0.208 2007 Planarity : 0.005 0.054 1956 Dihedral : 20.203 86.533 2467 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 6.52 % Allowed : 34.42 % 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: -0.34 (0.22), residues: 1362 helix: 0.87 (0.28), residues: 332 sheet: -0.38 (0.33), residues: 251 loop : -0.61 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 58 TYR 0.022 0.001 TYR E 64 PHE 0.014 0.001 PHE B 11 TRP 0.021 0.002 TRP C 5 HIS 0.006 0.001 HIS D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.18 (12429) covalent geometry : angle 0.65227 / 0.36 (17313) hydrogen bonds : bond 0.07138 / 4.70 ( 469) hydrogen bonds : angle 6.32507 / 4.40 ( 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 365 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 301 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9171 (OUTLIER) cc_final: 0.8883 (pt0) REVERT: A 102 ASP cc_start: 0.8782 (OUTLIER) cc_final: 0.8548 (p0) REVERT: A 144 ASN cc_start: 0.9261 (t0) cc_final: 0.8989 (t0) REVERT: A 145 LYS cc_start: 0.9431 (ptmm) cc_final: 0.9225 (ptpp) REVERT: A 183 GLN cc_start: 0.9030 (pt0) cc_final: 0.8808 (pp30) REVERT: B 147 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.8744 (mtt90) REVERT: B 185 VAL cc_start: 0.9065 (OUTLIER) cc_final: 0.8760 (m) REVERT: C 8 SER cc_start: 0.8809 (m) cc_final: 0.8296 (t) REVERT: C 154 LYS cc_start: 0.7543 (tttt) cc_final: 0.7084 (tttt) REVERT: C 221 GLU cc_start: 0.9111 (tt0) cc_final: 0.8848 (tp30) REVERT: D 8 SER cc_start: 0.9111 (p) cc_final: 0.8822 (p) REVERT: D 64 TYR cc_start: 0.8067 (t80) cc_final: 0.7856 (t80) REVERT: D 88 ARG cc_start: 0.8513 (tpt-90) cc_final: 0.7782 (tpp-160) REVERT: D 113 GLU cc_start: 0.8062 (tt0) cc_final: 0.7775 (pt0) REVERT: D 120 LYS cc_start: 0.9441 (OUTLIER) cc_final: 0.8830 (ttpt) REVERT: D 154 LYS cc_start: 0.8350 (ptmt) cc_final: 0.8143 (ptmt) REVERT: E 44 TYR cc_start: 0.8481 (m-80) cc_final: 0.8263 (m-80) REVERT: E 172 GLU cc_start: 0.9168 (OUTLIER) cc_final: 0.8877 (tt0) REVERT: E 177 ASP cc_start: 0.9164 (t0) cc_final: 0.8602 (p0) REVERT: F 2 ARG cc_start: 0.9108 (mtp-110) cc_final: 0.8844 (mtp-110) REVERT: F 160 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7806 (mt-10) REVERT: F 182 ASP cc_start: 0.8951 (m-30) cc_final: 0.8662 (m-30) outliers start: 64 outliers final: 34 residues processed: 335 average time/residue: 0.4437 time to fit residues: 162.1993 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 : 0.367 ------------------------------------------------------------------------------- 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 74 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 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 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: 0.9990 chunk 16 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 114 optimal weight: 0.0870 chunk 33 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.126857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.081987 restraints weight = 21518.788| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 3.05 r_work: 0.2882 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12429 Z= 0.197 Angle : 0.620 7.823 17313 Z= 0.344 Chirality : 0.045 0.172 2007 Planarity : 0.004 0.045 1956 Dihedral : 20.507 86.379 2452 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 7.33 % Allowed : 34.11 % Favored : 58.55 % 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: -0.33 (0.22), residues: 1362 helix: 1.01 (0.28), residues: 341 sheet: -0.21 (0.35), residues: 228 loop : -0.76 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 58 TYR 0.017 0.001 TYR D 211 PHE 0.016 0.001 PHE B 11 TRP 0.027 0.002 TRP C 5 HIS 0.018 0.001 HIS D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.20 (12429) covalent geometry : angle 0.61992 / 0.34 (17313) hydrogen bonds : bond 0.05490 / 3.63 ( 469) hydrogen bonds : angle 5.87181 / 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 364 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 292 time to evaluate : 0.366 Fit side-chains REVERT: A 94 GLU cc_start: 0.9115 (OUTLIER) cc_final: 0.8766 (pt0) REVERT: A 144 ASN cc_start: 0.9241 (t0) cc_final: 0.8955 (t0) REVERT: A 183 GLN cc_start: 0.9068 (pt0) cc_final: 0.8802 (pp30) REVERT: B 185 VAL cc_start: 0.9086 (OUTLIER) cc_final: 0.8762 (m) REVERT: C 8 SER cc_start: 0.8898 (OUTLIER) cc_final: 0.8437 (t) REVERT: C 60 LEU cc_start: 0.7214 (mm) cc_final: 0.6749 (tm) REVERT: C 159 ARG cc_start: 0.7960 (mtp180) cc_final: 0.7367 (mtp85) REVERT: C 221 GLU cc_start: 0.9089 (tt0) cc_final: 0.8847 (tp30) REVERT: D 8 SER cc_start: 0.9168 (p) cc_final: 0.8896 (p) REVERT: D 88 ARG cc_start: 0.8397 (tpt-90) cc_final: 0.7753 (tpp-160) REVERT: D 113 GLU cc_start: 0.8049 (tt0) cc_final: 0.7745 (pt0) REVERT: D 120 LYS cc_start: 0.9461 (OUTLIER) cc_final: 0.8903 (ttpt) REVERT: D 174 ARG cc_start: 0.8617 (ttm110) cc_final: 0.8391 (mtt-85) REVERT: E 172 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.8896 (tt0) REVERT: E 177 ASP cc_start: 0.9174 (t0) cc_final: 0.8557 (p0) REVERT: E 182 ASP cc_start: 0.8575 (m-30) cc_final: 0.8157 (m-30) REVERT: F 1 MET cc_start: 0.6635 (OUTLIER) cc_final: 0.6150 (mtm) REVERT: F 2 ARG cc_start: 0.9081 (mtp-110) cc_final: 0.8851 (mtp-110) REVERT: F 160 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7898 (mt-10) REVERT: F 182 ASP cc_start: 0.8952 (m-30) cc_final: 0.8715 (m-30) outliers start: 72 outliers final: 40 residues processed: 324 average time/residue: 0.4378 time to fit residues: 154.5863 Evaluate side-chains 319 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 273 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 137 ILE 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 42 ILE Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 118 SER 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 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 109 SER Chi-restraints excluded: chain D residue 120 LYS 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 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 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: 0.5980 chunk 30 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 128 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 = 0.3769 r_free = 0.3769 target = 0.126440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.081604 restraints weight = 21467.680| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.04 r_work: 0.2874 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12429 Z= 0.202 Angle : 0.611 9.848 17313 Z= 0.336 Chirality : 0.045 0.170 2007 Planarity : 0.004 0.046 1956 Dihedral : 20.608 86.139 2444 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 8.35 % Allowed : 33.10 % Favored : 58.55 % 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: -0.30 (0.22), residues: 1362 helix: 1.10 (0.28), residues: 342 sheet: -0.23 (0.34), residues: 231 loop : -0.76 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 58 TYR 0.023 0.001 TYR E 64 PHE 0.017 0.001 PHE B 11 TRP 0.028 0.002 TRP C 5 HIS 0.005 0.001 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.20 (12429) covalent geometry : angle 0.61053 / 0.34 (17313) hydrogen bonds : bond 0.04937 / 3.22 ( 469) hydrogen bonds : angle 5.68664 / 3.97 ( 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: 82 poor density : 281 time to evaluate : 0.391 Fit side-chains REVERT: A 144 ASN cc_start: 0.9234 (t0) cc_final: 0.8947 (t0) REVERT: A 183 GLN cc_start: 0.9083 (pt0) cc_final: 0.8730 (pp30) REVERT: B 185 VAL cc_start: 0.9079 (OUTLIER) cc_final: 0.8757 (m) REVERT: C 8 SER cc_start: 0.8897 (OUTLIER) cc_final: 0.8442 (t) REVERT: C 154 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7480 (tttp) REVERT: C 159 ARG cc_start: 0.8005 (mtp180) cc_final: 0.7418 (mtp85) REVERT: C 221 GLU cc_start: 0.9085 (tt0) cc_final: 0.8833 (tp30) REVERT: D 8 SER cc_start: 0.9172 (p) cc_final: 0.8905 (p) REVERT: D 88 ARG cc_start: 0.8377 (tpt-90) cc_final: 0.7737 (tpp-160) REVERT: D 113 GLU cc_start: 0.8075 (tt0) cc_final: 0.7750 (pt0) REVERT: D 132 THR cc_start: 0.8901 (t) cc_final: 0.8638 (p) REVERT: D 166 THR cc_start: 0.9221 (m) cc_final: 0.8820 (p) REVERT: E 172 GLU cc_start: 0.9156 (OUTLIER) cc_final: 0.8906 (tt0) REVERT: E 177 ASP cc_start: 0.9181 (t0) cc_final: 0.8550 (p0) REVERT: E 194 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.7814 (tmm) REVERT: F 1 MET cc_start: 0.6663 (OUTLIER) cc_final: 0.6280 (mtm) REVERT: F 160 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7893 (mt-10) REVERT: F 182 ASP cc_start: 0.8958 (m-30) cc_final: 0.8719 (m-30) outliers start: 82 outliers final: 50 residues processed: 320 average time/residue: 0.4448 time to fit residues: 155.0666 Evaluate side-chains 337 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 281 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 81 SER Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 137 ILE 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 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 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 151 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 211 TYR 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 72 VAL Chi-restraints excluded: chain D residue 109 SER 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 116 SER Chi-restraints excluded: chain E residue 135 MET 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 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 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 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: 0.0020 chunk 6 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 52 optimal weight: 20.0000 chunk 94 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 165 HIS 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 = 0.3776 r_free = 0.3776 target = 0.126987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.082490 restraints weight = 21566.697| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.04 r_work: 0.2886 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12429 Z= 0.170 Angle : 0.602 8.837 17313 Z= 0.332 Chirality : 0.044 0.173 2007 Planarity : 0.004 0.048 1956 Dihedral : 20.714 86.524 2441 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 7.94 % Allowed : 32.99 % 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: -0.24 (0.22), residues: 1362 helix: 1.26 (0.28), residues: 342 sheet: -0.23 (0.35), residues: 215 loop : -0.76 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 58 TYR 0.019 0.001 TYR C 215 PHE 0.015 0.001 PHE D 11 TRP 0.031 0.002 TRP C 5 HIS 0.007 0.001 HIS D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 (12429) covalent geometry : angle 0.60215 / 0.33 (17313) hydrogen bonds : bond 0.04542 / 2.94 ( 469) hydrogen bonds : angle 5.50855 / 3.85 ( 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 370 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 292 time to evaluate : 0.312 Fit side-chains REVERT: A 144 ASN cc_start: 0.9228 (t0) cc_final: 0.8931 (t0) REVERT: A 183 GLN cc_start: 0.9063 (pt0) cc_final: 0.8697 (pp30) REVERT: A 185 VAL cc_start: 0.9568 (OUTLIER) cc_final: 0.9323 (m) REVERT: A 200 ASP cc_start: 0.9105 (m-30) cc_final: 0.8882 (m-30) REVERT: B 185 VAL cc_start: 0.9077 (OUTLIER) cc_final: 0.8727 (m) REVERT: C 8 SER cc_start: 0.8896 (OUTLIER) cc_final: 0.8446 (t) REVERT: C 159 ARG cc_start: 0.7972 (mtp180) cc_final: 0.7387 (mtp85) REVERT: C 160 GLU cc_start: 0.7455 (tp30) cc_final: 0.6972 (tp30) REVERT: C 221 GLU cc_start: 0.9080 (tt0) cc_final: 0.8830 (tp30) REVERT: D 6 THR cc_start: 0.8727 (t) cc_final: 0.8482 (m) REVERT: D 8 SER cc_start: 0.9168 (p) cc_final: 0.8882 (p) REVERT: D 88 ARG cc_start: 0.8362 (tpt-90) cc_final: 0.7746 (tpp-160) REVERT: D 113 GLU cc_start: 0.8051 (tt0) cc_final: 0.7752 (pt0) REVERT: D 120 LYS cc_start: 0.9460 (OUTLIER) cc_final: 0.8880 (ttpt) REVERT: D 154 LYS cc_start: 0.8195 (ptmt) cc_final: 0.7701 (pttt) REVERT: D 162 MET cc_start: 0.9207 (mtp) cc_final: 0.8919 (mtm) REVERT: E 172 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.8816 (tt0) REVERT: E 177 ASP cc_start: 0.9192 (t0) cc_final: 0.8547 (p0) REVERT: F 1 MET cc_start: 0.6648 (OUTLIER) cc_final: 0.6268 (mtm) REVERT: F 76 ASP cc_start: 0.8291 (m-30) cc_final: 0.7357 (p0) REVERT: F 82 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8645 (mm) REVERT: F 160 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7892 (mt-10) REVERT: F 182 ASP cc_start: 0.8962 (m-30) cc_final: 0.8729 (m-30) REVERT: F 197 GLN cc_start: 0.9218 (mp10) cc_final: 0.8614 (mp10) REVERT: F 200 ASP cc_start: 0.9260 (m-30) cc_final: 0.8867 (m-30) outliers start: 78 outliers final: 45 residues processed: 328 average time/residue: 0.4380 time to fit residues: 156.4627 Evaluate side-chains 330 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 278 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 102 ASP Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 223 ILE 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 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 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 211 TYR 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 135 MET 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 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 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: 3.9990 chunk 84 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 74 optimal weight: 10.0000 chunk 49 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3772 r_free = 0.3772 target = 0.126703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.082262 restraints weight = 21570.444| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 3.04 r_work: 0.2886 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12429 Z= 0.179 Angle : 0.610 9.687 17313 Z= 0.336 Chirality : 0.044 0.175 2007 Planarity : 0.004 0.050 1956 Dihedral : 20.732 86.845 2441 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 7.13 % Allowed : 34.93 % Favored : 57.94 % 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: -0.24 (0.22), residues: 1362 helix: 1.31 (0.28), residues: 342 sheet: -0.32 (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 D 108 TYR 0.027 0.001 TYR F 122 PHE 0.016 0.001 PHE E 11 TRP 0.031 0.002 TRP C 5 HIS 0.015 0.001 HIS D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 (12429) covalent geometry : angle 0.60980 / 0.34 (17313) hydrogen bonds : bond 0.04435 / 2.85 ( 469) hydrogen bonds : angle 5.44026 / 3.81 ( 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 356 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 286 time to evaluate : 0.411 Fit side-chains REVERT: A 144 ASN cc_start: 0.9233 (t0) cc_final: 0.8952 (t0) REVERT: A 183 GLN cc_start: 0.9041 (pt0) cc_final: 0.8666 (pp30) REVERT: A 200 ASP cc_start: 0.9095 (m-30) cc_final: 0.8867 (m-30) REVERT: B 147 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.8653 (mtm-85) REVERT: B 185 VAL cc_start: 0.9047 (OUTLIER) cc_final: 0.8729 (m) REVERT: C 8 SER cc_start: 0.8890 (m) cc_final: 0.8450 (t) REVERT: C 154 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.7412 (tttt) REVERT: C 159 ARG cc_start: 0.8005 (mtp180) cc_final: 0.7448 (mtp85) REVERT: C 221 GLU cc_start: 0.9080 (tt0) cc_final: 0.8827 (tp30) REVERT: D 8 SER cc_start: 0.9176 (p) cc_final: 0.8892 (p) REVERT: D 88 ARG cc_start: 0.8329 (tpt-90) cc_final: 0.7745 (tpp-160) REVERT: D 113 GLU cc_start: 0.8059 (tt0) cc_final: 0.7758 (pt0) REVERT: D 120 LYS cc_start: 0.9463 (OUTLIER) cc_final: 0.8880 (ttpt) REVERT: D 132 THR cc_start: 0.8893 (t) cc_final: 0.8643 (p) REVERT: D 162 MET cc_start: 0.9204 (mtp) cc_final: 0.8920 (mtm) REVERT: E 172 GLU cc_start: 0.9153 (OUTLIER) cc_final: 0.8827 (tt0) REVERT: E 177 ASP cc_start: 0.9195 (t0) cc_final: 0.8542 (p0) REVERT: F 1 MET cc_start: 0.6566 (OUTLIER) cc_final: 0.6195 (mtm) REVERT: F 76 ASP cc_start: 0.8351 (m-30) cc_final: 0.7453 (p0) REVERT: F 82 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8629 (mm) REVERT: F 160 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7855 (mt-10) REVERT: F 182 ASP cc_start: 0.8973 (m-30) cc_final: 0.8732 (m-30) REVERT: F 197 GLN cc_start: 0.9234 (OUTLIER) cc_final: 0.8700 (mp10) outliers start: 70 outliers final: 47 residues processed: 318 average time/residue: 0.4375 time to fit residues: 151.6630 Evaluate side-chains 339 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 284 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 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 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 211 TYR 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 120 LYS Chi-restraints excluded: chain D residue 137 ILE 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 168 LEU 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 96 VAL Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 185 VAL 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: 2.9990 chunk 121 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 48 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.3751 r_free = 0.3751 target = 0.125109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.080522 restraints weight = 21487.685| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.02 r_work: 0.2854 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 12429 Z= 0.251 Angle : 0.652 9.505 17313 Z= 0.357 Chirality : 0.045 0.176 2007 Planarity : 0.005 0.052 1956 Dihedral : 20.772 86.462 2441 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 7.74 % Allowed : 35.54 % Favored : 56.72 % 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: -0.24 (0.22), residues: 1362 helix: 1.29 (0.28), residues: 342 sheet: -0.23 (0.34), residues: 235 loop : -0.79 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 2 TYR 0.032 0.002 TYR F 122 PHE 0.020 0.002 PHE E 11 TRP 0.035 0.002 TRP C 5 HIS 0.015 0.001 HIS D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.25 (12429) covalent geometry : angle 0.65244 / 0.36 (17313) hydrogen bonds : bond 0.04559 / 2.93 ( 469) hydrogen bonds : angle 5.44145 / 3.82 ( 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 356 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 280 time to evaluate : 0.364 Fit side-chains REVERT: A 144 ASN cc_start: 0.9247 (t0) cc_final: 0.8955 (t0) REVERT: A 183 GLN cc_start: 0.9072 (pt0) cc_final: 0.8638 (pp30) REVERT: A 185 VAL cc_start: 0.9562 (OUTLIER) cc_final: 0.9338 (m) REVERT: A 188 LYS cc_start: 0.8871 (mmtp) cc_final: 0.8659 (mmtt) REVERT: A 200 ASP cc_start: 0.9096 (m-30) cc_final: 0.8868 (m-30) REVERT: B 147 ARG cc_start: 0.9071 (OUTLIER) cc_final: 0.8685 (mtm-85) REVERT: B 162 MET cc_start: 0.9455 (OUTLIER) cc_final: 0.9245 (ttp) REVERT: B 185 VAL cc_start: 0.9048 (OUTLIER) cc_final: 0.8803 (m) REVERT: C 8 SER cc_start: 0.8902 (m) cc_final: 0.8442 (t) REVERT: C 154 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7504 (tttt) REVERT: C 159 ARG cc_start: 0.8031 (mtp180) cc_final: 0.7489 (mtp85) REVERT: C 221 GLU cc_start: 0.9089 (tt0) cc_final: 0.8827 (tp30) REVERT: D 6 THR cc_start: 0.8694 (t) cc_final: 0.8386 (m) REVERT: D 8 SER cc_start: 0.9202 (p) cc_final: 0.8932 (p) REVERT: D 88 ARG cc_start: 0.8326 (tpt-90) cc_final: 0.7720 (tpp-160) REVERT: D 113 GLU cc_start: 0.8088 (tt0) cc_final: 0.7790 (pt0) REVERT: D 120 LYS cc_start: 0.9462 (OUTLIER) cc_final: 0.8881 (ttpt) REVERT: D 132 THR cc_start: 0.8849 (t) cc_final: 0.8578 (p) REVERT: D 154 LYS cc_start: 0.8211 (ptmt) cc_final: 0.7843 (pttp) REVERT: D 162 MET cc_start: 0.9223 (mtp) cc_final: 0.8947 (mtm) REVERT: D 166 THR cc_start: 0.9222 (m) cc_final: 0.8817 (p) REVERT: D 174 ARG cc_start: 0.8599 (ptp90) cc_final: 0.8264 (ptp90) REVERT: D 205 ASP cc_start: 0.8220 (t0) cc_final: 0.7844 (t0) REVERT: E 172 GLU cc_start: 0.9162 (OUTLIER) cc_final: 0.8827 (tt0) REVERT: E 177 ASP cc_start: 0.9190 (t0) cc_final: 0.8531 (p0) REVERT: F 1 MET cc_start: 0.6607 (OUTLIER) cc_final: 0.6177 (mtm) REVERT: F 76 ASP cc_start: 0.8303 (m-30) cc_final: 0.7401 (p0) REVERT: F 160 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7962 (mt-10) REVERT: F 172 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8813 (mt-10) REVERT: F 182 ASP cc_start: 0.8985 (m-30) cc_final: 0.8743 (m-30) outliers start: 76 outliers final: 53 residues processed: 318 average time/residue: 0.4479 time to fit residues: 155.5099 Evaluate side-chains 333 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 272 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 81 SER 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 6 THR 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 142 LEU Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 183 GLN 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 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 120 LYS 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 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 Chi-restraints excluded: chain F residue 227 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 111 optimal weight: 0.6980 chunk 99 optimal weight: 0.5980 chunk 29 optimal weight: 0.0570 chunk 112 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 109 optimal weight: 0.0570 chunk 51 optimal weight: 20.0000 chunk 135 optimal weight: 8.9990 chunk 103 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.127313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.082783 restraints weight = 21322.323| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 3.02 r_work: 0.2900 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12429 Z= 0.142 Angle : 0.634 10.816 17313 Z= 0.348 Chirality : 0.044 0.178 2007 Planarity : 0.005 0.049 1956 Dihedral : 20.787 87.362 2441 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 5.91 % Allowed : 36.76 % Favored : 57.33 % 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: -0.28 (0.35), residues: 220 loop : -0.75 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 2 TYR 0.027 0.001 TYR F 122 PHE 0.013 0.001 PHE D 11 TRP 0.036 0.002 TRP C 5 HIS 0.019 0.001 HIS D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (12429) covalent geometry : angle 0.63409 / 0.35 (17313) hydrogen bonds : bond 0.04185 / 2.67 ( 469) hydrogen bonds : angle 5.34291 / 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 343 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 285 time to evaluate : 0.430 Fit side-chains REVERT: A 94 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8451 (pt0) REVERT: A 102 ASP cc_start: 0.8820 (OUTLIER) cc_final: 0.8611 (p0) REVERT: A 144 ASN cc_start: 0.9207 (t0) cc_final: 0.8932 (t0) REVERT: A 183 GLN cc_start: 0.9016 (pt0) cc_final: 0.8606 (pp30) REVERT: A 185 VAL cc_start: 0.9582 (OUTLIER) cc_final: 0.9314 (m) REVERT: A 200 ASP cc_start: 0.9070 (m-30) cc_final: 0.8829 (m-30) REVERT: B 147 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8609 (mtm-85) REVERT: C 8 SER cc_start: 0.8934 (m) cc_final: 0.8497 (t) REVERT: C 154 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7528 (tttt) REVERT: C 159 ARG cc_start: 0.7986 (mtp180) cc_final: 0.7457 (mtp85) REVERT: C 174 ARG cc_start: 0.7917 (mmm-85) cc_final: 0.7706 (mmm-85) REVERT: C 221 GLU cc_start: 0.9091 (tt0) cc_final: 0.8842 (tp30) REVERT: D 6 THR cc_start: 0.8598 (t) cc_final: 0.8307 (m) REVERT: D 8 SER cc_start: 0.9150 (p) cc_final: 0.8850 (p) REVERT: D 88 ARG cc_start: 0.8309 (tpt-90) cc_final: 0.7717 (tpp-160) REVERT: D 113 GLU cc_start: 0.8064 (tt0) cc_final: 0.7740 (pt0) REVERT: D 120 LYS cc_start: 0.9445 (OUTLIER) cc_final: 0.8861 (ttpt) REVERT: D 154 LYS cc_start: 0.8132 (ptmt) cc_final: 0.7706 (pttt) REVERT: D 162 MET cc_start: 0.9202 (mtp) cc_final: 0.8926 (mtm) REVERT: D 174 ARG cc_start: 0.8596 (ptp90) cc_final: 0.8281 (ptp90) REVERT: E 44 TYR cc_start: 0.8355 (m-80) cc_final: 0.8123 (m-80) REVERT: E 172 GLU cc_start: 0.9184 (OUTLIER) cc_final: 0.8892 (tt0) REVERT: E 177 ASP cc_start: 0.9176 (t0) cc_final: 0.8524 (p0) REVERT: F 1 MET cc_start: 0.6604 (mtm) cc_final: 0.6150 (mtm) REVERT: F 76 ASP cc_start: 0.8306 (m-30) cc_final: 0.7396 (p0) REVERT: F 160 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7862 (mt-10) REVERT: F 182 ASP cc_start: 0.8972 (m-30) cc_final: 0.8732 (m-30) outliers start: 58 outliers final: 35 residues processed: 314 average time/residue: 0.4599 time to fit residues: 157.5431 Evaluate side-chains 319 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 277 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 B residue 75 THR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 202 MET 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 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 211 TYR 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 139 optimal weight: 8.9990 chunk 140 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 71 optimal weight: 20.0000 chunk 107 optimal weight: 0.0980 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 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 = 0.3764 r_free = 0.3764 target = 0.126026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.081391 restraints weight = 21457.453| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 3.04 r_work: 0.2875 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12429 Z= 0.193 Angle : 0.654 10.114 17313 Z= 0.355 Chirality : 0.045 0.185 2007 Planarity : 0.005 0.048 1956 Dihedral : 20.770 87.566 2438 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 6.01 % Allowed : 36.66 % Favored : 57.33 % 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: -0.27 (0.22), residues: 1362 helix: 1.20 (0.28), residues: 356 sheet: -0.22 (0.34), residues: 222 loop : -0.82 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 2 TYR 0.032 0.002 TYR E 64 PHE 0.020 0.001 PHE B 11 TRP 0.041 0.002 TRP C 5 HIS 0.008 0.001 HIS D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 (12429) covalent geometry : angle 0.65406 / 0.36 (17313) hydrogen bonds : bond 0.04287 / 2.74 ( 469) hydrogen bonds : angle 5.35174 / 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 336 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 277 time to evaluate : 0.556 Fit side-chains REVERT: A 102 ASP cc_start: 0.8818 (OUTLIER) cc_final: 0.8606 (p0) REVERT: A 144 ASN cc_start: 0.9245 (t0) cc_final: 0.8931 (t0) REVERT: A 163 MET cc_start: 0.9359 (mtm) cc_final: 0.9158 (ttm) REVERT: A 183 GLN cc_start: 0.9021 (pt0) cc_final: 0.8586 (pp30) REVERT: A 185 VAL cc_start: 0.9561 (OUTLIER) cc_final: 0.9331 (m) REVERT: A 188 LYS cc_start: 0.8776 (mmtp) cc_final: 0.8566 (mmtt) REVERT: A 200 ASP cc_start: 0.9094 (m-30) cc_final: 0.8856 (m-30) REVERT: B 147 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8643 (mtm-85) REVERT: C 8 SER cc_start: 0.8959 (m) cc_final: 0.8528 (t) REVERT: C 154 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7552 (tttt) REVERT: C 159 ARG cc_start: 0.8001 (mtp180) cc_final: 0.7465 (mtp85) REVERT: C 221 GLU cc_start: 0.9088 (tt0) cc_final: 0.8845 (tp30) REVERT: D 6 THR cc_start: 0.8596 (t) cc_final: 0.8283 (m) REVERT: D 8 SER cc_start: 0.9204 (p) cc_final: 0.8902 (p) REVERT: D 88 ARG cc_start: 0.8357 (tpt-90) cc_final: 0.7767 (tpp-160) REVERT: D 113 GLU cc_start: 0.8121 (tt0) cc_final: 0.7801 (pt0) REVERT: D 120 LYS cc_start: 0.9459 (OUTLIER) cc_final: 0.8885 (ttpt) REVERT: D 132 THR cc_start: 0.8898 (t) cc_final: 0.8676 (p) REVERT: D 162 MET cc_start: 0.9184 (mtp) cc_final: 0.8908 (mtm) REVERT: D 172 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8231 (mt-10) REVERT: D 174 ARG cc_start: 0.8619 (ptp90) cc_final: 0.8296 (ptp90) REVERT: E 58 ARG cc_start: 0.8795 (mmp80) cc_final: 0.8395 (mmp80) REVERT: E 172 GLU cc_start: 0.9207 (OUTLIER) cc_final: 0.8908 (tt0) REVERT: E 177 ASP cc_start: 0.9179 (t0) cc_final: 0.8507 (p0) REVERT: F 1 MET cc_start: 0.6601 (mtm) cc_final: 0.6154 (mtm) REVERT: F 76 ASP cc_start: 0.8349 (m-30) cc_final: 0.7423 (p0) REVERT: F 160 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7807 (mt-10) REVERT: F 182 ASP cc_start: 0.8975 (m-30) cc_final: 0.8731 (m-30) REVERT: F 200 ASP cc_start: 0.9242 (m-30) cc_final: 0.8855 (m-30) outliers start: 59 outliers final: 34 residues processed: 309 average time/residue: 0.4792 time to fit residues: 160.9752 Evaluate side-chains 317 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 277 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER 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 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 147 ARG 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 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 211 TYR 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 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 185 VAL 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 89 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 70 optimal weight: 20.0000 chunk 84 optimal weight: 0.2980 chunk 88 optimal weight: 10.0000 chunk 23 optimal weight: 0.0470 chunk 130 optimal weight: 2.9990 chunk 50 optimal weight: 20.0000 chunk 124 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 overall best weight: 1.4482 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.125147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.080523 restraints weight = 21534.424| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.03 r_work: 0.2862 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 12429 Z= 0.227 Angle : 0.681 10.835 17313 Z= 0.368 Chirality : 0.045 0.199 2007 Planarity : 0.005 0.055 1956 Dihedral : 20.767 87.186 2438 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.58 % Allowed : 38.39 % Favored : 57.03 % 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: -0.26 (0.22), residues: 1362 helix: 1.34 (0.28), residues: 342 sheet: -0.30 (0.34), residues: 234 loop : -0.81 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 2 TYR 0.034 0.002 TYR F 122 PHE 0.022 0.002 PHE B 11 TRP 0.049 0.002 TRP C 5 HIS 0.011 0.001 HIS D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.23 (12429) covalent geometry : angle 0.68107 / 0.37 (17313) hydrogen bonds : bond 0.04301 / 2.75 ( 469) hydrogen bonds : angle 5.37799 / 3.76 ( 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 324 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 279 time to evaluate : 0.426 Fit side-chains REVERT: A 102 ASP cc_start: 0.8810 (OUTLIER) cc_final: 0.8605 (p0) REVERT: A 144 ASN cc_start: 0.9243 (t0) cc_final: 0.8957 (t0) REVERT: A 183 GLN cc_start: 0.9040 (pt0) cc_final: 0.8585 (pp30) REVERT: A 185 VAL cc_start: 0.9574 (OUTLIER) cc_final: 0.9295 (m) REVERT: A 188 LYS cc_start: 0.8792 (mmtp) cc_final: 0.8557 (mmtt) REVERT: A 200 ASP cc_start: 0.9097 (m-30) cc_final: 0.8873 (m-30) REVERT: B 147 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.8645 (mtm-85) REVERT: C 8 SER cc_start: 0.8970 (OUTLIER) cc_final: 0.8562 (t) REVERT: C 154 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7626 (tttt) REVERT: C 159 ARG cc_start: 0.7995 (mtp180) cc_final: 0.7454 (mtp85) REVERT: C 160 GLU cc_start: 0.7910 (tp30) cc_final: 0.7508 (tp30) REVERT: C 221 GLU cc_start: 0.9098 (tt0) cc_final: 0.8850 (tp30) REVERT: D 6 THR cc_start: 0.8608 (t) cc_final: 0.8288 (m) REVERT: D 8 SER cc_start: 0.9195 (p) cc_final: 0.8909 (p) REVERT: D 88 ARG cc_start: 0.8334 (tpt-90) cc_final: 0.7747 (tpp-160) REVERT: D 113 GLU cc_start: 0.8139 (tt0) cc_final: 0.7822 (pt0) REVERT: D 120 LYS cc_start: 0.9461 (OUTLIER) cc_final: 0.8886 (ttpt) REVERT: D 132 THR cc_start: 0.8886 (t) cc_final: 0.8645 (p) REVERT: D 162 MET cc_start: 0.9188 (mtp) cc_final: 0.8906 (mtm) REVERT: D 166 THR cc_start: 0.9210 (m) cc_final: 0.8862 (p) REVERT: D 172 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8268 (mt-10) REVERT: D 174 ARG cc_start: 0.8625 (ptp90) cc_final: 0.8292 (ptp90) REVERT: E 44 TYR cc_start: 0.8284 (m-80) cc_final: 0.8071 (m-80) REVERT: E 71 MET cc_start: 0.7773 (pmt) cc_final: 0.7392 (pmm) REVERT: E 172 GLU cc_start: 0.9207 (OUTLIER) cc_final: 0.8896 (tt0) REVERT: E 177 ASP cc_start: 0.9189 (t0) cc_final: 0.8529 (p0) REVERT: F 1 MET cc_start: 0.6753 (OUTLIER) cc_final: 0.6354 (mtm) REVERT: F 76 ASP cc_start: 0.8425 (m-30) cc_final: 0.7485 (p0) REVERT: F 160 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7776 (mt-10) REVERT: F 182 ASP cc_start: 0.8988 (m-30) cc_final: 0.8739 (m-30) outliers start: 45 outliers final: 34 residues processed: 301 average time/residue: 0.4477 time to fit residues: 146.9681 Evaluate side-chains 313 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 271 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER 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 B residue 118 SER Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 60 LEU 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 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 1 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 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 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: 1.9990 chunk 54 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 109 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.126065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.082362 restraints weight = 21120.385| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.98 r_work: 0.2878 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2603 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= 0.164 Angle : 0.668 10.771 17313 Z= 0.360 Chirality : 0.045 0.198 2007 Planarity : 0.005 0.059 1956 Dihedral : 20.770 87.598 2438 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.38 % Allowed : 38.80 % 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: -0.33 (0.22), residues: 1362 helix: 1.19 (0.28), residues: 356 sheet: -0.29 (0.34), residues: 220 loop : -0.86 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 2 TYR 0.035 0.002 TYR E 64 PHE 0.022 0.001 PHE C 178 TRP 0.046 0.002 TRP C 5 HIS 0.028 0.001 HIS D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (12429) covalent geometry : angle 0.66840 / 0.36 (17313) hydrogen bonds : bond 0.04086 / 2.62 ( 469) hydrogen bonds : angle 5.33113 / 3.72 ( 1246) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4169.72 seconds wall clock time: 71 minutes 27.44 seconds (4287.44 seconds total)