Starting phenix.real_space_refine on Fri Aug 7 11:15:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tm4_41378/08_2026/8tm4_41378.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tm4_41378/08_2026/8tm4_41378.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tm4_41378/08_2026/8tm4_41378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tm4_41378/08_2026/8tm4_41378.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tm4_41378/08_2026/8tm4_41378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tm4_41378/08_2026/8tm4_41378.map" } resolution = 3.0 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 133 5.16 5 C 13612 2.51 5 N 3650 2.21 5 O 3972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21367 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1813 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 222} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1901 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 5, 'TRANS': 244} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "C" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1819 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 6, 'TRANS': 231} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 Chain: "D" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1742 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 7, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 32 Chain: "E" Number of atoms: 1832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1832 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 10, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "F" Number of atoms: 1868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1868 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 237} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 1892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1892 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 236} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 1480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1480 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "I" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1342 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 9, 'TRANS': 165} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "J" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 904 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain breaks: 2 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 1, 'ARG:plan': 1, 'TYR:plan': 2, 'ASP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "c" Number of atoms: 2100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2100 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 13, 'TRANS': 261} Chain breaks: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 11, 'ARG:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 71 Chain: "d" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1906 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 15, 'TRANS': 230} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "e" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 768 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 91} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 4.47, per 1000 atoms: 0.21 Number of scatterers: 21367 At special positions: 0 Unit cell: (130.38, 132.5, 138.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 133 16.00 O 3972 8.00 N 3650 7.00 C 13612 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS G 115 " - pdb=" SG CYS G 154 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 956.8 milliseconds 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5214 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 36 sheets defined 41.0% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 19 through 30 removed outlier: 3.635A pdb=" N GLU A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 101 Processing helix chain 'A' and resid 106 through 124 Processing helix chain 'A' and resid 166 through 178 Processing helix chain 'A' and resid 183 through 198 removed outlier: 4.429A pdb=" N HIS A 189 " --> pdb=" O GLU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 232 Processing helix chain 'B' and resid 18 through 30 Processing helix chain 'B' and resid 79 through 101 Processing helix chain 'B' and resid 106 through 124 removed outlier: 3.667A pdb=" N LEU B 110 " --> pdb=" O PRO B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 179 Processing helix chain 'B' and resid 185 through 201 Processing helix chain 'B' and resid 229 through 251 Processing helix chain 'C' and resid 16 through 28 Processing helix chain 'C' and resid 76 through 99 removed outlier: 3.760A pdb=" N ALA C 80 " --> pdb=" O LEU C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 118 removed outlier: 3.848A pdb=" N ILE C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 176 removed outlier: 3.641A pdb=" N VAL C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS C 174 " --> pdb=" O GLU C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 181 removed outlier: 3.716A pdb=" N ILE C 181 " --> pdb=" O ASP C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 199 removed outlier: 3.704A pdb=" N THR C 187 " --> pdb=" O THR C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 239 Processing helix chain 'D' and resid 21 through 32 removed outlier: 3.873A pdb=" N GLU D 25 " --> pdb=" O LEU D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 103 removed outlier: 4.135A pdb=" N THR D 87 " --> pdb=" O ALA D 83 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU D 88 " --> pdb=" O ASP D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 120 Processing helix chain 'D' and resid 173 through 185 removed outlier: 4.178A pdb=" N SER D 180 " --> pdb=" O GLY D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 206 Processing helix chain 'D' and resid 230 through 241 Processing helix chain 'E' and resid 2 through 7 removed outlier: 3.590A pdb=" N ASP E 7 " --> pdb=" O ASN E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 29 removed outlier: 3.847A pdb=" N GLU E 23 " --> pdb=" O ILE E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 99 Processing helix chain 'E' and resid 104 through 116 Processing helix chain 'E' and resid 118 through 122 Processing helix chain 'E' and resid 165 through 175 Processing helix chain 'E' and resid 175 through 181 removed outlier: 4.011A pdb=" N MET E 180 " --> pdb=" O MET E 176 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU E 181 " --> pdb=" O SER E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 199 Processing helix chain 'E' and resid 229 through 234 Processing helix chain 'F' and resid 22 through 34 removed outlier: 3.909A pdb=" N SER F 34 " --> pdb=" O ALA F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 103 Processing helix chain 'F' and resid 108 through 126 removed outlier: 3.519A pdb=" N TYR F 123 " --> pdb=" O TYR F 119 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TYR F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 178 Processing helix chain 'F' and resid 186 through 202 Processing helix chain 'F' and resid 229 through 246 Processing helix chain 'G' and resid 25 through 35 Processing helix chain 'G' and resid 83 through 106 Processing helix chain 'G' and resid 110 through 128 Processing helix chain 'G' and resid 171 through 185 Processing helix chain 'G' and resid 190 through 206 Processing helix chain 'G' and resid 211 through 213 No H-bonds generated for 'chain 'G' and resid 211 through 213' Processing helix chain 'G' and resid 231 through 245 Processing helix chain 'H' and resid -26 through -11 Processing helix chain 'H' and resid 47 through 70 Processing helix chain 'H' and resid 74 through 89 Processing helix chain 'H' and resid 129 through 140 Processing helix chain 'H' and resid 146 through 162 Processing helix chain 'I' and resid 56 through 79 Processing helix chain 'I' and resid 83 through 97 Processing helix chain 'I' and resid 142 through 154 removed outlier: 4.160A pdb=" N MET I 146 " --> pdb=" O CYS I 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 174 removed outlier: 4.430A pdb=" N GLU I 165 " --> pdb=" O ASP I 161 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR I 166 " --> pdb=" O HIS I 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 72 removed outlier: 3.678A pdb=" N GLN J 65 " --> pdb=" O GLN J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 95 removed outlier: 3.635A pdb=" N ASP J 90 " --> pdb=" O ARG J 86 " (cutoff:3.500A) Processing helix chain 'c' and resid 17 through 31 removed outlier: 5.697A pdb=" N ARG c 28 " --> pdb=" O GLU c 24 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ARG c 29 " --> pdb=" O GLU c 25 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR c 31 " --> pdb=" O GLY c 27 " (cutoff:3.500A) Processing helix chain 'c' and resid 31 through 45 Processing helix chain 'c' and resid 76 through 86 Processing helix chain 'c' and resid 87 through 90 removed outlier: 3.966A pdb=" N SER c 90 " --> pdb=" O VAL c 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 87 through 90' Processing helix chain 'c' and resid 144 through 151 removed outlier: 4.100A pdb=" N GLN c 148 " --> pdb=" O ASP c 144 " (cutoff:3.500A) Processing helix chain 'c' and resid 173 through 175 No H-bonds generated for 'chain 'c' and resid 173 through 175' Processing helix chain 'c' and resid 214 through 226 Processing helix chain 'c' and resid 243 through 248 Processing helix chain 'c' and resid 250 through 255 removed outlier: 4.277A pdb=" N LEU c 254 " --> pdb=" O PHE c 250 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N SER c 255 " --> pdb=" O LYS c 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 250 through 255' Processing helix chain 'c' and resid 256 through 260 Processing helix chain 'c' and resid 265 through 279 Processing helix chain 'd' and resid 23 through 25 No H-bonds generated for 'chain 'd' and resid 23 through 25' Processing helix chain 'd' and resid 26 through 39 Processing helix chain 'd' and resid 98 through 114 Processing helix chain 'd' and resid 130 through 136 Processing helix chain 'd' and resid 148 through 158 Processing helix chain 'd' and resid 186 through 198 Processing helix chain 'd' and resid 213 through 229 removed outlier: 3.517A pdb=" N ALA d 217 " --> pdb=" O ASN d 213 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP d 227 " --> pdb=" O TYR d 223 " (cutoff:3.500A) Processing helix chain 'e' and resid 47 through 54 removed outlier: 3.850A pdb=" N SER e 51 " --> pdb=" O PRO e 47 " (cutoff:3.500A) Processing helix chain 'e' and resid 56 through 71 removed outlier: 5.107A pdb=" N MET e 62 " --> pdb=" O ASN e 58 " (cutoff:3.500A) Processing helix chain 'e' and resid 73 through 87 removed outlier: 3.549A pdb=" N LEU e 77 " --> pdb=" O LEU e 73 " (cutoff:3.500A) Processing helix chain 'e' and resid 99 through 107 Processing helix chain 'e' and resid 113 through 118 removed outlier: 3.537A pdb=" N ILE e 117 " --> pdb=" O GLY e 113 " (cutoff:3.500A) Processing helix chain 'e' and resid 129 through 139 Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 163 Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 67 Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 77 removed outlier: 3.533A pdb=" N SER A 77 " --> pdb=" O SER A 133 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 162 through 164 Processing sheet with id=AA5, first strand: chain 'B' and resid 66 through 69 removed outlier: 6.733A pdb=" N MET B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU B 147 " --> pdb=" O TRP B 159 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLY B 158 " --> pdb=" O ASP C 55 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 77 through 78 Processing sheet with id=AA7, first strand: chain 'C' and resid 158 through 161 removed outlier: 3.800A pdb=" N ILE C 40 " --> pdb=" O GLY C 37 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 62 through 66 removed outlier: 6.365A pdb=" N VAL C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 145 through 147 Processing sheet with id=AB1, first strand: chain 'D' and resid 167 through 170 Processing sheet with id=AB2, first strand: chain 'D' and resid 67 through 69 removed outlier: 3.522A pdb=" N GLY D 75 " --> pdb=" O GLY D 144 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE D 143 " --> pdb=" O PHE D 154 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU D 153 " --> pdb=" O CYS D 165 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 158 through 161 Processing sheet with id=AB4, first strand: chain 'E' and resid 63 through 67 removed outlier: 6.909A pdb=" N ILE E 70 " --> pdb=" O VAL E 66 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 63 through 67 removed outlier: 6.909A pdb=" N ILE E 70 " --> pdb=" O VAL E 66 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 37 through 38 removed outlier: 3.699A pdb=" N GLY F 49 " --> pdb=" O ILE F 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 74 through 75 removed outlier: 4.230A pdb=" N LEU F 149 " --> pdb=" O TYR F 161 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR F 159 " --> pdb=" O MET F 151 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 165 through 169 removed outlier: 5.554A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 69 through 73 removed outlier: 7.182A pdb=" N ILE G 76 " --> pdb=" O ILE G 72 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 69 through 73 removed outlier: 7.182A pdb=" N ILE G 76 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL G 151 " --> pdb=" O PHE G 163 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.597A pdb=" N VAL H 12 " --> pdb=" O VAL H 5 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 34 through 35 Processing sheet with id=AC4, first strand: chain 'H' and resid 45 through 46 Processing sheet with id=AC5, first strand: chain 'I' and resid 10 through 14 Processing sheet with id=AC6, first strand: chain 'I' and resid 19 through 24 removed outlier: 3.726A pdb=" N ILE I 22 " --> pdb=" O HIS I 188 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 42 through 46 removed outlier: 6.780A pdb=" N LEU I 49 " --> pdb=" O MET I 45 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR I 50 " --> pdb=" O ALA I 110 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N CYS I 122 " --> pdb=" O ILE I 109 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ILE I 121 " --> pdb=" O VAL I 132 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N VAL I 132 " --> pdb=" O ILE I 121 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N SER I 123 " --> pdb=" O PRO I 130 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 54 through 55 removed outlier: 3.909A pdb=" N ALA I 54 " --> pdb=" O GLU I 106 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 5 through 7 removed outlier: 3.568A pdb=" N ALA J 16 " --> pdb=" O ILE J 5 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 45 through 48 Processing sheet with id=AD2, first strand: chain 'J' and resid 105 through 107 Processing sheet with id=AD3, first strand: chain 'J' and resid 182 through 184 removed outlier: 3.585A pdb=" N ILE J 182 " --> pdb=" O HIS J 189 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'c' and resid 94 through 98 removed outlier: 5.479A pdb=" N GLU c 95 " --> pdb=" O HIS c 125 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N HIS c 125 " --> pdb=" O GLU c 95 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY c 97 " --> pdb=" O PHE c 123 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LYS c 70 " --> pdb=" O PHE c 133 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N CYS c 135 " --> pdb=" O LYS c 70 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE c 72 " --> pdb=" O CYS c 135 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N CYS c 137 " --> pdb=" O ILE c 72 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA c 74 " --> pdb=" O CYS c 137 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE c 164 " --> pdb=" O ILE c 231 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N TYR c 233 " --> pdb=" O ILE c 164 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE c 166 " --> pdb=" O TYR c 233 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N CYS c 235 " --> pdb=" O ILE c 166 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N THR c 168 " --> pdb=" O CYS c 235 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N THR c 237 " --> pdb=" O THR c 168 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ARG c 170 " --> pdb=" O THR c 237 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'c' and resid 212 through 213 Processing sheet with id=AD6, first strand: chain 'd' and resid 3 through 4 removed outlier: 7.326A pdb=" N VAL d 77 " --> pdb=" O ILE d 44 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N TYR d 46 " --> pdb=" O ALA d 75 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ALA d 75 " --> pdb=" O TYR d 46 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N THR d 16 " --> pdb=" O VAL d 86 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N LEU d 88 " --> pdb=" O THR d 16 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU d 18 " --> pdb=" O LEU d 88 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N LEU d 90 " --> pdb=" O LEU d 18 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'd' and resid 120 through 121 removed outlier: 5.634A pdb=" N VAL d 120 " --> pdb=" O LEU d 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'd' and resid 124 through 125 removed outlier: 6.399A pdb=" N SER d 124 " --> pdb=" O VAL d 208 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'd' and resid 140 through 141 1048 hydrogen bonds defined for protein. 2970 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.40 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4058 1.33 - 1.45: 5039 1.45 - 1.57: 12454 1.57 - 1.70: 0 1.70 - 1.82: 208 Bond restraints: 21759 Sorted by residual: bond pdb=" N GLY I 46 " pdb=" CA GLY I 46 " ideal model delta sigma weight residual 1.442 1.477 -0.035 7.70e-03 1.69e+04 2.03e+01 bond pdb=" N GLY A 32 " pdb=" CA GLY A 32 " ideal model delta sigma weight residual 1.442 1.476 -0.034 7.70e-03 1.69e+04 1.97e+01 bond pdb=" N ARG G 132 " pdb=" CA ARG G 132 " ideal model delta sigma weight residual 1.453 1.488 -0.035 8.30e-03 1.45e+04 1.73e+01 bond pdb=" N CYS c 157 " pdb=" CA CYS c 157 " ideal model delta sigma weight residual 1.458 1.487 -0.030 7.40e-03 1.83e+04 1.61e+01 bond pdb=" N SER C 11 " pdb=" CA SER C 11 " ideal model delta sigma weight residual 1.453 1.486 -0.033 8.30e-03 1.45e+04 1.54e+01 ... (remaining 21754 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 15139 1.32 - 2.65: 9284 2.65 - 3.97: 4082 3.97 - 5.29: 910 5.29 - 6.62: 53 Bond angle restraints: 29468 Sorted by residual: angle pdb=" C GLY B 157 " pdb=" N GLY B 158 " pdb=" CA GLY B 158 " ideal model delta sigma weight residual 121.61 126.28 -4.67 7.70e-01 1.69e+00 3.67e+01 angle pdb=" N ASN e 58 " pdb=" CA ASN e 58 " pdb=" C ASN e 58 " ideal model delta sigma weight residual 112.97 107.29 5.68 1.06e+00 8.90e-01 2.87e+01 angle pdb=" CA GLY A 43 " pdb=" C GLY A 43 " pdb=" O GLY A 43 " ideal model delta sigma weight residual 122.16 117.92 4.24 8.20e-01 1.49e+00 2.67e+01 angle pdb=" CA GLY B 158 " pdb=" C GLY B 158 " pdb=" O GLY B 158 " ideal model delta sigma weight residual 121.57 117.12 4.45 8.70e-01 1.32e+00 2.61e+01 angle pdb=" CA VAL I 185 " pdb=" C VAL I 185 " pdb=" O VAL I 185 " ideal model delta sigma weight residual 121.68 117.80 3.88 7.90e-01 1.60e+00 2.42e+01 ... (remaining 29463 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 11610 17.75 - 35.49: 1229 35.49 - 53.24: 203 53.24 - 70.99: 64 70.99 - 88.74: 16 Dihedral angle restraints: 13122 sinusoidal: 5025 harmonic: 8097 Sorted by residual: dihedral pdb=" CA GLY F 167 " pdb=" C GLY F 167 " pdb=" N LYS F 168 " pdb=" CA LYS F 168 " ideal model delta harmonic sigma weight residual -180.00 -144.18 -35.82 0 5.00e+00 4.00e-02 5.13e+01 dihedral pdb=" CA PRO c 187 " pdb=" C PRO c 187 " pdb=" N PHE c 188 " pdb=" CA PHE c 188 " ideal model delta harmonic sigma weight residual 180.00 144.76 35.24 0 5.00e+00 4.00e-02 4.97e+01 dihedral pdb=" CA ILE A 72 " pdb=" C ILE A 72 " pdb=" N GLY A 73 " pdb=" CA GLY A 73 " ideal model delta harmonic sigma weight residual 180.00 146.38 33.62 0 5.00e+00 4.00e-02 4.52e+01 ... (remaining 13119 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1103 0.053 - 0.105: 1214 0.105 - 0.158: 840 0.158 - 0.211: 217 0.211 - 0.264: 13 Chirality restraints: 3387 Sorted by residual: chirality pdb=" CB ILE F 4 " pdb=" CA ILE F 4 " pdb=" CG1 ILE F 4 " pdb=" CG2 ILE F 4 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA ILE c 228 " pdb=" N ILE c 228 " pdb=" C ILE c 228 " pdb=" CB ILE c 228 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA ILE H 177 " pdb=" N ILE H 177 " pdb=" C ILE H 177 " pdb=" CB ILE H 177 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 3384 not shown) Planarity restraints: 3773 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU d 17 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.92e+00 pdb=" C LEU d 17 " 0.049 2.00e-02 2.50e+03 pdb=" O LEU d 17 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU d 18 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE d 181 " 0.008 2.00e-02 2.50e+03 1.58e-02 2.51e+00 pdb=" C ILE d 181 " -0.027 2.00e-02 2.50e+03 pdb=" O ILE d 181 " 0.010 2.00e-02 2.50e+03 pdb=" N PRO d 182 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP I 159 " -0.007 2.00e-02 2.50e+03 1.43e-02 2.05e+00 pdb=" C ASP I 159 " 0.025 2.00e-02 2.50e+03 pdb=" O ASP I 159 " -0.009 2.00e-02 2.50e+03 pdb=" N PRO I 160 " -0.009 2.00e-02 2.50e+03 ... (remaining 3770 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 9473 2.98 - 3.46: 23148 3.46 - 3.94: 41213 3.94 - 4.42: 45604 4.42 - 4.90: 71116 Nonbonded interactions: 190554 Sorted by model distance: nonbonded pdb=" O GLU E 238 " pdb=" C ARG E 239 " model vdw 2.497 3.270 nonbonded pdb=" N ASP E 67 " pdb=" O ASP E 67 " model vdw 2.526 2.496 nonbonded pdb=" N THR A 69 " pdb=" O THR A 69 " model vdw 2.529 2.496 nonbonded pdb=" CD PRO E 200 " pdb=" OE1 GLN E 203 " model vdw 2.530 3.440 nonbonded pdb=" N VAL J 47 " pdb=" O VAL J 47 " model vdw 2.564 2.496 ... (remaining 190549 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 6.120 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: 0.030 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 20.880 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:11.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 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 : 0.013 0.046 21760 Z= 0.994 Angle : 1.886 6.619 29470 Z= 1.369 Chirality : 0.095 0.264 3387 Planarity : 0.004 0.028 3773 Dihedral : 15.392 88.736 7905 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 1.64 % Allowed : 9.29 % Favored : 89.08 % Rotamer: Outliers : 3.99 % Allowed : 9.52 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.03 (0.11), residues: 2746 helix: -3.16 (0.11), residues: 1084 sheet: -3.51 (0.21), residues: 388 loop : -3.38 (0.12), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG d 129 TYR 0.023 0.002 TYR C 110 PHE 0.020 0.002 PHE C 171 TRP 0.014 0.002 TRP F 162 HIS 0.006 0.001 HIS D 73 Details of bonding type rmsd/Z covalent geometry : bond 0.01299 / 0.99 (21759) covalent geometry : angle 1.88612 / 1.37 (29468) SS BOND : bond 0.00192 / 0.10 ( 1) SS BOND : angle 1.34088 / 0.72 ( 2) hydrogen bonds : bond 0.20383 / 13.51 ( 1038) hydrogen bonds : angle 9.67409 / 6.75 ( 2970) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 744 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 TYR cc_start: 0.8853 (t80) cc_final: 0.8230 (t80) REVERT: A 226 VAL cc_start: 0.9309 (t) cc_final: 0.8988 (t) REVERT: B 230 GLN cc_start: 0.6534 (tp40) cc_final: 0.6300 (tp40) REVERT: C 159 ASN cc_start: 0.7964 (t0) cc_final: 0.7582 (t0) REVERT: D 109 VAL cc_start: 0.8891 (t) cc_final: 0.8639 (t) REVERT: D 157 ASP cc_start: 0.6131 (p0) cc_final: 0.5804 (p0) REVERT: D 202 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7753 (mt) REVERT: D 229 PHE cc_start: 0.7614 (OUTLIER) cc_final: 0.7116 (t80) REVERT: E 117 GLN cc_start: 0.8623 (tm-30) cc_final: 0.8034 (tp40) REVERT: E 195 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8535 (tp) REVERT: F 64 ASN cc_start: 0.7773 (m-40) cc_final: 0.7530 (m110) REVERT: F 94 GLU cc_start: 0.8133 (tp30) cc_final: 0.7897 (tp30) REVERT: F 118 MET cc_start: 0.8529 (mmp) cc_final: 0.8232 (mmt) REVERT: G 53 GLN cc_start: 0.8537 (pt0) cc_final: 0.8253 (pt0) REVERT: G 101 TRP cc_start: 0.8772 (t-100) cc_final: 0.8246 (t-100) REVERT: G 107 TYR cc_start: 0.8181 (p90) cc_final: 0.7945 (p90) REVERT: H -15 PHE cc_start: 0.9045 (m-80) cc_final: 0.8584 (m-80) REVERT: H 1 THR cc_start: 0.7100 (OUTLIER) cc_final: 0.6827 (t) REVERT: H 63 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7701 (mm-30) REVERT: H 85 MET cc_start: 0.8769 (ttp) cc_final: 0.8555 (ttp) REVERT: H 89 TYR cc_start: 0.8624 (m-80) cc_final: 0.8265 (m-80) REVERT: H 118 THR cc_start: 0.6540 (t) cc_final: 0.6231 (t) REVERT: I 169 GLN cc_start: 0.8323 (mm110) cc_final: 0.8062 (tp40) REVERT: I 186 ILE cc_start: 0.8846 (mt) cc_final: 0.8541 (mp) REVERT: J 85 ARG cc_start: 0.8156 (ttp80) cc_final: 0.7948 (ttp-110) REVERT: J 104 LEU cc_start: 0.7879 (tt) cc_final: 0.7571 (tm) REVERT: J 118 MET cc_start: 0.7546 (ttm) cc_final: 0.7183 (ttp) REVERT: c 40 GLN cc_start: 0.8294 (mm-40) cc_final: 0.8043 (mm-40) REVERT: c 121 CYS cc_start: 0.6727 (OUTLIER) cc_final: 0.6430 (m) REVERT: c 134 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8066 (tt) REVERT: c 184 LEU cc_start: 0.7315 (mt) cc_final: 0.6854 (mt) REVERT: c 186 SER cc_start: 0.7234 (OUTLIER) cc_final: 0.6906 (p) REVERT: c 236 TYR cc_start: 0.8611 (m-80) cc_final: 0.8388 (m-80) REVERT: c 273 LEU cc_start: 0.9423 (tp) cc_final: 0.9191 (tm) REVERT: d 41 MET cc_start: 0.8040 (mmm) cc_final: 0.7818 (mmm) REVERT: d 49 THR cc_start: 0.7904 (t) cc_final: 0.7700 (t) REVERT: d 61 TYR cc_start: 0.8756 (m-80) cc_final: 0.8319 (m-80) REVERT: d 130 ASN cc_start: 0.8413 (t0) cc_final: 0.7991 (t0) REVERT: e 56 GLN cc_start: 0.8113 (tp-100) cc_final: 0.7657 (tp40) REVERT: e 58 ASN cc_start: 0.8869 (OUTLIER) cc_final: 0.8159 (m-40) REVERT: e 62 MET cc_start: 0.7111 (mtp) cc_final: 0.6903 (mtp) REVERT: e 119 ASN cc_start: 0.8107 (t0) cc_final: 0.7885 (t0) outliers start: 89 outliers final: 16 residues processed: 795 average time/residue: 0.5236 time to fit residues: 480.5232 Evaluate side-chains 428 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 404 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 154 HIS Chi-restraints excluded: chain D residue 158 PRO Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 160 TYR Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain H residue 1 THR Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain c residue 121 CYS Chi-restraints excluded: chain c residue 134 LEU Chi-restraints excluded: chain c residue 186 SER Chi-restraints excluded: chain d residue 115 CYS Chi-restraints excluded: chain e residue 58 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 GLN B 123 GLN B 146 GLN C 23 GLN C 54 GLN ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN C 146 GLN D 104 ASN E 69 HIS E 121 GLN E 175 HIS F 64 ASN F 222 ASN ** G 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 GLN J 71 ASN J 82 ASN J 87 ASN J 110 HIS d 29 GLN d 128 GLN d 133 GLN ** d 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.095739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.081009 restraints weight = 55312.124| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.30 r_work: 0.3209 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 21760 Z= 0.196 Angle : 0.780 13.470 29470 Z= 0.401 Chirality : 0.045 0.173 3387 Planarity : 0.005 0.052 3773 Dihedral : 6.925 59.679 3047 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.35 % Favored : 96.47 % Rotamer: Outliers : 5.61 % Allowed : 20.42 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.14), residues: 2746 helix: -0.69 (0.14), residues: 1092 sheet: -2.53 (0.19), residues: 594 loop : -2.19 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 60 TYR 0.022 0.002 TYR C 118 PHE 0.031 0.002 PHE I 43 TRP 0.022 0.002 TRP F 162 HIS 0.013 0.001 HIS F 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.20 (21759) covalent geometry : angle 0.77997 / 0.40 (29468) SS BOND : bond 0.00582 / 0.31 ( 1) SS BOND : angle 0.94431 / 0.53 ( 2) hydrogen bonds : bond 0.04763 / 3.24 ( 1038) hydrogen bonds : angle 5.78217 / 4.06 ( 2970) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 455 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 ASP cc_start: 0.8464 (m-30) cc_final: 0.8220 (m-30) REVERT: A 166 ASN cc_start: 0.8427 (m-40) cc_final: 0.8062 (t0) REVERT: B 71 ASP cc_start: 0.8847 (m-30) cc_final: 0.8620 (m-30) REVERT: B 199 LYS cc_start: 0.8491 (ttpt) cc_final: 0.8247 (ptmt) REVERT: B 231 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8792 (tptp) REVERT: C 146 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8591 (tp40) REVERT: C 211 MET cc_start: 0.8255 (tpp) cc_final: 0.8002 (tpt) REVERT: D 25 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8152 (mt-10) REVERT: D 152 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7766 (mt0) REVERT: D 178 GLN cc_start: 0.8840 (tp40) cc_final: 0.8010 (tp40) REVERT: D 202 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8259 (mt) REVERT: D 215 ILE cc_start: 0.8588 (tt) cc_final: 0.8116 (tp) REVERT: D 229 PHE cc_start: 0.8601 (OUTLIER) cc_final: 0.7999 (t80) REVERT: D 231 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7779 (tppt) REVERT: F 51 GLU cc_start: 0.7968 (tt0) cc_final: 0.7635 (tt0) REVERT: F 94 GLU cc_start: 0.9096 (tp30) cc_final: 0.8711 (tm-30) REVERT: F 118 MET cc_start: 0.9242 (mmp) cc_final: 0.8946 (mmt) REVERT: G 101 TRP cc_start: 0.9415 (t-100) cc_final: 0.8684 (t-100) REVERT: G 107 TYR cc_start: 0.8479 (p90) cc_final: 0.7937 (p90) REVERT: G 123 GLN cc_start: 0.9476 (OUTLIER) cc_final: 0.9222 (tm-30) REVERT: G 128 ASN cc_start: 0.8882 (t0) cc_final: 0.8569 (t0) REVERT: H 63 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8319 (mm-30) REVERT: H 79 ASN cc_start: 0.9132 (t0) cc_final: 0.8724 (t0) REVERT: H 126 MET cc_start: 0.7686 (mtp) cc_final: 0.7447 (mtp) REVERT: H 134 MET cc_start: 0.7944 (tpt) cc_final: 0.7736 (tpt) REVERT: H 175 CYS cc_start: 0.8325 (m) cc_final: 0.7662 (t) REVERT: H 180 ASN cc_start: 0.7892 (p0) cc_final: 0.7664 (p0) REVERT: I 104 TYR cc_start: 0.7962 (m-80) cc_final: 0.7657 (m-80) REVERT: I 131 MET cc_start: 0.6239 (ppp) cc_final: 0.5872 (pp-130) REVERT: I 134 ASP cc_start: 0.8920 (t70) cc_final: 0.8647 (t0) REVERT: I 149 MET cc_start: 0.8151 (tpt) cc_final: 0.7636 (tpp) REVERT: I 169 GLN cc_start: 0.8226 (mm110) cc_final: 0.7940 (tp40) REVERT: J 42 ILE cc_start: 0.6653 (mt) cc_final: 0.6452 (mt) REVERT: c 210 ASN cc_start: 0.8474 (m-40) cc_final: 0.8240 (m-40) REVERT: c 236 TYR cc_start: 0.8871 (m-80) cc_final: 0.8484 (m-80) REVERT: c 243 ASP cc_start: 0.8081 (t0) cc_final: 0.7576 (t0) REVERT: c 256 THR cc_start: 0.8170 (p) cc_final: 0.7781 (p) REVERT: d 41 MET cc_start: 0.8854 (mmm) cc_final: 0.8114 (mmm) REVERT: d 83 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8608 (mmm160) REVERT: d 200 GLN cc_start: 0.8212 (mt0) cc_final: 0.7994 (mt0) REVERT: d 264 PHE cc_start: 0.8384 (m-80) cc_final: 0.8133 (m-80) REVERT: e 58 ASN cc_start: 0.9137 (m-40) cc_final: 0.8817 (m-40) REVERT: e 59 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8396 (mm110) REVERT: e 90 GLN cc_start: 0.8766 (pm20) cc_final: 0.8379 (pm20) REVERT: e 119 ASN cc_start: 0.7648 (t0) cc_final: 0.7228 (t0) outliers start: 125 outliers final: 35 residues processed: 530 average time/residue: 0.4431 time to fit residues: 275.0643 Evaluate side-chains 414 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 369 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 146 GLN Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 47 CYS Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 152 GLN Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 160 TYR Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain H residue 156 GLU Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain J residue 39 SER Chi-restraints excluded: chain J residue 182 ILE Chi-restraints excluded: chain c residue 176 LYS Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 63 THR Chi-restraints excluded: chain d residue 83 ARG Chi-restraints excluded: chain d residue 115 CYS Chi-restraints excluded: chain d residue 187 THR Chi-restraints excluded: chain e residue 59 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 169 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 238 optimal weight: 0.9980 chunk 198 optimal weight: 0.1980 chunk 205 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 GLN C 23 GLN ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN D 104 ASN F 98 ASN G 147 GLN G 238 HIS ** I 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 HIS d 128 GLN ** d 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 88 GLN e 108 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.088926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.074629 restraints weight = 56791.349| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 3.23 r_work: 0.3082 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 21760 Z= 0.165 Angle : 0.709 15.958 29470 Z= 0.358 Chirality : 0.044 0.271 3387 Planarity : 0.005 0.056 3773 Dihedral : 5.704 59.459 3027 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.46 % Favored : 96.39 % Rotamer: Outliers : 5.70 % Allowed : 21.45 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.15), residues: 2746 helix: 0.59 (0.15), residues: 1099 sheet: -2.14 (0.19), residues: 609 loop : -1.55 (0.17), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 3 TYR 0.020 0.002 TYR C 118 PHE 0.018 0.002 PHE d 102 TRP 0.013 0.001 TRP F 162 HIS 0.009 0.001 HIS F 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (21759) covalent geometry : angle 0.70846 / 0.36 (29468) SS BOND : bond 0.03307 / 1.74 ( 1) SS BOND : angle 2.60150 / 1.53 ( 2) hydrogen bonds : bond 0.04356 / 3.00 ( 1038) hydrogen bonds : angle 5.14473 / 3.61 ( 2970) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 404 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 TYR cc_start: 0.9026 (t80) cc_final: 0.8593 (t80) REVERT: A 166 ASN cc_start: 0.8736 (m-40) cc_final: 0.8448 (t0) REVERT: B 51 ASN cc_start: 0.8409 (m-40) cc_final: 0.7865 (p0) REVERT: B 231 LYS cc_start: 0.9311 (OUTLIER) cc_final: 0.8971 (tppp) REVERT: C 66 ASP cc_start: 0.7175 (t0) cc_final: 0.6845 (t0) REVERT: C 211 MET cc_start: 0.8396 (tpp) cc_final: 0.8129 (tpt) REVERT: C 225 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8815 (pp) REVERT: D 178 GLN cc_start: 0.9089 (tp40) cc_final: 0.8854 (tp40) REVERT: D 202 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8437 (mt) REVERT: D 229 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.8074 (t80) REVERT: E 3 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7997 (ptp-170) REVERT: E 77 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8948 (mp) REVERT: E 85 CYS cc_start: 0.9418 (p) cc_final: 0.9155 (t) REVERT: E 178 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7558 (mp0) REVERT: F 94 GLU cc_start: 0.9147 (tp30) cc_final: 0.8944 (tm-30) REVERT: F 118 MET cc_start: 0.9344 (mmp) cc_final: 0.9113 (mmt) REVERT: G 101 TRP cc_start: 0.9458 (t-100) cc_final: 0.8770 (t-100) REVERT: G 107 TYR cc_start: 0.8634 (p90) cc_final: 0.8049 (p90) REVERT: G 123 GLN cc_start: 0.9480 (OUTLIER) cc_final: 0.9202 (tm-30) REVERT: H 56 GLN cc_start: 0.8991 (tt0) cc_final: 0.8553 (tp40) REVERT: H 63 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8356 (mm-30) REVERT: H 79 ASN cc_start: 0.9162 (t0) cc_final: 0.8781 (t0) REVERT: H 84 GLN cc_start: 0.8715 (mt0) cc_final: 0.8337 (mm-40) REVERT: H 123 TYR cc_start: 0.8610 (p90) cc_final: 0.7974 (p90) REVERT: H 126 MET cc_start: 0.7840 (mtp) cc_final: 0.7635 (mtp) REVERT: H 137 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.7775 (t80) REVERT: H 139 ASP cc_start: 0.8845 (t0) cc_final: 0.8460 (t0) REVERT: H 140 LYS cc_start: 0.8163 (mmmm) cc_final: 0.7863 (mmmt) REVERT: H 145 MET cc_start: 0.8082 (tpp) cc_final: 0.7841 (tpp) REVERT: H 146 GLU cc_start: 0.8109 (pm20) cc_final: 0.7819 (pm20) REVERT: H 175 CYS cc_start: 0.8308 (m) cc_final: 0.7630 (t) REVERT: I 75 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8134 (tp30) REVERT: I 131 MET cc_start: 0.6545 (ppp) cc_final: 0.6093 (pp-130) REVERT: I 146 MET cc_start: 0.8389 (pmm) cc_final: 0.8128 (pmm) REVERT: I 149 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7781 (tpp) REVERT: I 169 GLN cc_start: 0.8185 (mm110) cc_final: 0.7903 (tp40) REVERT: I 171 MET cc_start: 0.7970 (mmm) cc_final: 0.7688 (mmm) REVERT: J 11 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7273 (m-30) REVERT: J 14 LEU cc_start: 0.8296 (tp) cc_final: 0.8091 (tm) REVERT: c 176 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8793 (mmtp) REVERT: c 210 ASN cc_start: 0.8600 (m-40) cc_final: 0.8374 (m-40) REVERT: c 236 TYR cc_start: 0.9007 (m-80) cc_final: 0.8589 (m-80) REVERT: d 83 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.8697 (mmm160) REVERT: d 200 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8286 (mt0) REVERT: e 59 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8475 (mm-40) REVERT: e 68 ARG cc_start: 0.8670 (tpt90) cc_final: 0.8333 (tpt90) REVERT: e 90 GLN cc_start: 0.8742 (pm20) cc_final: 0.7998 (pm20) outliers start: 127 outliers final: 40 residues processed: 483 average time/residue: 0.4394 time to fit residues: 247.3612 Evaluate side-chains 409 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 354 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 139 ASP Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain H residue 0 THR Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain c residue 77 ASN Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 92 VAL Chi-restraints excluded: chain c residue 153 VAL Chi-restraints excluded: chain c residue 176 LYS Chi-restraints excluded: chain d residue 5 CYS Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 26 ASN Chi-restraints excluded: chain d residue 63 THR Chi-restraints excluded: chain d residue 83 ARG Chi-restraints excluded: chain d residue 115 CYS Chi-restraints excluded: chain d residue 187 THR Chi-restraints excluded: chain d residue 189 THR Chi-restraints excluded: chain d residue 200 GLN Chi-restraints excluded: chain d residue 209 SER Chi-restraints excluded: chain d residue 228 LEU Chi-restraints excluded: chain e residue 59 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 18 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 243 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN A 112 GLN ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN D 104 ASN ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 157 ASN I 162 HIS J 110 HIS c 136 GLN ** d 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 108 ASN e 119 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.082251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.068171 restraints weight = 58073.626| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 3.17 r_work: 0.2949 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 21760 Z= 0.216 Angle : 0.704 12.301 29470 Z= 0.356 Chirality : 0.044 0.297 3387 Planarity : 0.005 0.054 3773 Dihedral : 5.322 58.922 3025 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.28 % Favored : 96.61 % Rotamer: Outliers : 5.52 % Allowed : 23.29 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.15), residues: 2746 helix: 1.14 (0.15), residues: 1086 sheet: -1.66 (0.19), residues: 606 loop : -1.18 (0.18), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 3 TYR 0.026 0.002 TYR C 118 PHE 0.017 0.002 PHE I 69 TRP 0.014 0.001 TRP F 162 HIS 0.007 0.001 HIS G 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.22 (21759) covalent geometry : angle 0.70360 / 0.36 (29468) SS BOND : bond 0.00187 / 0.10 ( 1) SS BOND : angle 3.26210 / 1.89 ( 2) hydrogen bonds : bond 0.04470 / 3.04 ( 1038) hydrogen bonds : angle 4.90760 / 3.46 ( 2970) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 380 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8805 (mmm) REVERT: A 103 GLU cc_start: 0.7788 (tp30) cc_final: 0.7585 (tm-30) REVERT: A 166 ASN cc_start: 0.8960 (m-40) cc_final: 0.8675 (t0) REVERT: B 51 ASN cc_start: 0.8368 (m-40) cc_final: 0.7982 (p0) REVERT: B 151 ASP cc_start: 0.8667 (m-30) cc_final: 0.8438 (m-30) REVERT: B 201 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.6757 (pp-130) REVERT: C 129 ILE cc_start: 0.9295 (OUTLIER) cc_final: 0.8905 (pp) REVERT: C 225 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8846 (pp) REVERT: D 215 ILE cc_start: 0.9245 (OUTLIER) cc_final: 0.8991 (tp) REVERT: E 3 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8154 (ptp-170) REVERT: E 16 GLN cc_start: 0.9494 (OUTLIER) cc_final: 0.9235 (mm-40) REVERT: E 91 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8609 (mp0) REVERT: F 94 GLU cc_start: 0.9145 (tp30) cc_final: 0.8943 (tm-30) REVERT: F 98 ASN cc_start: 0.9128 (t0) cc_final: 0.8811 (t0) REVERT: F 111 HIS cc_start: 0.8840 (t-170) cc_final: 0.8570 (t-170) REVERT: F 170 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8357 (ppt-90) REVERT: G 123 GLN cc_start: 0.9508 (OUTLIER) cc_final: 0.9265 (tm-30) REVERT: G 138 MET cc_start: 0.8963 (ttm) cc_final: 0.8587 (ttp) REVERT: H 56 GLN cc_start: 0.8958 (tt0) cc_final: 0.8623 (tp40) REVERT: H 63 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8313 (mm-30) REVERT: H 79 ASN cc_start: 0.9206 (t0) cc_final: 0.8838 (t0) REVERT: H 84 GLN cc_start: 0.8680 (mt0) cc_final: 0.8267 (mm-40) REVERT: H 88 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8337 (ttt90) REVERT: H 123 TYR cc_start: 0.8867 (p90) cc_final: 0.8000 (p90) REVERT: H 137 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.7965 (t80) REVERT: H 145 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.7836 (tpp) REVERT: H 146 GLU cc_start: 0.8194 (pm20) cc_final: 0.7961 (pm20) REVERT: H 175 CYS cc_start: 0.8471 (m) cc_final: 0.7781 (t) REVERT: I 75 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8281 (tp30) REVERT: I 80 ARG cc_start: 0.9042 (ptp90) cc_final: 0.8616 (ptp90) REVERT: I 149 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.7906 (tpp) REVERT: I 165 GLU cc_start: 0.8322 (mp0) cc_final: 0.7815 (mp0) REVERT: I 169 GLN cc_start: 0.8137 (mm110) cc_final: 0.7867 (tp40) REVERT: I 193 ASP cc_start: 0.8700 (m-30) cc_final: 0.8378 (m-30) REVERT: J 65 GLN cc_start: 0.7612 (tm-30) cc_final: 0.6982 (tm-30) REVERT: J 121 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8463 (mt) REVERT: c 52 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7228 (mmt180) REVERT: c 181 THR cc_start: 0.9028 (p) cc_final: 0.8784 (p) REVERT: c 236 TYR cc_start: 0.9126 (m-80) cc_final: 0.8784 (m-80) REVERT: d 83 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.8881 (mmm160) REVERT: d 148 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8686 (tm-30) REVERT: d 153 ASN cc_start: 0.9205 (OUTLIER) cc_final: 0.8938 (m110) REVERT: d 200 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8291 (mt0) REVERT: e 68 ARG cc_start: 0.8959 (tpt90) cc_final: 0.8558 (tpt90) REVERT: e 90 GLN cc_start: 0.8813 (pm20) cc_final: 0.8091 (pm20) outliers start: 123 outliers final: 39 residues processed: 462 average time/residue: 0.4531 time to fit residues: 242.4272 Evaluate side-chains 388 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 329 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 201 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 16 GLN Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 170 ARG Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain H residue 0 THR Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 88 ARG Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 191 GLU Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain c residue 52 ARG Chi-restraints excluded: chain c residue 92 VAL Chi-restraints excluded: chain c residue 186 SER Chi-restraints excluded: chain c residue 212 VAL Chi-restraints excluded: chain d residue 5 CYS Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 63 THR Chi-restraints excluded: chain d residue 77 VAL Chi-restraints excluded: chain d residue 83 ARG Chi-restraints excluded: chain d residue 148 GLN Chi-restraints excluded: chain d residue 151 VAL Chi-restraints excluded: chain d residue 153 ASN Chi-restraints excluded: chain d residue 187 THR Chi-restraints excluded: chain d residue 189 THR Chi-restraints excluded: chain d residue 199 ILE Chi-restraints excluded: chain d residue 200 GLN Chi-restraints excluded: chain d residue 209 SER Chi-restraints excluded: chain e residue 122 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 175 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 245 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 127 optimal weight: 0.7980 chunk 190 optimal weight: 0.8980 chunk 251 optimal weight: 5.9990 chunk 260 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 GLN C 23 GLN D 104 ASN ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 GLN J 110 HIS ** d 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 108 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.082283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.068379 restraints weight = 57394.118| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.18 r_work: 0.2959 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.5642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21760 Z= 0.156 Angle : 0.666 12.780 29470 Z= 0.332 Chirality : 0.043 0.251 3387 Planarity : 0.004 0.060 3773 Dihedral : 5.001 59.343 3020 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.46 % Favored : 96.47 % Rotamer: Outliers : 5.16 % Allowed : 24.01 % Favored : 70.83 % 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: -0.25 (0.16), residues: 2746 helix: 1.42 (0.16), residues: 1087 sheet: -1.37 (0.20), residues: 599 loop : -1.02 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG G 3 TYR 0.028 0.001 TYR C 153 PHE 0.015 0.001 PHE I 69 TRP 0.008 0.001 TRP c 105 HIS 0.007 0.001 HIS E 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (21759) covalent geometry : angle 0.66581 / 0.33 (29468) SS BOND : bond 0.00130 / 0.07 ( 1) SS BOND : angle 2.92874 / 1.71 ( 2) hydrogen bonds : bond 0.03974 / 2.70 ( 1038) hydrogen bonds : angle 4.66678 / 3.29 ( 2970) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 375 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8740 (mt-10) REVERT: A 83 TYR cc_start: 0.8999 (t80) cc_final: 0.8659 (t80) REVERT: A 163 MET cc_start: 0.8626 (ptp) cc_final: 0.7948 (ptp) REVERT: A 166 ASN cc_start: 0.8944 (m-40) cc_final: 0.8679 (t0) REVERT: B 51 ASN cc_start: 0.8314 (m-40) cc_final: 0.8029 (p0) REVERT: B 151 ASP cc_start: 0.8735 (m-30) cc_final: 0.8529 (m-30) REVERT: C 129 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.8958 (pp) REVERT: C 159 ASN cc_start: 0.9063 (t0) cc_final: 0.8828 (t160) REVERT: D 141 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8834 (mt) REVERT: E 88 MET cc_start: 0.9393 (mtm) cc_final: 0.9047 (mtm) REVERT: E 91 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8673 (mm-30) REVERT: F 28 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.7684 (mpt) REVERT: F 94 GLU cc_start: 0.9154 (tp30) cc_final: 0.8935 (tm-30) REVERT: F 98 ASN cc_start: 0.9119 (t0) cc_final: 0.8770 (t0) REVERT: F 111 HIS cc_start: 0.8842 (t-170) cc_final: 0.8599 (t-170) REVERT: F 170 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8247 (ppp80) REVERT: G 138 MET cc_start: 0.8940 (ttm) cc_final: 0.8602 (ttp) REVERT: H 56 GLN cc_start: 0.8966 (tt0) cc_final: 0.8617 (tp-100) REVERT: H 79 ASN cc_start: 0.9209 (t0) cc_final: 0.8926 (t0) REVERT: H 84 GLN cc_start: 0.8652 (mt0) cc_final: 0.8296 (mm-40) REVERT: H 88 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8355 (ttt90) REVERT: H 123 TYR cc_start: 0.8885 (p90) cc_final: 0.8525 (p90) REVERT: H 145 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.7865 (tpp) REVERT: H 146 GLU cc_start: 0.8151 (pm20) cc_final: 0.7927 (pm20) REVERT: H 175 CYS cc_start: 0.8572 (m) cc_final: 0.7822 (t) REVERT: I 12 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7540 (mtm) REVERT: I 27 ARG cc_start: 0.3805 (tpm170) cc_final: 0.3381 (mmp-170) REVERT: I 68 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8810 (tmtm) REVERT: I 146 MET cc_start: 0.8746 (pmm) cc_final: 0.8503 (pmm) REVERT: I 149 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.7973 (tpp) REVERT: I 165 GLU cc_start: 0.8359 (mp0) cc_final: 0.7845 (mp0) REVERT: I 169 GLN cc_start: 0.8073 (mm110) cc_final: 0.7798 (tp40) REVERT: I 193 ASP cc_start: 0.8742 (m-30) cc_final: 0.8532 (m-30) REVERT: J 73 TYR cc_start: 0.7457 (p90) cc_final: 0.7176 (p90) REVERT: J 189 HIS cc_start: 0.6474 (m170) cc_final: 0.6260 (m170) REVERT: c 66 TYR cc_start: 0.8209 (m-10) cc_final: 0.7968 (m-10) REVERT: c 181 THR cc_start: 0.9120 (p) cc_final: 0.8915 (p) REVERT: c 236 TYR cc_start: 0.9110 (m-80) cc_final: 0.8783 (m-80) REVERT: d 83 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8852 (mmm160) REVERT: d 148 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8696 (tm-30) REVERT: d 153 ASN cc_start: 0.9224 (OUTLIER) cc_final: 0.8966 (m110) REVERT: d 200 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8260 (mt0) REVERT: e 68 ARG cc_start: 0.8871 (tpt90) cc_final: 0.8585 (tpt90) REVERT: e 90 GLN cc_start: 0.8818 (pm20) cc_final: 0.8028 (pm20) REVERT: e 124 SER cc_start: 0.9004 (t) cc_final: 0.8703 (t) outliers start: 115 outliers final: 45 residues processed: 456 average time/residue: 0.4436 time to fit residues: 235.5229 Evaluate side-chains 387 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 329 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain E residue 4 ASN Chi-restraints excluded: chain E residue 183 ASN Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain F residue 28 MET Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 170 ARG Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 0 THR Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 88 ARG Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain H residue 180 ASN Chi-restraints excluded: chain I residue 12 MET Chi-restraints excluded: chain I residue 68 LYS Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain c residue 77 ASN Chi-restraints excluded: chain c residue 92 VAL Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain c residue 186 SER Chi-restraints excluded: chain c residue 212 VAL Chi-restraints excluded: chain c residue 241 LYS Chi-restraints excluded: chain d residue 5 CYS Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 63 THR Chi-restraints excluded: chain d residue 77 VAL Chi-restraints excluded: chain d residue 83 ARG Chi-restraints excluded: chain d residue 148 GLN Chi-restraints excluded: chain d residue 153 ASN Chi-restraints excluded: chain d residue 187 THR Chi-restraints excluded: chain d residue 189 THR Chi-restraints excluded: chain d residue 199 ILE Chi-restraints excluded: chain d residue 200 GLN Chi-restraints excluded: chain e residue 122 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 261 optimal weight: 0.8980 chunk 265 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 35 optimal weight: 0.0980 chunk 158 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 204 optimal weight: 0.9980 chunk 256 optimal weight: 0.8980 chunk 249 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN D 104 ASN E 59 HIS H 65 HIS J 110 HIS ** d 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 108 ASN e 119 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.082671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.068789 restraints weight = 57771.865| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.20 r_work: 0.2975 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.5865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21760 Z= 0.135 Angle : 0.653 11.458 29470 Z= 0.325 Chirality : 0.042 0.222 3387 Planarity : 0.004 0.062 3773 Dihedral : 4.880 59.975 3020 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.61 % Favored : 96.36 % Rotamer: Outliers : 4.31 % Allowed : 25.40 % Favored : 70.29 % 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: -0.06 (0.16), residues: 2746 helix: 1.57 (0.16), residues: 1090 sheet: -1.20 (0.20), residues: 605 loop : -0.96 (0.18), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 3 TYR 0.030 0.001 TYR C 153 PHE 0.015 0.001 PHE I 69 TRP 0.009 0.001 TRP c 105 HIS 0.007 0.001 HIS E 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (21759) covalent geometry : angle 0.65279 / 0.33 (29468) SS BOND : bond 0.00088 / 0.05 ( 1) SS BOND : angle 3.12534 / 1.83 ( 2) hydrogen bonds : bond 0.03796 / 2.57 ( 1038) hydrogen bonds : angle 4.54814 / 3.23 ( 2970) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 374 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8785 (mt-10) REVERT: A 83 TYR cc_start: 0.9011 (t80) cc_final: 0.8428 (t80) REVERT: A 103 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7832 (tp30) REVERT: A 166 ASN cc_start: 0.8964 (m-40) cc_final: 0.8715 (t0) REVERT: B 51 ASN cc_start: 0.8249 (m-40) cc_final: 0.8031 (p0) REVERT: C 23 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8397 (mp10) REVERT: C 129 ILE cc_start: 0.9341 (OUTLIER) cc_final: 0.8987 (pp) REVERT: C 159 ASN cc_start: 0.9091 (t0) cc_final: 0.8840 (t160) REVERT: D 141 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8787 (mt) REVERT: E 88 MET cc_start: 0.9293 (mtm) cc_final: 0.8731 (mtm) REVERT: E 91 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8701 (mm-30) REVERT: E 197 GLU cc_start: 0.8829 (tt0) cc_final: 0.8532 (tt0) REVERT: F 28 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.7685 (mpt) REVERT: F 94 GLU cc_start: 0.9137 (tp30) cc_final: 0.8917 (tm-30) REVERT: F 98 ASN cc_start: 0.9127 (t0) cc_final: 0.8738 (t0) REVERT: F 111 HIS cc_start: 0.8829 (t-170) cc_final: 0.8616 (t-170) REVERT: F 170 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8300 (ppp80) REVERT: G 46 ASP cc_start: 0.8753 (m-30) cc_final: 0.8385 (m-30) REVERT: G 138 MET cc_start: 0.8918 (ttm) cc_final: 0.8602 (ttp) REVERT: H 56 GLN cc_start: 0.8979 (tt0) cc_final: 0.8620 (tp-100) REVERT: H 79 ASN cc_start: 0.9228 (t0) cc_final: 0.8799 (t0) REVERT: H 84 GLN cc_start: 0.8635 (mt0) cc_final: 0.8291 (mm-40) REVERT: H 88 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8383 (ttt90) REVERT: H 123 TYR cc_start: 0.8905 (p90) cc_final: 0.8539 (p90) REVERT: H 145 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.7855 (tpp) REVERT: H 175 CYS cc_start: 0.8563 (m) cc_final: 0.7775 (t) REVERT: I 12 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.7152 (mtm) REVERT: I 14 MET cc_start: 0.7963 (mmm) cc_final: 0.7597 (mtm) REVERT: I 27 ARG cc_start: 0.3946 (tpm170) cc_final: 0.3563 (mmp-170) REVERT: I 68 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8778 (tmtm) REVERT: I 75 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8167 (tp30) REVERT: I 80 ARG cc_start: 0.9088 (ptp90) cc_final: 0.8701 (ptp90) REVERT: I 149 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7992 (tpp) REVERT: I 153 LEU cc_start: 0.9131 (mt) cc_final: 0.8842 (pp) REVERT: I 165 GLU cc_start: 0.8407 (mp0) cc_final: 0.7825 (mp0) REVERT: I 169 GLN cc_start: 0.8079 (mm110) cc_final: 0.7790 (tp40) REVERT: J 65 GLN cc_start: 0.7937 (tt0) cc_final: 0.7478 (tm-30) REVERT: J 189 HIS cc_start: 0.6749 (m170) cc_final: 0.6520 (m170) REVERT: c 66 TYR cc_start: 0.8251 (m-10) cc_final: 0.8026 (m-10) REVERT: c 236 TYR cc_start: 0.9123 (m-80) cc_final: 0.8894 (m-80) REVERT: c 243 ASP cc_start: 0.8576 (t0) cc_final: 0.8002 (t0) REVERT: d 127 TYR cc_start: 0.9348 (p90) cc_final: 0.9113 (p90) REVERT: d 148 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.8710 (tm-30) REVERT: d 153 ASN cc_start: 0.9249 (OUTLIER) cc_final: 0.9015 (m110) REVERT: d 156 LYS cc_start: 0.9418 (tmmm) cc_final: 0.8892 (mptt) REVERT: d 200 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8273 (mt0) REVERT: e 68 ARG cc_start: 0.8915 (tpt90) cc_final: 0.8605 (tpt90) REVERT: e 90 GLN cc_start: 0.8828 (pm20) cc_final: 0.8025 (pm20) REVERT: e 124 SER cc_start: 0.8998 (t) cc_final: 0.8668 (t) outliers start: 96 outliers final: 44 residues processed: 441 average time/residue: 0.4294 time to fit residues: 220.6871 Evaluate side-chains 395 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 337 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain E residue 4 ASN Chi-restraints excluded: chain E residue 183 ASN Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain F residue 28 MET Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 170 ARG Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain H residue 0 THR Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 88 ARG Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain H residue 180 ASN Chi-restraints excluded: chain I residue 12 MET Chi-restraints excluded: chain I residue 68 LYS Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain c residue 92 VAL Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain c residue 186 SER Chi-restraints excluded: chain c residue 212 VAL Chi-restraints excluded: chain c residue 241 LYS Chi-restraints excluded: chain d residue 5 CYS Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 63 THR Chi-restraints excluded: chain d residue 77 VAL Chi-restraints excluded: chain d residue 148 GLN Chi-restraints excluded: chain d residue 151 VAL Chi-restraints excluded: chain d residue 153 ASN Chi-restraints excluded: chain d residue 187 THR Chi-restraints excluded: chain d residue 200 GLN Chi-restraints excluded: chain d residue 209 SER Chi-restraints excluded: chain d residue 228 LEU Chi-restraints excluded: chain e residue 122 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 195 optimal weight: 0.0770 chunk 78 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 229 optimal weight: 0.5980 chunk 189 optimal weight: 3.9990 chunk 264 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 61.6796 > 50:) chunk 37 optimal weight: 4.9990 chunk 252 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 110 optimal weight: 0.2980 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN D 104 ASN G 172 GLN I 72 ASN I 93 ASN ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 HIS ** d 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 69 ASN e 108 ASN e 119 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.083049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.069238 restraints weight = 57674.122| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.19 r_work: 0.2984 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.6017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21760 Z= 0.130 Angle : 0.653 11.361 29470 Z= 0.324 Chirality : 0.043 0.424 3387 Planarity : 0.004 0.069 3773 Dihedral : 4.809 59.086 3020 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.28 % Favored : 96.69 % Rotamer: Outliers : 4.40 % Allowed : 25.31 % Favored : 70.29 % 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: 0.02 (0.16), residues: 2746 helix: 1.60 (0.16), residues: 1094 sheet: -1.07 (0.20), residues: 593 loop : -0.96 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG G 3 TYR 0.030 0.001 TYR C 153 PHE 0.015 0.001 PHE G 187 TRP 0.009 0.001 TRP c 105 HIS 0.006 0.001 HIS E 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (21759) covalent geometry : angle 0.65206 / 0.32 (29468) SS BOND : bond 0.00119 / 0.06 ( 1) SS BOND : angle 3.08617 / 1.81 ( 2) hydrogen bonds : bond 0.03672 / 2.49 ( 1038) hydrogen bonds : angle 4.48919 / 3.19 ( 2970) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 365 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8831 (mt-10) REVERT: A 83 TYR cc_start: 0.9021 (t80) cc_final: 0.8419 (t80) REVERT: A 166 ASN cc_start: 0.8958 (m-40) cc_final: 0.8726 (t0) REVERT: A 182 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7795 (tm) REVERT: B 90 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8648 (mm) REVERT: C 23 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8304 (mm110) REVERT: C 66 ASP cc_start: 0.6949 (t0) cc_final: 0.6725 (t0) REVERT: C 129 ILE cc_start: 0.9342 (OUTLIER) cc_final: 0.9013 (pp) REVERT: C 159 ASN cc_start: 0.9092 (t0) cc_final: 0.8860 (t160) REVERT: D 202 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9019 (mt) REVERT: E 16 GLN cc_start: 0.9365 (OUTLIER) cc_final: 0.9159 (mm-40) REVERT: E 91 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8721 (mm-30) REVERT: E 164 ARG cc_start: 0.9408 (OUTLIER) cc_final: 0.9156 (mtt-85) REVERT: E 197 GLU cc_start: 0.8837 (tt0) cc_final: 0.8546 (tt0) REVERT: F 28 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.7699 (mpt) REVERT: F 94 GLU cc_start: 0.9126 (tp30) cc_final: 0.8913 (tm-30) REVERT: F 98 ASN cc_start: 0.9127 (t0) cc_final: 0.8765 (t0) REVERT: F 111 HIS cc_start: 0.8797 (t-170) cc_final: 0.8556 (t-170) REVERT: F 170 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8376 (ppp80) REVERT: G 46 ASP cc_start: 0.8676 (m-30) cc_final: 0.8301 (m-30) REVERT: G 138 MET cc_start: 0.8914 (ttm) cc_final: 0.8557 (ttp) REVERT: H -18 GLU cc_start: 0.8973 (tt0) cc_final: 0.8662 (mt-10) REVERT: H 56 GLN cc_start: 0.8981 (tt0) cc_final: 0.8623 (tp40) REVERT: H 79 ASN cc_start: 0.9229 (t0) cc_final: 0.8789 (t0) REVERT: H 84 GLN cc_start: 0.8590 (mt0) cc_final: 0.8254 (mm-40) REVERT: H 88 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.8370 (ttt90) REVERT: H 123 TYR cc_start: 0.8966 (p90) cc_final: 0.8621 (p90) REVERT: H 140 LYS cc_start: 0.8413 (mtmm) cc_final: 0.7871 (mtmm) REVERT: H 145 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.7971 (tpp) REVERT: H 146 GLU cc_start: 0.7889 (pm20) cc_final: 0.7387 (pm20) REVERT: H 175 CYS cc_start: 0.8554 (m) cc_final: 0.7815 (t) REVERT: I 12 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.7156 (mtm) REVERT: I 14 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7590 (mtm) REVERT: I 27 ARG cc_start: 0.4071 (tpm170) cc_final: 0.3729 (mmp-170) REVERT: I 45 MET cc_start: 0.8690 (mmm) cc_final: 0.8480 (mmp) REVERT: I 68 LYS cc_start: 0.9350 (OUTLIER) cc_final: 0.8881 (tmtm) REVERT: I 75 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8157 (tp30) REVERT: I 153 LEU cc_start: 0.9062 (mt) cc_final: 0.8833 (pp) REVERT: I 165 GLU cc_start: 0.8448 (mp0) cc_final: 0.7848 (mp0) REVERT: I 169 GLN cc_start: 0.8006 (mm110) cc_final: 0.7771 (tp40) REVERT: J 65 GLN cc_start: 0.8013 (tt0) cc_final: 0.7499 (tm-30) REVERT: J 189 HIS cc_start: 0.6994 (m170) cc_final: 0.6713 (m170) REVERT: c 41 LEU cc_start: 0.8773 (tp) cc_final: 0.8530 (tt) REVERT: c 44 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8181 (tttm) REVERT: c 66 TYR cc_start: 0.8375 (m-10) cc_final: 0.8151 (m-10) REVERT: c 236 TYR cc_start: 0.9119 (m-80) cc_final: 0.8892 (m-80) REVERT: c 243 ASP cc_start: 0.8603 (t0) cc_final: 0.7757 (t0) REVERT: d 127 TYR cc_start: 0.9357 (p90) cc_final: 0.9135 (p90) REVERT: d 148 GLN cc_start: 0.9107 (OUTLIER) cc_final: 0.8731 (tm-30) REVERT: d 153 ASN cc_start: 0.9241 (OUTLIER) cc_final: 0.9019 (m110) REVERT: d 156 LYS cc_start: 0.9428 (tmmm) cc_final: 0.8962 (mptt) REVERT: d 200 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8243 (mt0) REVERT: e 68 ARG cc_start: 0.8889 (tpt90) cc_final: 0.8619 (tpt90) REVERT: e 90 GLN cc_start: 0.8884 (pm20) cc_final: 0.8055 (pm20) REVERT: e 124 SER cc_start: 0.9016 (t) cc_final: 0.8678 (t) outliers start: 98 outliers final: 44 residues processed: 431 average time/residue: 0.4567 time to fit residues: 228.4228 Evaluate side-chains 402 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 339 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain E residue 4 ASN Chi-restraints excluded: chain E residue 16 GLN Chi-restraints excluded: chain E residue 164 ARG Chi-restraints excluded: chain E residue 183 ASN Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain F residue 28 MET Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 170 ARG Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 0 THR Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 88 ARG Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 12 MET Chi-restraints excluded: chain I residue 14 MET Chi-restraints excluded: chain I residue 68 LYS Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain c residue 44 LYS Chi-restraints excluded: chain c residue 92 VAL Chi-restraints excluded: chain c residue 186 SER Chi-restraints excluded: chain c residue 212 VAL Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 77 VAL Chi-restraints excluded: chain d residue 148 GLN Chi-restraints excluded: chain d residue 151 VAL Chi-restraints excluded: chain d residue 153 ASN Chi-restraints excluded: chain d residue 187 THR Chi-restraints excluded: chain d residue 200 GLN Chi-restraints excluded: chain d residue 209 SER Chi-restraints excluded: chain d residue 228 LEU Chi-restraints excluded: chain e residue 50 LEU Chi-restraints excluded: chain e residue 122 SER Chi-restraints excluded: chain e residue 140 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 213 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 165 optimal weight: 0.0770 chunk 176 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 206 optimal weight: 0.0050 chunk 76 optimal weight: 3.9990 chunk 210 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 overall best weight: 0.7354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 GLN ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 ASN B 84 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN D 104 ASN G 100 ASN G 172 GLN ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 HIS d 67 ASN ** d 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 108 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.082597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.068829 restraints weight = 57808.910| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.21 r_work: 0.2979 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.6182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21760 Z= 0.139 Angle : 0.678 15.092 29470 Z= 0.336 Chirality : 0.043 0.410 3387 Planarity : 0.005 0.078 3773 Dihedral : 4.769 57.684 3019 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.24 % Favored : 96.72 % Rotamer: Outliers : 4.31 % Allowed : 26.12 % Favored : 69.57 % 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: 0.12 (0.16), residues: 2746 helix: 1.70 (0.16), residues: 1087 sheet: -1.05 (0.20), residues: 596 loop : -0.88 (0.18), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG G 3 TYR 0.030 0.001 TYR C 153 PHE 0.025 0.001 PHE H 87 TRP 0.007 0.001 TRP c 105 HIS 0.007 0.001 HIS E 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (21759) covalent geometry : angle 0.67778 / 0.34 (29468) SS BOND : bond 0.00131 / 0.07 ( 1) SS BOND : angle 3.18821 / 1.87 ( 2) hydrogen bonds : bond 0.03705 / 2.51 ( 1038) hydrogen bonds : angle 4.46228 / 3.16 ( 2970) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 361 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8833 (mt-10) REVERT: A 83 TYR cc_start: 0.8976 (t80) cc_final: 0.8376 (t80) REVERT: A 166 ASN cc_start: 0.8951 (m-40) cc_final: 0.8690 (t0) REVERT: A 182 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7859 (tm) REVERT: C 23 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8430 (mm110) REVERT: C 66 ASP cc_start: 0.6881 (t0) cc_final: 0.6569 (t0) REVERT: C 129 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.9003 (pp) REVERT: C 159 ASN cc_start: 0.9121 (t0) cc_final: 0.8896 (t160) REVERT: D 141 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8773 (mt) REVERT: E 16 GLN cc_start: 0.9369 (OUTLIER) cc_final: 0.9167 (mm-40) REVERT: E 91 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8747 (mm-30) REVERT: E 178 GLU cc_start: 0.7808 (mp0) cc_final: 0.7580 (mp0) REVERT: E 197 GLU cc_start: 0.8838 (tt0) cc_final: 0.8542 (tt0) REVERT: F 28 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.7705 (mpt) REVERT: F 94 GLU cc_start: 0.9126 (tp30) cc_final: 0.8913 (tm-30) REVERT: F 98 ASN cc_start: 0.9134 (t0) cc_final: 0.8771 (t0) REVERT: F 111 HIS cc_start: 0.8791 (t-170) cc_final: 0.8203 (t-170) REVERT: F 170 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8409 (ppp80) REVERT: G 46 ASP cc_start: 0.8648 (m-30) cc_final: 0.8321 (m-30) REVERT: G 138 MET cc_start: 0.8918 (ttm) cc_final: 0.8581 (ttp) REVERT: H -18 GLU cc_start: 0.8992 (tt0) cc_final: 0.8742 (mt-10) REVERT: H 79 ASN cc_start: 0.9232 (t0) cc_final: 0.8799 (t0) REVERT: H 84 GLN cc_start: 0.8577 (mt0) cc_final: 0.8268 (mm-40) REVERT: H 123 TYR cc_start: 0.8970 (p90) cc_final: 0.8557 (p90) REVERT: H 140 LYS cc_start: 0.8459 (mtmm) cc_final: 0.7934 (mtmm) REVERT: H 145 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.7904 (tpp) REVERT: H 146 GLU cc_start: 0.7919 (pm20) cc_final: 0.7417 (pm20) REVERT: H 175 CYS cc_start: 0.8477 (m) cc_final: 0.7835 (t) REVERT: I 12 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7168 (mtm) REVERT: I 14 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7634 (mtm) REVERT: I 27 ARG cc_start: 0.4310 (tpm170) cc_final: 0.3917 (mmp-170) REVERT: I 45 MET cc_start: 0.8712 (mmm) cc_final: 0.8509 (mmp) REVERT: I 68 LYS cc_start: 0.9385 (OUTLIER) cc_final: 0.8916 (tmtm) REVERT: I 75 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8143 (tp30) REVERT: I 80 ARG cc_start: 0.9065 (ptp90) cc_final: 0.8807 (ptt90) REVERT: I 88 MET cc_start: 0.9049 (ttp) cc_final: 0.8667 (ttt) REVERT: I 149 MET cc_start: 0.8557 (tpt) cc_final: 0.8000 (tpp) REVERT: I 165 GLU cc_start: 0.8456 (mp0) cc_final: 0.7861 (mp0) REVERT: I 169 GLN cc_start: 0.8012 (mm110) cc_final: 0.7693 (tp40) REVERT: J 65 GLN cc_start: 0.8151 (tt0) cc_final: 0.7557 (tm-30) REVERT: J 118 MET cc_start: 0.7957 (ttm) cc_final: 0.7502 (tpp) REVERT: J 189 HIS cc_start: 0.7256 (m170) cc_final: 0.6950 (m170) REVERT: c 41 LEU cc_start: 0.8814 (tp) cc_final: 0.8588 (tt) REVERT: c 44 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8323 (tttm) REVERT: c 66 TYR cc_start: 0.8427 (m-10) cc_final: 0.8141 (m-10) REVERT: c 236 TYR cc_start: 0.9133 (m-80) cc_final: 0.8907 (m-80) REVERT: c 243 ASP cc_start: 0.8621 (t0) cc_final: 0.7951 (t0) REVERT: d 148 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.8846 (tm-30) REVERT: d 153 ASN cc_start: 0.9233 (OUTLIER) cc_final: 0.9016 (m110) REVERT: d 156 LYS cc_start: 0.9453 (tmmm) cc_final: 0.8998 (mptt) REVERT: d 200 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8246 (mt0) REVERT: e 68 ARG cc_start: 0.8902 (tpt90) cc_final: 0.8601 (tpt90) REVERT: e 90 GLN cc_start: 0.8879 (pm20) cc_final: 0.8069 (pm20) REVERT: e 119 ASN cc_start: 0.7707 (t0) cc_final: 0.7391 (t0) REVERT: e 124 SER cc_start: 0.9037 (t) cc_final: 0.8689 (t) outliers start: 96 outliers final: 46 residues processed: 427 average time/residue: 0.4585 time to fit residues: 227.7532 Evaluate side-chains 406 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 344 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain E residue 4 ASN Chi-restraints excluded: chain E residue 16 GLN Chi-restraints excluded: chain E residue 183 ASN Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain F residue 28 MET Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 170 ARG Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 0 THR Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain H residue 180 ASN Chi-restraints excluded: chain I residue 12 MET Chi-restraints excluded: chain I residue 14 MET Chi-restraints excluded: chain I residue 68 LYS Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 158 MET Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain c residue 44 LYS Chi-restraints excluded: chain c residue 92 VAL Chi-restraints excluded: chain c residue 186 SER Chi-restraints excluded: chain c residue 212 VAL Chi-restraints excluded: chain c residue 259 LEU Chi-restraints excluded: chain d residue 19 MET Chi-restraints excluded: chain d residue 77 VAL Chi-restraints excluded: chain d residue 148 GLN Chi-restraints excluded: chain d residue 151 VAL Chi-restraints excluded: chain d residue 153 ASN Chi-restraints excluded: chain d residue 187 THR Chi-restraints excluded: chain d residue 199 ILE Chi-restraints excluded: chain d residue 200 GLN Chi-restraints excluded: chain d residue 209 SER Chi-restraints excluded: chain d residue 228 LEU Chi-restraints excluded: chain e residue 50 LEU Chi-restraints excluded: chain e residue 122 SER Chi-restraints excluded: chain e residue 140 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 45 optimal weight: 8.9990 chunk 214 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 120 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 chunk 245 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 256 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 203 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 ASN B 146 GLN C 23 GLN H 56 GLN ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 80 GLN e 108 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.082360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.068653 restraints weight = 57417.216| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.19 r_work: 0.2977 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.6366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21760 Z= 0.142 Angle : 0.682 14.405 29470 Z= 0.341 Chirality : 0.043 0.370 3387 Planarity : 0.004 0.049 3773 Dihedral : 4.739 56.293 3019 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.28 % Favored : 96.69 % Rotamer: Outliers : 3.59 % Allowed : 27.38 % Favored : 69.03 % Cbeta Deviations : 0.04 % 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: 0.16 (0.16), residues: 2746 helix: 1.76 (0.16), residues: 1080 sheet: -0.98 (0.20), residues: 594 loop : -0.89 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 107 TYR 0.031 0.002 TYR H 7 PHE 0.032 0.001 PHE H 87 TRP 0.010 0.001 TRP c 105 HIS 0.007 0.001 HIS E 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (21759) covalent geometry : angle 0.68195 / 0.34 (29468) SS BOND : bond 0.00058 / 0.03 ( 1) SS BOND : angle 3.25273 / 1.91 ( 2) hydrogen bonds : bond 0.03714 / 2.52 ( 1038) hydrogen bonds : angle 4.45358 / 3.15 ( 2970) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 362 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8836 (mt-10) REVERT: A 83 TYR cc_start: 0.8979 (t80) cc_final: 0.8388 (t80) REVERT: A 166 ASN cc_start: 0.8956 (m-40) cc_final: 0.8722 (t0) REVERT: A 182 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7877 (tm) REVERT: B 151 ASP cc_start: 0.8510 (m-30) cc_final: 0.7991 (p0) REVERT: C 23 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8286 (mm110) REVERT: C 129 ILE cc_start: 0.9285 (OUTLIER) cc_final: 0.8972 (pp) REVERT: C 159 ASN cc_start: 0.9157 (t0) cc_final: 0.8934 (t160) REVERT: C 211 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8361 (ttt) REVERT: D 141 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8736 (mt) REVERT: E 16 GLN cc_start: 0.9375 (OUTLIER) cc_final: 0.9174 (mm-40) REVERT: E 91 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8769 (mm-30) REVERT: E 178 GLU cc_start: 0.7843 (mp0) cc_final: 0.7597 (mp0) REVERT: E 197 GLU cc_start: 0.8863 (tt0) cc_final: 0.8555 (tt0) REVERT: F 28 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.7699 (mpt) REVERT: F 68 PHE cc_start: 0.9295 (m-80) cc_final: 0.9079 (m-80) REVERT: F 94 GLU cc_start: 0.9129 (tp30) cc_final: 0.8903 (tm-30) REVERT: F 98 ASN cc_start: 0.9136 (t0) cc_final: 0.8771 (t0) REVERT: G 58 ASP cc_start: 0.8132 (t0) cc_final: 0.7921 (t0) REVERT: G 123 GLN cc_start: 0.9498 (OUTLIER) cc_final: 0.9255 (tm-30) REVERT: G 138 MET cc_start: 0.8900 (ttm) cc_final: 0.8567 (ttp) REVERT: G 172 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8336 (tp-100) REVERT: H 79 ASN cc_start: 0.9223 (t0) cc_final: 0.8779 (t0) REVERT: H 84 GLN cc_start: 0.8592 (mt0) cc_final: 0.8266 (mm-40) REVERT: H 123 TYR cc_start: 0.9023 (p90) cc_final: 0.8627 (p90) REVERT: H 140 LYS cc_start: 0.8432 (mtmm) cc_final: 0.7907 (mtmm) REVERT: H 145 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7907 (tpp) REVERT: H 146 GLU cc_start: 0.7958 (pm20) cc_final: 0.7508 (pm20) REVERT: H 175 CYS cc_start: 0.8565 (m) cc_final: 0.7900 (t) REVERT: I 14 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7673 (mtm) REVERT: I 27 ARG cc_start: 0.4439 (tpm170) cc_final: 0.4106 (mmp-170) REVERT: I 45 MET cc_start: 0.8713 (mmm) cc_final: 0.8505 (mmp) REVERT: I 75 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8200 (tp30) REVERT: I 80 ARG cc_start: 0.9059 (ptp90) cc_final: 0.8591 (ptt-90) REVERT: I 88 MET cc_start: 0.9045 (ttp) cc_final: 0.8675 (ttt) REVERT: I 149 MET cc_start: 0.8586 (tpt) cc_final: 0.8184 (tpp) REVERT: I 169 GLN cc_start: 0.7779 (mm110) cc_final: 0.7564 (tp40) REVERT: J 59 TYR cc_start: 0.8222 (t80) cc_final: 0.8019 (t80) REVERT: J 65 GLN cc_start: 0.8083 (tt0) cc_final: 0.7585 (tm-30) REVERT: J 73 TYR cc_start: 0.7599 (p90) cc_final: 0.7389 (p90) REVERT: J 118 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7439 (tpp) REVERT: J 121 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8398 (mt) REVERT: J 189 HIS cc_start: 0.7333 (m170) cc_final: 0.7081 (m90) REVERT: c 41 LEU cc_start: 0.8816 (tp) cc_final: 0.8611 (tt) REVERT: c 44 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8304 (tttm) REVERT: d 148 GLN cc_start: 0.9127 (OUTLIER) cc_final: 0.8876 (tm-30) REVERT: d 153 ASN cc_start: 0.9220 (OUTLIER) cc_final: 0.9020 (m110) REVERT: d 156 LYS cc_start: 0.9453 (tmmm) cc_final: 0.9013 (mptt) REVERT: d 200 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8230 (mt0) REVERT: e 68 ARG cc_start: 0.8907 (tpt90) cc_final: 0.8558 (tpt90) REVERT: e 90 GLN cc_start: 0.8886 (pm20) cc_final: 0.8040 (pm20) REVERT: e 124 SER cc_start: 0.9034 (t) cc_final: 0.8667 (t) outliers start: 80 outliers final: 43 residues processed: 414 average time/residue: 0.5611 time to fit residues: 269.3665 Evaluate side-chains 401 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 340 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 51 ASN Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain E residue 4 ASN Chi-restraints excluded: chain E residue 16 GLN Chi-restraints excluded: chain E residue 183 ASN Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain F residue 28 MET Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 172 GLN Chi-restraints excluded: chain H residue 0 THR Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain H residue 180 ASN Chi-restraints excluded: chain I residue 14 MET Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain c residue 44 LYS Chi-restraints excluded: chain c residue 92 VAL Chi-restraints excluded: chain c residue 186 SER Chi-restraints excluded: chain c residue 212 VAL Chi-restraints excluded: chain c residue 259 LEU Chi-restraints excluded: chain d residue 77 VAL Chi-restraints excluded: chain d residue 148 GLN Chi-restraints excluded: chain d residue 151 VAL Chi-restraints excluded: chain d residue 153 ASN Chi-restraints excluded: chain d residue 187 THR Chi-restraints excluded: chain d residue 199 ILE Chi-restraints excluded: chain d residue 200 GLN Chi-restraints excluded: chain d residue 209 SER Chi-restraints excluded: chain d residue 228 LEU Chi-restraints excluded: chain e residue 50 LEU Chi-restraints excluded: chain e residue 122 SER Chi-restraints excluded: chain e residue 140 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 242 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 204 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 184 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 265 optimal weight: 0.9980 chunk 206 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN C 116 GLN C 120 GLN G 100 ASN ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 80 GLN e 108 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.081748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.068013 restraints weight = 58013.667| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 3.19 r_work: 0.2955 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.6506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21760 Z= 0.164 Angle : 0.703 13.944 29470 Z= 0.349 Chirality : 0.044 0.358 3387 Planarity : 0.005 0.054 3773 Dihedral : 4.722 55.168 3017 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.20 % Favored : 96.76 % Rotamer: Outliers : 3.37 % Allowed : 27.78 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.16), residues: 2746 helix: 1.79 (0.16), residues: 1079 sheet: -0.94 (0.20), residues: 589 loop : -0.90 (0.18), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 3 TYR 0.025 0.002 TYR G 160 PHE 0.034 0.001 PHE H 87 TRP 0.010 0.001 TRP c 105 HIS 0.006 0.001 HIS E 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (21759) covalent geometry : angle 0.70247 / 0.35 (29468) SS BOND : bond 0.00169 / 0.09 ( 1) SS BOND : angle 3.38345 / 1.98 ( 2) hydrogen bonds : bond 0.03828 / 2.60 ( 1038) hydrogen bonds : angle 4.47957 / 3.16 ( 2970) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 353 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8837 (mt-10) REVERT: A 83 TYR cc_start: 0.8977 (t80) cc_final: 0.8404 (t80) REVERT: A 166 ASN cc_start: 0.8941 (m-40) cc_final: 0.8688 (t0) REVERT: A 182 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7857 (tm) REVERT: A 183 GLU cc_start: 0.8230 (pt0) cc_final: 0.7823 (pm20) REVERT: B 151 ASP cc_start: 0.8575 (m-30) cc_final: 0.8097 (p0) REVERT: C 23 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8396 (mm110) REVERT: C 129 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.8968 (pp) REVERT: C 159 ASN cc_start: 0.9167 (t0) cc_final: 0.8963 (t160) REVERT: C 211 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8358 (ttt) REVERT: D 189 MET cc_start: 0.7406 (mtp) cc_final: 0.6997 (mtt) REVERT: E 16 GLN cc_start: 0.9387 (OUTLIER) cc_final: 0.9184 (mm-40) REVERT: E 91 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8789 (mm-30) REVERT: E 176 MET cc_start: 0.7395 (ttp) cc_final: 0.7183 (mtp) REVERT: E 178 GLU cc_start: 0.7884 (mp0) cc_final: 0.7632 (mp0) REVERT: E 197 GLU cc_start: 0.8873 (tt0) cc_final: 0.8566 (tt0) REVERT: F 94 GLU cc_start: 0.9132 (tp30) cc_final: 0.8925 (tm-30) REVERT: F 98 ASN cc_start: 0.9142 (t0) cc_final: 0.8783 (t0) REVERT: G 123 GLN cc_start: 0.9514 (OUTLIER) cc_final: 0.9262 (tm-30) REVERT: G 138 MET cc_start: 0.8909 (ttm) cc_final: 0.8576 (ttp) REVERT: G 172 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8337 (tp-100) REVERT: G 209 ASP cc_start: 0.8739 (OUTLIER) cc_final: 0.8338 (p0) REVERT: H -37 TYR cc_start: 0.8719 (OUTLIER) cc_final: 0.8429 (m-80) REVERT: H 79 ASN cc_start: 0.9229 (t0) cc_final: 0.8786 (t0) REVERT: H 84 GLN cc_start: 0.8624 (mt0) cc_final: 0.8308 (mm-40) REVERT: H 123 TYR cc_start: 0.9048 (p90) cc_final: 0.8659 (p90) REVERT: H 140 LYS cc_start: 0.8489 (mtmm) cc_final: 0.7978 (mtmm) REVERT: H 146 GLU cc_start: 0.7962 (pm20) cc_final: 0.7458 (pm20) REVERT: H 175 CYS cc_start: 0.8597 (m) cc_final: 0.7934 (t) REVERT: I 27 ARG cc_start: 0.4557 (tpm170) cc_final: 0.4187 (mmp-170) REVERT: I 75 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8045 (tp30) REVERT: I 80 ARG cc_start: 0.9043 (ptp90) cc_final: 0.8676 (ptp90) REVERT: I 165 GLU cc_start: 0.8460 (mp0) cc_final: 0.7826 (mp0) REVERT: I 169 GLN cc_start: 0.7770 (mm110) cc_final: 0.7560 (tp40) REVERT: J 59 TYR cc_start: 0.8229 (t80) cc_final: 0.8010 (t80) REVERT: J 65 GLN cc_start: 0.8058 (tt0) cc_final: 0.7625 (tm130) REVERT: J 73 TYR cc_start: 0.7645 (p90) cc_final: 0.7444 (p90) REVERT: J 118 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7547 (ttm) REVERT: J 121 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8421 (mt) REVERT: J 189 HIS cc_start: 0.7263 (m170) cc_final: 0.7018 (m90) REVERT: c 44 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8426 (tttm) REVERT: d 148 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.8870 (tm-30) REVERT: d 153 ASN cc_start: 0.9211 (OUTLIER) cc_final: 0.9004 (m110) REVERT: d 156 LYS cc_start: 0.9468 (tmmm) cc_final: 0.9027 (mptt) REVERT: d 200 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8278 (mt0) REVERT: e 68 ARG cc_start: 0.8904 (tpt90) cc_final: 0.8586 (tpt90) REVERT: e 90 GLN cc_start: 0.8876 (pm20) cc_final: 0.8048 (pm20) REVERT: e 124 SER cc_start: 0.9032 (t) cc_final: 0.8681 (t) outliers start: 75 outliers final: 47 residues processed: 407 average time/residue: 0.5545 time to fit residues: 261.3046 Evaluate side-chains 404 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 341 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain E residue 4 ASN Chi-restraints excluded: chain E residue 16 GLN Chi-restraints excluded: chain E residue 183 ASN Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 172 GLN Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain H residue -37 TYR Chi-restraints excluded: chain H residue 0 THR Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 180 ASN Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain c residue 44 LYS Chi-restraints excluded: chain c residue 77 ASN Chi-restraints excluded: chain c residue 92 VAL Chi-restraints excluded: chain c residue 186 SER Chi-restraints excluded: chain c residue 212 VAL Chi-restraints excluded: chain c residue 244 LEU Chi-restraints excluded: chain c residue 259 LEU Chi-restraints excluded: chain d residue 77 VAL Chi-restraints excluded: chain d residue 148 GLN Chi-restraints excluded: chain d residue 151 VAL Chi-restraints excluded: chain d residue 153 ASN Chi-restraints excluded: chain d residue 187 THR Chi-restraints excluded: chain d residue 199 ILE Chi-restraints excluded: chain d residue 200 GLN Chi-restraints excluded: chain d residue 209 SER Chi-restraints excluded: chain d residue 228 LEU Chi-restraints excluded: chain e residue 50 LEU Chi-restraints excluded: chain e residue 122 SER Chi-restraints excluded: chain e residue 140 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 183 optimal weight: 10.0000 chunk 188 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 245 optimal weight: 0.8980 chunk 269 optimal weight: 1.9990 chunk 179 optimal weight: 0.5980 chunk 127 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 250 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN C 116 GLN C 120 GLN ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.081699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.067959 restraints weight = 57862.137| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.18 r_work: 0.2950 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.6610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21760 Z= 0.155 Angle : 0.701 13.974 29470 Z= 0.349 Chirality : 0.044 0.348 3387 Planarity : 0.005 0.062 3773 Dihedral : 4.719 54.551 3017 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.31 % Favored : 96.65 % Rotamer: Outliers : 3.46 % Allowed : 28.14 % Favored : 68.40 % 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: 0.23 (0.16), residues: 2746 helix: 1.78 (0.16), residues: 1079 sheet: -0.87 (0.21), residues: 582 loop : -0.88 (0.18), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 3 TYR 0.033 0.002 TYR H 7 PHE 0.034 0.001 PHE H 87 TRP 0.009 0.001 TRP c 105 HIS 0.006 0.001 HIS E 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (21759) covalent geometry : angle 0.70054 / 0.35 (29468) SS BOND : bond 0.00177 / 0.09 ( 1) SS BOND : angle 3.39962 / 1.99 ( 2) hydrogen bonds : bond 0.03812 / 2.59 ( 1038) hydrogen bonds : angle 4.47747 / 3.16 ( 2970) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6054.02 seconds wall clock time: 104 minutes 15.14 seconds (6255.14 seconds total)