Starting phenix.real_space_refine on Wed Jun 18 14:34:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tm4_41378/06_2025/8tm4_41378.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tm4_41378/06_2025/8tm4_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tm4_41378/06_2025/8tm4_41378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tm4_41378/06_2025/8tm4_41378.map" model { file = "/net/cci-nas-00/data/ceres_data/8tm4_41378/06_2025/8tm4_41378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tm4_41378/06_2025/8tm4_41378.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 6, 'ARG:plan': 3, '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: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 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: {'GLN:plan1': 3, 'GLU:plan': 5} 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: {'GLU:plan': 6, 'ARG:plan': 2, '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: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP: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: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 3} 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: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG: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: {'GLU:plan': 11, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 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: 13.44, per 1000 atoms: 0.63 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: 5.05 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 2.55 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: 7.36 Time building geometry restraints manager: 6.08 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: 2.630 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: 0.020 Extract box with map and model: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 49.490 Find NCS groups from input model: 0.660 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:12.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.014 0.002 TRP F 162 HIS 0.006 0.001 HIS D 73 PHE 0.020 0.002 PHE C 171 TYR 0.023 0.002 TYR C 110 ARG 0.008 0.001 ARG d 129 Details of bonding type rmsd hydrogen bonds : bond 0.20383 ( 1038) hydrogen bonds : angle 9.67409 ( 2970) SS BOND : bond 0.00192 ( 1) SS BOND : angle 1.34088 ( 2) covalent geometry : bond 0.01299 (21759) covalent geometry : angle 1.88612 (29468) *********************** 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 : 2.260 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: 0.8638 (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: 0.7117 (t80) REVERT: E 117 GLN cc_start: 0.8623 (tm-30) cc_final: 0.8035 (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: 0.7182 (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: 0.6429 (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: 1.2259 time to fit residues: 1119.1495 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 : 2.387 ------------------------------------------------------------------------------- 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 230 optimal weight: 4.9990 chunk 206 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 213 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 247 optimal weight: 0.8980 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 B 198 ASN C 23 GLN C 54 GLN ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN C 146 GLN C 154 HIS D 104 ASN D 186 HIS E 69 HIS E 121 GLN F 64 ASN F 222 ASN ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN 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: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.097207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.082560 restraints weight = 54186.628| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 3.28 r_work: 0.3239 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 21760 Z= 0.179 Angle : 0.765 13.229 29470 Z= 0.394 Chirality : 0.044 0.171 3387 Planarity : 0.005 0.055 3773 Dihedral : 7.022 59.926 3047 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.64 % Favored : 96.18 % Rotamer: Outliers : 5.75 % Allowed : 20.69 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.14), residues: 2746 helix: -0.71 (0.14), residues: 1094 sheet: -2.59 (0.19), residues: 592 loop : -2.24 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 162 HIS 0.014 0.001 HIS F 73 PHE 0.030 0.002 PHE I 43 TYR 0.022 0.002 TYR C 118 ARG 0.008 0.001 ARG F 72 Details of bonding type rmsd hydrogen bonds : bond 0.04974 ( 1038) hydrogen bonds : angle 5.83541 ( 2970) SS BOND : bond 0.01100 ( 1) SS BOND : angle 1.08969 ( 2) covalent geometry : bond 0.00400 (21759) covalent geometry : angle 0.76490 (29468) *********************** 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 579 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 451 time to evaluate : 2.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8204 (mmm) REVERT: A 150 ASP cc_start: 0.8495 (m-30) cc_final: 0.8258 (m-30) REVERT: A 166 ASN cc_start: 0.8446 (m-40) cc_final: 0.8113 (t0) REVERT: B 146 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7283 (mp10) REVERT: B 230 GLN cc_start: 0.6982 (tp40) cc_final: 0.6631 (tp40) REVERT: C 211 MET cc_start: 0.8123 (tpp) cc_final: 0.7896 (tpt) REVERT: D 25 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8154 (mt-10) REVERT: D 178 GLN cc_start: 0.8831 (tp40) cc_final: 0.7987 (tp40) REVERT: D 202 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8248 (mt) REVERT: D 215 ILE cc_start: 0.8597 (tt) cc_final: 0.8136 (tp) REVERT: D 229 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.7885 (t80) REVERT: D 231 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.8052 (tppt) REVERT: F 94 GLU cc_start: 0.9089 (tp30) cc_final: 0.8700 (tm-30) REVERT: F 118 MET cc_start: 0.9223 (mmp) cc_final: 0.8918 (mmt) REVERT: F 181 GLN cc_start: 0.7399 (OUTLIER) cc_final: 0.7180 (pp30) REVERT: G 101 TRP cc_start: 0.9394 (t-100) cc_final: 0.8639 (t-100) REVERT: G 107 TYR cc_start: 0.8465 (p90) cc_final: 0.7930 (p90) REVERT: G 123 GLN cc_start: 0.9486 (OUTLIER) cc_final: 0.9211 (tm-30) REVERT: G 128 ASN cc_start: 0.8810 (t0) cc_final: 0.8478 (t0) REVERT: H 63 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8243 (mm-30) REVERT: H 79 ASN cc_start: 0.9144 (t0) cc_final: 0.8758 (t0) REVERT: H 126 MET cc_start: 0.7691 (mtp) cc_final: 0.7477 (mtp) REVERT: H 175 CYS cc_start: 0.8429 (m) cc_final: 0.7821 (t) REVERT: H 180 ASN cc_start: 0.7910 (p0) cc_final: 0.7687 (p0) REVERT: I 104 TYR cc_start: 0.7958 (m-80) cc_final: 0.7655 (m-80) REVERT: I 131 MET cc_start: 0.6463 (ppp) cc_final: 0.6089 (pp-130) REVERT: I 146 MET cc_start: 0.7972 (pmm) cc_final: 0.7729 (pmm) REVERT: I 149 MET cc_start: 0.8179 (tpt) cc_final: 0.7656 (tpp) REVERT: I 169 GLN cc_start: 0.8276 (mm110) cc_final: 0.7955 (tp40) REVERT: J 118 MET cc_start: 0.7858 (ttm) cc_final: 0.7604 (ttp) REVERT: c 210 ASN cc_start: 0.8483 (m-40) cc_final: 0.8259 (m-40) REVERT: c 236 TYR cc_start: 0.8879 (m-80) cc_final: 0.8542 (m-80) REVERT: c 243 ASP cc_start: 0.8110 (t0) cc_final: 0.7620 (t0) REVERT: c 256 THR cc_start: 0.8187 (p) cc_final: 0.7804 (p) REVERT: d 83 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8607 (mmm160) REVERT: d 200 GLN cc_start: 0.8222 (mt0) cc_final: 0.7982 (mt0) REVERT: d 264 PHE cc_start: 0.8384 (m-80) cc_final: 0.8131 (m-80) REVERT: e 57 LEU cc_start: 0.8856 (mm) cc_final: 0.8394 (tm) REVERT: e 58 ASN cc_start: 0.9101 (m-40) cc_final: 0.8835 (m-40) REVERT: e 59 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8391 (mm110) REVERT: e 90 GLN cc_start: 0.8768 (pm20) cc_final: 0.8388 (pm20) REVERT: e 119 ASN cc_start: 0.7664 (t0) cc_final: 0.7378 (t0) outliers start: 128 outliers final: 39 residues processed: 531 average time/residue: 1.0853 time to fit residues: 672.5306 Evaluate side-chains 423 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 374 time to evaluate : 2.758 ------------------------------------------------------------------------------- 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 A residue 186 ASP Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 47 CYS Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 204 GLN 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 181 GLN 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 20 VAL 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 d residue 189 THR Chi-restraints excluded: chain d residue 209 SER Chi-restraints excluded: chain e residue 59 GLN Chi-restraints excluded: chain e residue 122 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 211 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 221 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 190 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN D 104 ASN D 186 HIS ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 157 ASN ** I 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 HIS c 195 GLN ** d 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 108 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.086820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.072586 restraints weight = 56608.572| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 3.20 r_work: 0.3045 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 21760 Z= 0.193 Angle : 0.734 15.000 29470 Z= 0.371 Chirality : 0.045 0.176 3387 Planarity : 0.005 0.051 3773 Dihedral : 5.711 59.500 3027 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.42 % Favored : 96.43 % Rotamer: Outliers : 5.70 % Allowed : 21.14 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.15), residues: 2746 helix: 0.58 (0.15), residues: 1094 sheet: -2.07 (0.19), residues: 604 loop : -1.61 (0.17), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP c 93 HIS 0.009 0.001 HIS F 73 PHE 0.019 0.002 PHE d 102 TYR 0.023 0.002 TYR C 118 ARG 0.010 0.001 ARG G 3 Details of bonding type rmsd hydrogen bonds : bond 0.04482 ( 1038) hydrogen bonds : angle 5.16158 ( 2970) SS BOND : bond 0.00737 ( 1) SS BOND : angle 2.30010 ( 2) covalent geometry : bond 0.00448 (21759) covalent geometry : angle 0.73382 (29468) *********************** 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 521 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 394 time to evaluate : 2.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8549 (mmm) REVERT: A 166 ASN cc_start: 0.8771 (m-40) cc_final: 0.8483 (t0) REVERT: B 51 ASN cc_start: 0.8405 (m-40) cc_final: 0.7877 (p0) REVERT: B 135 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8245 (mp) REVERT: C 63 CYS cc_start: 0.7742 (t) cc_final: 0.7127 (t) REVERT: C 116 GLN cc_start: 0.9356 (OUTLIER) cc_final: 0.9073 (tp40) REVERT: C 225 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8804 (pp) REVERT: D 178 GLN cc_start: 0.9115 (tp40) cc_final: 0.8898 (tp40) REVERT: D 202 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8563 (mt) REVERT: D 215 ILE cc_start: 0.8971 (tt) cc_final: 0.8724 (tp) REVERT: D 228 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8339 (mpp) REVERT: E 3 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.8028 (ptp-170) REVERT: E 77 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8992 (mp) REVERT: E 85 CYS cc_start: 0.9398 (OUTLIER) cc_final: 0.9195 (t) REVERT: E 171 TYR cc_start: 0.8684 (t80) cc_final: 0.8411 (t80) REVERT: E 184 LEU cc_start: 0.7981 (pt) cc_final: 0.7777 (tm) REVERT: F 28 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8588 (mpt) REVERT: F 94 GLU cc_start: 0.9141 (tp30) cc_final: 0.8928 (tm-30) REVERT: F 98 ASN cc_start: 0.9121 (t0) cc_final: 0.8906 (t0) REVERT: F 118 MET cc_start: 0.9370 (mmp) cc_final: 0.9169 (mmt) REVERT: G 83 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8760 (mtp) REVERT: G 101 TRP cc_start: 0.9469 (t-100) cc_final: 0.8795 (t-100) REVERT: G 107 TYR cc_start: 0.8708 (p90) cc_final: 0.8143 (p90) REVERT: G 123 GLN cc_start: 0.9494 (OUTLIER) cc_final: 0.9209 (tm-30) REVERT: H 56 GLN cc_start: 0.9005 (tt0) cc_final: 0.8580 (tp40) REVERT: H 63 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8379 (mm-30) REVERT: H 79 ASN cc_start: 0.9182 (t0) cc_final: 0.8801 (t0) REVERT: H 84 GLN cc_start: 0.8728 (mt0) cc_final: 0.8317 (mm-40) REVERT: H 123 TYR cc_start: 0.8645 (p90) cc_final: 0.8059 (p90) REVERT: H 126 MET cc_start: 0.7887 (mtp) cc_final: 0.7633 (mtp) REVERT: H 137 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.7729 (t80) REVERT: H 139 ASP cc_start: 0.8859 (t0) cc_final: 0.8603 (t0) REVERT: H 175 CYS cc_start: 0.8394 (m) cc_final: 0.7712 (t) REVERT: I 75 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8185 (tp30) REVERT: I 80 ARG cc_start: 0.8777 (ptt90) cc_final: 0.8516 (ptp90) REVERT: I 83 LYS cc_start: 0.7964 (mtmt) cc_final: 0.7541 (mtmm) REVERT: I 149 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7773 (tpp) REVERT: I 169 GLN cc_start: 0.8190 (mm110) cc_final: 0.7896 (tp40) REVERT: J 11 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7197 (m-30) REVERT: J 14 LEU cc_start: 0.8257 (tp) cc_final: 0.8052 (tm) REVERT: J 70 ARG cc_start: 0.8237 (ttm-80) cc_final: 0.8002 (ttp-170) REVERT: J 118 MET cc_start: 0.8284 (ttm) cc_final: 0.7944 (mtp) REVERT: c 176 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8821 (mmtp) REVERT: c 236 TYR cc_start: 0.9031 (m-80) cc_final: 0.8581 (m-80) REVERT: d 83 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8726 (mmm160) REVERT: d 200 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8193 (mt0) REVERT: e 90 GLN cc_start: 0.8730 (pm20) cc_final: 0.7954 (pm20) outliers start: 127 outliers final: 39 residues processed: 472 average time/residue: 1.1612 time to fit residues: 634.9731 Evaluate side-chains 398 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 340 time to evaluate : 2.311 ------------------------------------------------------------------------------- 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 75 SER Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 116 GLN 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 228 MET 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 85 CYS 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 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 83 MET 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 176 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 77 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 146 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 187 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 GLN ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN D 104 ASN ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 ASN I 162 HIS J 110 HIS c 136 GLN ** d 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 108 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.086599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.072289 restraints weight = 57721.317| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.25 r_work: 0.3033 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21760 Z= 0.146 Angle : 0.667 12.791 29470 Z= 0.333 Chirality : 0.043 0.288 3387 Planarity : 0.004 0.053 3773 Dihedral : 5.264 58.779 3025 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.17 % Favored : 96.72 % Rotamer: Outliers : 4.89 % Allowed : 23.52 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.16), residues: 2746 helix: 1.17 (0.15), residues: 1090 sheet: -1.68 (0.19), residues: 600 loop : -1.24 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 100 HIS 0.006 0.001 HIS F 73 PHE 0.016 0.002 PHE I 69 TYR 0.023 0.001 TYR C 118 ARG 0.012 0.001 ARG G 3 Details of bonding type rmsd hydrogen bonds : bond 0.03956 ( 1038) hydrogen bonds : angle 4.80952 ( 2970) SS BOND : bond 0.01236 ( 1) SS BOND : angle 3.00384 ( 2) covalent geometry : bond 0.00339 (21759) covalent geometry : angle 0.66666 (29468) *********************** 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 492 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 383 time to evaluate : 2.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8809 (mt-10) REVERT: A 83 TYR cc_start: 0.9001 (t80) cc_final: 0.8488 (t80) REVERT: A 166 ASN cc_start: 0.8873 (m-40) cc_final: 0.8610 (t0) REVERT: B 51 ASN cc_start: 0.8348 (m-40) cc_final: 0.7900 (p0) REVERT: B 146 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8133 (mp10) REVERT: B 151 ASP cc_start: 0.8527 (m-30) cc_final: 0.8238 (m-30) REVERT: B 174 MET cc_start: 0.8896 (mmp) cc_final: 0.8533 (mmp) REVERT: C 129 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.8900 (pp) REVERT: C 225 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8831 (pp) REVERT: D 20 ARG cc_start: 0.8598 (mmm-85) cc_final: 0.8033 (mtp85) REVERT: D 107 MET cc_start: 0.7997 (ttp) cc_final: 0.7440 (ttp) REVERT: D 178 GLN cc_start: 0.9227 (tp40) cc_final: 0.9019 (tp40) REVERT: D 215 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8880 (tp) REVERT: E 3 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8046 (ptp-170) REVERT: E 91 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8543 (mp0) REVERT: F 94 GLU cc_start: 0.9188 (tp30) cc_final: 0.8919 (tm-30) REVERT: F 137 MET cc_start: 0.8509 (mtm) cc_final: 0.8288 (mtm) REVERT: G 83 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8714 (mtp) REVERT: G 101 TRP cc_start: 0.9465 (t-100) cc_final: 0.8833 (t-100) REVERT: G 107 TYR cc_start: 0.8841 (p90) cc_final: 0.8328 (p90) REVERT: G 209 ASP cc_start: 0.8722 (p0) cc_final: 0.8510 (p0) REVERT: H 56 GLN cc_start: 0.8968 (tt0) cc_final: 0.8581 (tp40) REVERT: H 63 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8242 (mm-30) REVERT: H 79 ASN cc_start: 0.9185 (t0) cc_final: 0.8813 (t0) REVERT: H 84 GLN cc_start: 0.8665 (mt0) cc_final: 0.8280 (mm-40) REVERT: H 123 TYR cc_start: 0.8683 (p90) cc_final: 0.8143 (p90) REVERT: H 137 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.7828 (t80) REVERT: H 146 GLU cc_start: 0.8062 (pm20) cc_final: 0.7767 (pm20) REVERT: H 175 CYS cc_start: 0.8443 (m) cc_final: 0.7753 (t) REVERT: I 12 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.7319 (mtm) REVERT: I 68 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.8834 (tmtm) REVERT: I 75 GLU cc_start: 0.8494 (tp30) cc_final: 0.8231 (tp30) REVERT: I 83 LYS cc_start: 0.7995 (mtmt) cc_final: 0.7558 (mtmm) REVERT: I 146 MET cc_start: 0.8430 (pmm) cc_final: 0.8138 (pmm) REVERT: I 149 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7822 (tpp) REVERT: I 169 GLN cc_start: 0.8127 (mm110) cc_final: 0.7861 (tp40) REVERT: I 193 ASP cc_start: 0.8685 (m-30) cc_final: 0.8357 (m-30) REVERT: J 118 MET cc_start: 0.8208 (ttm) cc_final: 0.7931 (mtp) REVERT: J 121 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8462 (mt) REVERT: c 52 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7047 (mmt180) REVERT: c 236 TYR cc_start: 0.9042 (m-80) cc_final: 0.8772 (m-80) REVERT: d 83 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8742 (mmm160) REVERT: d 148 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8615 (tm-30) REVERT: d 153 ASN cc_start: 0.9248 (OUTLIER) cc_final: 0.9008 (m110) REVERT: d 200 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8281 (mt0) REVERT: e 90 GLN cc_start: 0.8776 (pm20) cc_final: 0.8030 (pm20) outliers start: 109 outliers final: 31 residues processed: 455 average time/residue: 1.1495 time to fit residues: 606.5130 Evaluate side-chains 393 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 346 time to evaluate : 2.732 ------------------------------------------------------------------------------- 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 146 GLN Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 53 LEU 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 215 ILE Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 83 MET 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 137 PHE Chi-restraints excluded: chain I residue 12 MET Chi-restraints excluded: chain I residue 68 LYS 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 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 200 GLN Chi-restraints excluded: chain d residue 228 LEU 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 123 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 269 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 157 optimal weight: 0.2980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN C 23 GLN C 92 GLN D 104 ASN E 21 GLN ** 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 88 GLN e 108 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.084542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.070348 restraints weight = 57502.619| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 3.23 r_work: 0.2999 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.5415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21760 Z= 0.150 Angle : 0.658 12.119 29470 Z= 0.328 Chirality : 0.043 0.250 3387 Planarity : 0.004 0.059 3773 Dihedral : 4.924 58.323 3018 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.46 % Favored : 96.47 % Rotamer: Outliers : 5.16 % Allowed : 23.83 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.16), residues: 2746 helix: 1.43 (0.16), residues: 1091 sheet: -1.40 (0.20), residues: 605 loop : -1.00 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 100 HIS 0.007 0.001 HIS E 65 PHE 0.016 0.001 PHE I 69 TYR 0.024 0.001 TYR C 153 ARG 0.016 0.001 ARG G 3 Details of bonding type rmsd hydrogen bonds : bond 0.03876 ( 1038) hydrogen bonds : angle 4.64932 ( 2970) SS BOND : bond 0.00003 ( 1) SS BOND : angle 3.11287 ( 2) covalent geometry : bond 0.00348 (21759) covalent geometry : angle 0.65724 (29468) *********************** 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 501 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 386 time to evaluate : 2.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8816 (mt-10) REVERT: A 83 TYR cc_start: 0.8979 (t80) cc_final: 0.8410 (t80) REVERT: A 166 ASN cc_start: 0.8915 (m-40) cc_final: 0.8657 (t0) REVERT: B 45 LEU cc_start: 0.9042 (mt) cc_final: 0.8775 (mt) REVERT: B 51 ASN cc_start: 0.8282 (m-40) cc_final: 0.7948 (p0) REVERT: B 92 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9295 (tt) REVERT: B 151 ASP cc_start: 0.8576 (m-30) cc_final: 0.8324 (m-30) REVERT: C 66 ASP cc_start: 0.7370 (t0) cc_final: 0.7072 (t0) REVERT: C 117 ARG cc_start: 0.9238 (OUTLIER) cc_final: 0.7870 (ttp-170) REVERT: C 129 ILE cc_start: 0.9281 (OUTLIER) cc_final: 0.8894 (pp) REVERT: C 146 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8529 (tm-30) REVERT: C 225 ILE cc_start: 0.9095 (pt) cc_final: 0.8833 (pp) REVERT: D 20 ARG cc_start: 0.8494 (mmm-85) cc_final: 0.8263 (mmm-85) REVERT: D 107 MET cc_start: 0.8197 (ttp) cc_final: 0.7929 (ttp) REVERT: D 215 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.9012 (tp) REVERT: E 16 GLN cc_start: 0.9425 (OUTLIER) cc_final: 0.9186 (mm-40) REVERT: E 91 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8647 (mm-30) REVERT: F 94 GLU cc_start: 0.9214 (tp30) cc_final: 0.8934 (tm-30) REVERT: F 111 HIS cc_start: 0.8706 (t-170) cc_final: 0.8406 (t-170) REVERT: G 83 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8653 (mtp) REVERT: G 123 GLN cc_start: 0.9486 (OUTLIER) cc_final: 0.9187 (tm-30) REVERT: G 138 MET cc_start: 0.8974 (ttm) cc_final: 0.8618 (ttp) REVERT: G 209 ASP cc_start: 0.8659 (p0) cc_final: 0.8440 (p0) REVERT: H 56 GLN cc_start: 0.9007 (tt0) cc_final: 0.8626 (tp-100) REVERT: H 79 ASN cc_start: 0.9196 (t0) cc_final: 0.8818 (t0) REVERT: H 84 GLN cc_start: 0.8605 (mt0) cc_final: 0.8236 (mm-40) REVERT: H 123 TYR cc_start: 0.8778 (p90) cc_final: 0.8496 (p90) REVERT: H 145 MET cc_start: 0.8102 (tpp) cc_final: 0.7889 (tpp) REVERT: H 146 GLU cc_start: 0.8156 (pm20) cc_final: 0.7905 (pm20) REVERT: H 175 CYS cc_start: 0.8477 (m) cc_final: 0.7755 (t) REVERT: I 12 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.7289 (mtm) REVERT: I 26 ARG cc_start: 0.8070 (mmm-85) cc_final: 0.7632 (mtm110) REVERT: I 65 GLN cc_start: 0.8630 (mt0) cc_final: 0.8317 (mt0) REVERT: I 68 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8865 (tmtm) REVERT: I 75 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8269 (tp30) REVERT: I 80 ARG cc_start: 0.9124 (ptp90) cc_final: 0.8711 (ptp90) REVERT: I 149 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7878 (tpp) REVERT: I 165 GLU cc_start: 0.8307 (mp0) cc_final: 0.7781 (mp0) REVERT: I 169 GLN cc_start: 0.8079 (mm110) cc_final: 0.7808 (tp40) REVERT: I 193 ASP cc_start: 0.8741 (m-30) cc_final: 0.8491 (m-30) REVERT: J 59 TYR cc_start: 0.8043 (t80) cc_final: 0.7823 (t80) REVERT: J 65 GLN cc_start: 0.7633 (tt0) cc_final: 0.7264 (tm-30) REVERT: J 118 MET cc_start: 0.8201 (ttm) cc_final: 0.7952 (mtp) REVERT: J 189 HIS cc_start: 0.5952 (m170) cc_final: 0.5692 (m170) REVERT: c 236 TYR cc_start: 0.9072 (m-80) cc_final: 0.8826 (m-80) REVERT: c 243 ASP cc_start: 0.8524 (t0) cc_final: 0.7942 (t0) REVERT: d 148 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8663 (tm-30) REVERT: d 153 ASN cc_start: 0.9220 (OUTLIER) cc_final: 0.8886 (m110) REVERT: d 200 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8212 (mt0) REVERT: e 90 GLN cc_start: 0.8788 (pm20) cc_final: 0.7981 (pm20) outliers start: 115 outliers final: 32 residues processed: 457 average time/residue: 1.1116 time to fit residues: 588.0268 Evaluate side-chains 379 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 332 time to evaluate : 2.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 92 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 129 ILE 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 215 ILE 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 186 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain H residue 0 THR Chi-restraints excluded: chain H residue 75 VAL 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 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 153 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 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 245 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 194 optimal weight: 0.6980 chunk 240 optimal weight: 4.9990 chunk 190 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 259 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 164 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN D 104 ASN E 59 HIS ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H -22 ASN H 56 GLN I 72 ASN I 93 ASN J 110 HIS d 128 GLN ** d 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 108 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.082765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.068821 restraints weight = 57655.772| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.21 r_work: 0.2974 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.5816 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= 0.154 Angle : 0.670 13.945 29470 Z= 0.333 Chirality : 0.043 0.305 3387 Planarity : 0.004 0.062 3773 Dihedral : 4.842 59.464 3018 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.64 % Favored : 96.29 % Rotamer: Outliers : 4.94 % Allowed : 24.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.16), residues: 2746 helix: 1.62 (0.16), residues: 1093 sheet: -1.14 (0.20), residues: 606 loop : -0.91 (0.18), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 100 HIS 0.007 0.001 HIS E 65 PHE 0.015 0.001 PHE I 164 TYR 0.029 0.001 TYR H 7 ARG 0.015 0.000 ARG G 3 Details of bonding type rmsd hydrogen bonds : bond 0.03870 ( 1038) hydrogen bonds : angle 4.55011 ( 2970) SS BOND : bond 0.00036 ( 1) SS BOND : angle 2.95312 ( 2) covalent geometry : bond 0.00361 (21759) covalent geometry : angle 0.66920 (29468) *********************** 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 476 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 366 time to evaluate : 2.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8807 (mt-10) REVERT: A 79 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8610 (mmm) REVERT: A 83 TYR cc_start: 0.8970 (t80) cc_final: 0.8367 (t80) REVERT: A 103 GLU cc_start: 0.7965 (tp30) cc_final: 0.7708 (tm-30) REVERT: A 166 ASN cc_start: 0.8971 (m-40) cc_final: 0.8740 (t0) REVERT: B 45 LEU cc_start: 0.9087 (mt) cc_final: 0.8835 (mt) REVERT: B 51 ASN cc_start: 0.8253 (m-40) cc_final: 0.8013 (p0) REVERT: B 114 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.9076 (tp) REVERT: B 151 ASP cc_start: 0.8701 (m-30) cc_final: 0.8496 (m-30) REVERT: C 129 ILE cc_start: 0.9340 (OUTLIER) cc_final: 0.8995 (pp) REVERT: C 146 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8516 (tm-30) REVERT: C 159 ASN cc_start: 0.8908 (t0) cc_final: 0.8695 (t160) REVERT: D 141 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8790 (mt) REVERT: E 91 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8716 (mm-30) REVERT: E 178 GLU cc_start: 0.7948 (mp0) cc_final: 0.7646 (mp0) REVERT: E 197 GLU cc_start: 0.8842 (tt0) cc_final: 0.8558 (tt0) REVERT: F 94 GLU cc_start: 0.9225 (tp30) cc_final: 0.8951 (tm-30) REVERT: F 111 HIS cc_start: 0.8805 (t-170) cc_final: 0.8522 (t-170) REVERT: G 83 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8639 (mtp) REVERT: G 123 GLN cc_start: 0.9489 (OUTLIER) cc_final: 0.9247 (tm-30) REVERT: G 138 MET cc_start: 0.8934 (ttm) cc_final: 0.8607 (ttp) REVERT: H -18 GLU cc_start: 0.9002 (tt0) cc_final: 0.8639 (mt-10) REVERT: H 56 GLN cc_start: 0.8975 (tt0) cc_final: 0.8625 (tp40) REVERT: H 79 ASN cc_start: 0.9215 (t0) cc_final: 0.8783 (t0) REVERT: H 84 GLN cc_start: 0.8552 (mt0) cc_final: 0.8186 (mm-40) REVERT: H 146 GLU cc_start: 0.8159 (pm20) cc_final: 0.7956 (pm20) REVERT: H 175 CYS cc_start: 0.8540 (m) cc_final: 0.7754 (t) REVERT: I 14 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7715 (mtm) REVERT: I 65 GLN cc_start: 0.8641 (mt0) cc_final: 0.8312 (mt0) REVERT: I 75 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8253 (tp30) REVERT: I 80 ARG cc_start: 0.9095 (ptp90) cc_final: 0.8690 (ptp90) REVERT: I 113 ASP cc_start: 0.8219 (t0) cc_final: 0.8017 (t0) REVERT: I 116 THR cc_start: 0.8546 (m) cc_final: 0.8288 (m) REVERT: I 149 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.7976 (tpp) REVERT: I 153 LEU cc_start: 0.9140 (mt) cc_final: 0.8863 (pp) REVERT: I 165 GLU cc_start: 0.8299 (mp0) cc_final: 0.7713 (mp0) REVERT: I 169 GLN cc_start: 0.8049 (mm110) cc_final: 0.7736 (tp40) REVERT: I 171 MET cc_start: 0.7959 (mmm) cc_final: 0.7686 (mmm) REVERT: J 17 SER cc_start: 0.5106 (OUTLIER) cc_final: 0.4828 (t) REVERT: J 59 TYR cc_start: 0.8122 (t80) cc_final: 0.7915 (t80) REVERT: J 65 GLN cc_start: 0.7865 (tt0) cc_final: 0.7406 (tm-30) REVERT: J 73 TYR cc_start: 0.7461 (p90) cc_final: 0.7173 (p90) REVERT: J 189 HIS cc_start: 0.6626 (m-70) cc_final: 0.6355 (m170) REVERT: c 66 TYR cc_start: 0.8137 (m-10) cc_final: 0.7927 (m-10) REVERT: c 236 TYR cc_start: 0.9104 (m-80) cc_final: 0.8835 (m-80) REVERT: c 243 ASP cc_start: 0.8594 (t0) cc_final: 0.8036 (t0) REVERT: d 148 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8741 (tm-30) REVERT: d 153 ASN cc_start: 0.9145 (OUTLIER) cc_final: 0.8928 (m110) REVERT: d 200 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8289 (mt0) REVERT: e 62 MET cc_start: 0.8562 (mpm) cc_final: 0.8354 (mpt) REVERT: e 90 GLN cc_start: 0.8790 (pm20) cc_final: 0.7978 (pm20) REVERT: e 124 SER cc_start: 0.8970 (t) cc_final: 0.8637 (t) outliers start: 110 outliers final: 40 residues processed: 434 average time/residue: 1.2515 time to fit residues: 630.3667 Evaluate side-chains 388 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 334 time to evaluate : 2.422 ------------------------------------------------------------------------------- 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 9 THR Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 114 LEU 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 146 GLN Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 219 ILE 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 50 VAL Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 123 GLN 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 14 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 199 THR Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain J residue 104 LEU 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 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 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 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 248 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 208 optimal weight: 2.9990 chunk 185 optimal weight: 0.8980 chunk 253 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 38 optimal weight: 0.0370 chunk 27 optimal weight: 0.7980 chunk 134 optimal weight: 0.9980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN D 104 ASN ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 GLN H 56 GLN H 65 HIS J 110 HIS d 152 GLN ** d 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 108 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.083254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.069371 restraints weight = 57408.053| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.20 r_work: 0.2987 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.5994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 21760 Z= 0.134 Angle : 0.664 12.740 29470 Z= 0.329 Chirality : 0.043 0.280 3387 Planarity : 0.004 0.072 3773 Dihedral : 4.722 59.077 3018 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.50 % Favored : 96.47 % Rotamer: Outliers : 4.49 % Allowed : 25.45 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.16), residues: 2746 helix: 1.76 (0.16), residues: 1085 sheet: -1.09 (0.20), residues: 601 loop : -0.86 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP c 105 HIS 0.007 0.001 HIS D 73 PHE 0.018 0.001 PHE I 164 TYR 0.030 0.001 TYR C 153 ARG 0.018 0.001 ARG G 3 Details of bonding type rmsd hydrogen bonds : bond 0.03677 ( 1038) hydrogen bonds : angle 4.46986 ( 2970) SS BOND : bond 0.00026 ( 1) SS BOND : angle 3.01492 ( 2) covalent geometry : bond 0.00313 (21759) covalent geometry : angle 0.66369 (29468) *********************** 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 476 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 376 time to evaluate : 3.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8793 (mt-10) REVERT: A 83 TYR cc_start: 0.8942 (t80) cc_final: 0.8327 (t80) REVERT: A 150 ASP cc_start: 0.8413 (m-30) cc_final: 0.8126 (m-30) REVERT: A 166 ASN cc_start: 0.8950 (m-40) cc_final: 0.8721 (t0) REVERT: A 182 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7813 (tm) REVERT: B 45 LEU cc_start: 0.9005 (mt) cc_final: 0.8776 (mt) REVERT: B 51 ASN cc_start: 0.8250 (m-40) cc_final: 0.8029 (p0) REVERT: B 151 ASP cc_start: 0.8659 (m-30) cc_final: 0.8443 (m-30) REVERT: C 23 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8359 (mp10) REVERT: C 117 ARG cc_start: 0.9266 (OUTLIER) cc_final: 0.7930 (ttp-170) REVERT: C 129 ILE cc_start: 0.9355 (OUTLIER) cc_final: 0.9021 (pp) REVERT: C 146 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8513 (tm-30) REVERT: D 141 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8775 (mt) REVERT: E 16 GLN cc_start: 0.9392 (OUTLIER) cc_final: 0.9181 (mm-40) REVERT: E 91 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8739 (mm-30) REVERT: E 178 GLU cc_start: 0.7985 (mp0) cc_final: 0.7669 (mp0) REVERT: E 197 GLU cc_start: 0.8833 (tt0) cc_final: 0.8541 (tt0) REVERT: F 94 GLU cc_start: 0.9199 (tp30) cc_final: 0.8878 (tm-30) REVERT: F 111 HIS cc_start: 0.8782 (t-170) cc_final: 0.8526 (t-170) REVERT: F 118 MET cc_start: 0.9474 (tpp) cc_final: 0.9157 (mmp) REVERT: G 83 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.8573 (mtp) REVERT: G 138 MET cc_start: 0.8907 (ttm) cc_final: 0.8533 (ttp) REVERT: H -18 GLU cc_start: 0.9044 (tt0) cc_final: 0.8759 (mt-10) REVERT: H 79 ASN cc_start: 0.9203 (t0) cc_final: 0.8768 (t0) REVERT: H 84 GLN cc_start: 0.8510 (mt0) cc_final: 0.8146 (mm-40) REVERT: H 88 ARG cc_start: 0.8725 (ttt180) cc_final: 0.8439 (ttt180) REVERT: H 123 TYR cc_start: 0.8899 (p90) cc_final: 0.8575 (p90) REVERT: H 146 GLU cc_start: 0.8118 (pm20) cc_final: 0.7856 (pm20) REVERT: H 175 CYS cc_start: 0.8521 (m) cc_final: 0.7782 (t) REVERT: I 14 MET cc_start: 0.7887 (mmm) cc_final: 0.7552 (mtm) REVERT: I 65 GLN cc_start: 0.8720 (mt0) cc_final: 0.8367 (mt0) REVERT: I 75 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8250 (tp30) REVERT: I 80 ARG cc_start: 0.9139 (ptp90) cc_final: 0.8319 (ptp90) REVERT: I 113 ASP cc_start: 0.8146 (t0) cc_final: 0.7831 (OUTLIER) REVERT: I 116 THR cc_start: 0.8515 (m) cc_final: 0.8160 (m) REVERT: I 131 MET cc_start: 0.7406 (ptt) cc_final: 0.6807 (pp-130) REVERT: I 146 MET cc_start: 0.8475 (pmm) cc_final: 0.8136 (pmm) REVERT: I 153 LEU cc_start: 0.9080 (mt) cc_final: 0.8864 (pp) REVERT: I 165 GLU cc_start: 0.8377 (mp0) cc_final: 0.7728 (mp0) REVERT: I 169 GLN cc_start: 0.7965 (mm110) cc_final: 0.7685 (tp40) REVERT: J 59 TYR cc_start: 0.8094 (t80) cc_final: 0.7873 (t80) REVERT: J 65 GLN cc_start: 0.7958 (tt0) cc_final: 0.7529 (tm-30) REVERT: J 73 TYR cc_start: 0.7619 (p90) cc_final: 0.7296 (p90) REVERT: J 189 HIS cc_start: 0.6953 (m-70) cc_final: 0.6634 (m170) REVERT: c 41 LEU cc_start: 0.8735 (tp) cc_final: 0.8514 (tt) REVERT: c 179 GLU cc_start: 0.8711 (mp0) cc_final: 0.8476 (pm20) REVERT: c 236 TYR cc_start: 0.9095 (m-80) cc_final: 0.8870 (m-80) REVERT: c 243 ASP cc_start: 0.8597 (t0) cc_final: 0.8045 (t0) REVERT: d 148 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8771 (tm-30) REVERT: d 153 ASN cc_start: 0.9184 (OUTLIER) cc_final: 0.8922 (m110) REVERT: d 200 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8249 (mt0) REVERT: e 90 GLN cc_start: 0.8810 (pm20) cc_final: 0.8014 (pm20) REVERT: e 124 SER cc_start: 0.8961 (t) cc_final: 0.8600 (t) outliers start: 100 outliers final: 45 residues processed: 444 average time/residue: 1.2068 time to fit residues: 625.2272 Evaluate side-chains 397 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 341 time to evaluate : 2.689 ------------------------------------------------------------------------------- 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 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 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 117 ARG Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 146 GLN 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 16 GLN Chi-restraints excluded: chain E residue 183 ASN Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain F residue 50 VAL 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 G residue 83 MET Chi-restraints excluded: chain H residue 0 THR Chi-restraints excluded: chain H residue 53 MET 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 191 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 45 optimal weight: 0.3980 chunk 172 optimal weight: 8.9990 chunk 156 optimal weight: 0.9990 chunk 176 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 199 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 140 optimal weight: 2.9990 chunk 237 optimal weight: 4.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN C 23 GLN D 104 ASN ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN G 172 GLN J 110 HIS ** d 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 108 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.081358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.067486 restraints weight = 58252.098| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.20 r_work: 0.2943 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.6211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 21760 Z= 0.173 Angle : 0.684 13.184 29470 Z= 0.340 Chirality : 0.044 0.346 3387 Planarity : 0.004 0.072 3773 Dihedral : 4.742 56.693 3018 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.46 % Favored : 96.50 % Rotamer: Outliers : 3.95 % Allowed : 26.44 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.16), residues: 2746 helix: 1.79 (0.16), residues: 1087 sheet: -1.07 (0.20), residues: 609 loop : -0.86 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 156 HIS 0.007 0.001 HIS E 65 PHE 0.019 0.001 PHE H 87 TYR 0.029 0.002 TYR C 153 ARG 0.019 0.001 ARG G 3 Details of bonding type rmsd hydrogen bonds : bond 0.03951 ( 1038) hydrogen bonds : angle 4.52375 ( 2970) SS BOND : bond 0.00077 ( 1) SS BOND : angle 3.29172 ( 2) covalent geometry : bond 0.00411 (21759) covalent geometry : angle 0.68349 (29468) *********************** 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 451 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 363 time to evaluate : 2.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8835 (mt-10) REVERT: A 83 TYR cc_start: 0.8960 (t80) cc_final: 0.8373 (t80) REVERT: A 150 ASP cc_start: 0.8542 (m-30) cc_final: 0.8263 (m-30) REVERT: A 166 ASN cc_start: 0.8941 (m-40) cc_final: 0.8707 (t0) REVERT: A 182 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7841 (tm) REVERT: B 45 LEU cc_start: 0.9069 (mt) cc_final: 0.8803 (mt) REVERT: B 51 ASN cc_start: 0.8263 (m-40) cc_final: 0.7990 (p0) REVERT: C 66 ASP cc_start: 0.6538 (t0) cc_final: 0.6297 (t0) REVERT: C 146 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8518 (tm-30) REVERT: D 107 MET cc_start: 0.8516 (ttp) cc_final: 0.7996 (ttp) REVERT: D 141 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8788 (mt) REVERT: E 16 GLN cc_start: 0.9422 (OUTLIER) cc_final: 0.9205 (mm-40) REVERT: E 91 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8734 (mm-30) REVERT: E 178 GLU cc_start: 0.8059 (mp0) cc_final: 0.7572 (mp0) REVERT: E 197 GLU cc_start: 0.8855 (tt0) cc_final: 0.8561 (tt0) REVERT: F 68 PHE cc_start: 0.9328 (m-80) cc_final: 0.9118 (m-80) REVERT: F 94 GLU cc_start: 0.9228 (tp30) cc_final: 0.8907 (tm-30) REVERT: G 46 ASP cc_start: 0.8813 (m-30) cc_final: 0.8542 (m-30) REVERT: G 83 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8700 (mtp) REVERT: G 123 GLN cc_start: 0.9507 (OUTLIER) cc_final: 0.9259 (tm-30) REVERT: G 138 MET cc_start: 0.8923 (ttm) cc_final: 0.8551 (ttp) REVERT: G 236 ASP cc_start: 0.9406 (t0) cc_final: 0.9147 (t0) REVERT: H -18 GLU cc_start: 0.9052 (tt0) cc_final: 0.8829 (mt-10) REVERT: H 79 ASN cc_start: 0.9208 (t0) cc_final: 0.8775 (t0) REVERT: H 84 GLN cc_start: 0.8526 (mt0) cc_final: 0.8156 (mm-40) REVERT: H 88 ARG cc_start: 0.8734 (ttt180) cc_final: 0.8492 (ttt180) REVERT: H 123 TYR cc_start: 0.8970 (p90) cc_final: 0.8688 (p90) REVERT: H 142 ARG cc_start: 0.8803 (ttp80) cc_final: 0.8080 (ttp80) REVERT: H 146 GLU cc_start: 0.8150 (pm20) cc_final: 0.7899 (pm20) REVERT: H 175 CYS cc_start: 0.8521 (m) cc_final: 0.7794 (t) REVERT: I 14 MET cc_start: 0.8023 (mmm) cc_final: 0.7774 (mtm) REVERT: I 65 GLN cc_start: 0.8779 (mt0) cc_final: 0.8414 (mt0) REVERT: I 75 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8217 (tp30) REVERT: I 80 ARG cc_start: 0.9000 (ptp90) cc_final: 0.8542 (ptp90) REVERT: I 113 ASP cc_start: 0.8083 (t0) cc_final: 0.7845 (t0) REVERT: I 116 THR cc_start: 0.8570 (m) cc_final: 0.8272 (m) REVERT: I 149 MET cc_start: 0.8559 (tpt) cc_final: 0.8031 (tpp) REVERT: I 153 LEU cc_start: 0.9060 (mt) cc_final: 0.8842 (pp) REVERT: I 165 GLU cc_start: 0.8410 (mp0) cc_final: 0.7770 (mp0) REVERT: I 169 GLN cc_start: 0.7847 (mm110) cc_final: 0.7549 (tp40) REVERT: I 171 MET cc_start: 0.7941 (mmm) cc_final: 0.7740 (mmm) REVERT: J 59 TYR cc_start: 0.8038 (t80) cc_final: 0.7810 (t80) REVERT: J 65 GLN cc_start: 0.8030 (tt0) cc_final: 0.7482 (tm-30) REVERT: J 73 TYR cc_start: 0.7714 (p90) cc_final: 0.7335 (p90) REVERT: J 189 HIS cc_start: 0.7081 (m-70) cc_final: 0.6758 (m170) REVERT: c 41 LEU cc_start: 0.8795 (tp) cc_final: 0.8584 (tt) REVERT: c 44 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8281 (tttm) REVERT: c 179 GLU cc_start: 0.8759 (mp0) cc_final: 0.8423 (pm20) REVERT: c 236 TYR cc_start: 0.9119 (m-80) cc_final: 0.8898 (m-80) REVERT: c 243 ASP cc_start: 0.8613 (t0) cc_final: 0.7969 (t0) REVERT: d 148 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8765 (tm-30) REVERT: d 153 ASN cc_start: 0.9183 (OUTLIER) cc_final: 0.8943 (m110) REVERT: d 200 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8224 (mt0) REVERT: e 90 GLN cc_start: 0.8885 (pm20) cc_final: 0.8025 (pm20) REVERT: e 124 SER cc_start: 0.8986 (t) cc_final: 0.8632 (t) outliers start: 88 outliers final: 45 residues processed: 426 average time/residue: 1.1404 time to fit residues: 562.9840 Evaluate side-chains 400 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 344 time to evaluate : 2.214 ------------------------------------------------------------------------------- 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 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 45 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 134 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 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 50 VAL 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 G residue 83 MET Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain H residue 0 THR Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 61 ASN Chi-restraints excluded: chain H residue 72 LEU 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 104 LEU Chi-restraints excluded: chain c residue 44 LYS 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 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 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 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 19 optimal weight: 0.7980 chunk 150 optimal weight: 0.7980 chunk 145 optimal weight: 6.9990 chunk 152 optimal weight: 0.9990 chunk 228 optimal weight: 0.5980 chunk 203 optimal weight: 6.9990 chunk 180 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 3 optimal weight: 0.0270 chunk 95 optimal weight: 0.8980 chunk 127 optimal weight: 4.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN H -22 ASN d 67 ASN ** d 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 80 GLN e 108 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.082719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.068923 restraints weight = 57479.312| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.20 r_work: 0.2973 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.6389 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= 0.134 Angle : 0.681 12.270 29470 Z= 0.338 Chirality : 0.043 0.359 3387 Planarity : 0.004 0.078 3773 Dihedral : 4.636 56.277 3016 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.50 % Favored : 96.47 % Rotamer: Outliers : 3.19 % Allowed : 27.42 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.16), residues: 2746 helix: 1.76 (0.16), residues: 1090 sheet: -1.04 (0.20), residues: 600 loop : -0.80 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP c 105 HIS 0.007 0.001 HIS D 186 PHE 0.014 0.001 PHE I 69 TYR 0.031 0.001 TYR H 7 ARG 0.020 0.001 ARG G 3 Details of bonding type rmsd hydrogen bonds : bond 0.03654 ( 1038) hydrogen bonds : angle 4.42356 ( 2970) SS BOND : bond 0.00369 ( 1) SS BOND : angle 3.11695 ( 2) covalent geometry : bond 0.00314 (21759) covalent geometry : angle 0.68096 (29468) *********************** 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 440 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 369 time to evaluate : 4.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8834 (mt-10) REVERT: A 83 TYR cc_start: 0.8929 (t80) cc_final: 0.8304 (t80) REVERT: A 150 ASP cc_start: 0.8481 (m-30) cc_final: 0.8161 (m-30) REVERT: A 166 ASN cc_start: 0.8945 (m-40) cc_final: 0.8697 (t0) REVERT: A 182 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7889 (tm) REVERT: B 45 LEU cc_start: 0.8965 (mt) cc_final: 0.8720 (mt) REVERT: B 51 ASN cc_start: 0.8176 (m-40) cc_final: 0.7928 (p0) REVERT: B 151 ASP cc_start: 0.8583 (m-30) cc_final: 0.8071 (p0) REVERT: C 23 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8436 (mm110) REVERT: C 117 ARG cc_start: 0.9279 (OUTLIER) cc_final: 0.7970 (ttp-170) REVERT: C 129 ILE cc_start: 0.9337 (OUTLIER) cc_final: 0.9009 (pp) REVERT: C 146 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8570 (tm-30) REVERT: D 141 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8767 (mt) REVERT: E 16 GLN cc_start: 0.9375 (OUTLIER) cc_final: 0.9162 (mm-40) REVERT: E 91 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8748 (mm-30) REVERT: E 178 GLU cc_start: 0.8010 (mp0) cc_final: 0.7450 (mp0) REVERT: E 197 GLU cc_start: 0.8841 (tt0) cc_final: 0.8538 (tt0) REVERT: F 94 GLU cc_start: 0.9208 (tp30) cc_final: 0.8891 (tm-30) REVERT: G 46 ASP cc_start: 0.8807 (m-30) cc_final: 0.8545 (m-30) REVERT: G 83 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8572 (mtp) REVERT: G 138 MET cc_start: 0.8919 (ttm) cc_final: 0.8578 (ttp) REVERT: G 236 ASP cc_start: 0.9415 (t0) cc_final: 0.9150 (t0) REVERT: H 79 ASN cc_start: 0.9199 (t0) cc_final: 0.8753 (t0) REVERT: H 84 GLN cc_start: 0.8487 (mt0) cc_final: 0.8120 (mm-40) REVERT: H 88 ARG cc_start: 0.8769 (ttt180) cc_final: 0.8480 (ttt180) REVERT: H 123 TYR cc_start: 0.8943 (p90) cc_final: 0.8655 (p90) REVERT: H 126 MET cc_start: 0.7941 (mtp) cc_final: 0.7682 (mtt) REVERT: H 142 ARG cc_start: 0.8849 (ttp80) cc_final: 0.8158 (ttp80) REVERT: H 145 MET cc_start: 0.8265 (tpp) cc_final: 0.7553 (tpp) REVERT: H 146 GLU cc_start: 0.8168 (pm20) cc_final: 0.7930 (pm20) REVERT: H 175 CYS cc_start: 0.8612 (m) cc_final: 0.7909 (t) REVERT: I 14 MET cc_start: 0.7883 (mmm) cc_final: 0.7638 (mtm) REVERT: I 75 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8213 (tp30) REVERT: I 78 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8151 (mt-10) REVERT: I 80 ARG cc_start: 0.9026 (ptp90) cc_final: 0.8553 (ptp90) REVERT: I 113 ASP cc_start: 0.8065 (t0) cc_final: 0.7802 (t0) REVERT: I 116 THR cc_start: 0.8587 (m) cc_final: 0.8260 (m) REVERT: I 138 VAL cc_start: 0.9113 (t) cc_final: 0.8859 (t) REVERT: I 149 MET cc_start: 0.8538 (tpt) cc_final: 0.7997 (tpp) REVERT: I 165 GLU cc_start: 0.8421 (mp0) cc_final: 0.7794 (mp0) REVERT: I 169 GLN cc_start: 0.7645 (mm110) cc_final: 0.7416 (tp40) REVERT: J 59 TYR cc_start: 0.8030 (t80) cc_final: 0.7770 (t80) REVERT: J 65 GLN cc_start: 0.7878 (tt0) cc_final: 0.7409 (tm-30) REVERT: J 69 MET cc_start: 0.7905 (ptt) cc_final: 0.7375 (ptp) REVERT: J 73 TYR cc_start: 0.7876 (p90) cc_final: 0.7438 (p90) REVERT: J 189 HIS cc_start: 0.7248 (m-70) cc_final: 0.6934 (m90) REVERT: c 41 LEU cc_start: 0.8803 (tp) cc_final: 0.8600 (tt) REVERT: c 44 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8355 (tttm) REVERT: c 179 GLU cc_start: 0.8775 (mp0) cc_final: 0.8471 (pm20) REVERT: c 184 LEU cc_start: 0.9194 (mm) cc_final: 0.8966 (mt) REVERT: d 148 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.8825 (tm-30) REVERT: d 153 ASN cc_start: 0.9175 (OUTLIER) cc_final: 0.8928 (m110) REVERT: d 200 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8245 (mt0) REVERT: e 90 GLN cc_start: 0.8887 (pm20) cc_final: 0.8033 (pm20) REVERT: e 124 SER cc_start: 0.8959 (t) cc_final: 0.8614 (t) REVERT: e 135 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8539 (mt-10) outliers start: 71 outliers final: 45 residues processed: 419 average time/residue: 1.2210 time to fit residues: 599.5758 Evaluate side-chains 404 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 346 time to evaluate : 2.298 ------------------------------------------------------------------------------- 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 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 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 117 ARG Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 146 GLN 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 78 MET 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 F residue 50 VAL 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 G residue 83 MET 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 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 104 LEU Chi-restraints excluded: chain c residue 44 LYS 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 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 189 THR Chi-restraints excluded: chain d residue 199 ILE Chi-restraints excluded: chain d residue 200 GLN Chi-restraints excluded: chain d residue 208 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 23 optimal weight: 0.2980 chunk 16 optimal weight: 2.9990 chunk 153 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 270 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 201 optimal weight: 0.6980 chunk 185 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN D 104 ASN ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 80 GLN e 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.082880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.069101 restraints weight = 57964.087| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.20 r_work: 0.2977 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.6493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21760 Z= 0.133 Angle : 0.681 12.821 29470 Z= 0.338 Chirality : 0.043 0.298 3387 Planarity : 0.004 0.056 3773 Dihedral : 4.598 55.835 3016 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.35 % Favored : 96.61 % Rotamer: Outliers : 2.78 % Allowed : 28.55 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.16), residues: 2746 helix: 1.79 (0.16), residues: 1089 sheet: -1.00 (0.20), residues: 601 loop : -0.74 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP c 105 HIS 0.006 0.001 HIS E 65 PHE 0.020 0.001 PHE H 87 TYR 0.025 0.001 TYR G 160 ARG 0.013 0.000 ARG B 8 Details of bonding type rmsd hydrogen bonds : bond 0.03656 ( 1038) hydrogen bonds : angle 4.40645 ( 2970) SS BOND : bond 0.00147 ( 1) SS BOND : angle 3.16567 ( 2) covalent geometry : bond 0.00310 (21759) covalent geometry : angle 0.68054 (29468) ********************** 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: 62 poor density : 366 time to evaluate : 2.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8795 (mt-10) REVERT: A 83 TYR cc_start: 0.8924 (t80) cc_final: 0.8316 (t80) REVERT: A 150 ASP cc_start: 0.8494 (m-30) cc_final: 0.8158 (m-30) REVERT: A 166 ASN cc_start: 0.8932 (m-40) cc_final: 0.8723 (t0) REVERT: A 182 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7882 (tm) REVERT: A 183 GLU cc_start: 0.8127 (pt0) cc_final: 0.7740 (pm20) REVERT: B 45 LEU cc_start: 0.8948 (mt) cc_final: 0.8734 (mt) REVERT: B 51 ASN cc_start: 0.8158 (m-40) cc_final: 0.7817 (p0) REVERT: B 151 ASP cc_start: 0.8546 (m-30) cc_final: 0.8003 (p0) REVERT: C 23 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8488 (mm110) REVERT: C 117 ARG cc_start: 0.9286 (OUTLIER) cc_final: 0.8002 (ttp-170) REVERT: C 129 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.9018 (pp) REVERT: C 146 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8522 (tm-30) REVERT: D 141 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8749 (mt) REVERT: D 189 MET cc_start: 0.7308 (mtp) cc_final: 0.7025 (mtt) REVERT: E 16 GLN cc_start: 0.9373 (OUTLIER) cc_final: 0.9171 (mm-40) REVERT: E 91 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8746 (mm-30) REVERT: E 178 GLU cc_start: 0.8010 (mp0) cc_final: 0.7447 (mp0) REVERT: E 197 GLU cc_start: 0.8827 (tt0) cc_final: 0.8530 (tt0) REVERT: F 72 ARG cc_start: 0.8730 (mtm110) cc_final: 0.8333 (ptp-170) REVERT: F 94 GLU cc_start: 0.9219 (tp30) cc_final: 0.8904 (tm-30) REVERT: G 83 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8556 (mtp) REVERT: G 138 MET cc_start: 0.8911 (ttm) cc_final: 0.8567 (ttp) REVERT: G 236 ASP cc_start: 0.9421 (t0) cc_final: 0.9142 (t0) REVERT: H -10 TYR cc_start: 0.6983 (m-10) cc_final: 0.6737 (m-10) REVERT: H -9 LYS cc_start: 0.9084 (mtpt) cc_final: 0.8797 (ttmt) REVERT: H 79 ASN cc_start: 0.9206 (t0) cc_final: 0.8762 (t0) REVERT: H 84 GLN cc_start: 0.8486 (mt0) cc_final: 0.8110 (mm-40) REVERT: H 88 ARG cc_start: 0.8744 (ttt180) cc_final: 0.8469 (ttt180) REVERT: H 123 TYR cc_start: 0.8950 (p90) cc_final: 0.8702 (p90) REVERT: H 142 ARG cc_start: 0.8867 (ttp80) cc_final: 0.8168 (ttp80) REVERT: H 145 MET cc_start: 0.8269 (tpp) cc_final: 0.7501 (tpp) REVERT: H 146 GLU cc_start: 0.8158 (pm20) cc_final: 0.7905 (pm20) REVERT: H 175 CYS cc_start: 0.8576 (m) cc_final: 0.7907 (t) REVERT: I 75 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8220 (tp30) REVERT: I 78 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8122 (mt-10) REVERT: I 80 ARG cc_start: 0.9021 (ptp90) cc_final: 0.8560 (ptp90) REVERT: I 113 ASP cc_start: 0.8094 (t0) cc_final: 0.7838 (t0) REVERT: I 116 THR cc_start: 0.8627 (m) cc_final: 0.8291 (m) REVERT: I 149 MET cc_start: 0.8451 (tpt) cc_final: 0.8061 (tpp) REVERT: I 165 GLU cc_start: 0.8426 (mp0) cc_final: 0.7781 (mp0) REVERT: I 169 GLN cc_start: 0.7637 (mm110) cc_final: 0.7423 (tp40) REVERT: J 59 TYR cc_start: 0.8005 (t80) cc_final: 0.7764 (t80) REVERT: J 65 GLN cc_start: 0.7990 (tt0) cc_final: 0.7399 (tm-30) REVERT: J 69 MET cc_start: 0.7955 (ptt) cc_final: 0.7749 (ptm) REVERT: J 73 TYR cc_start: 0.7699 (p90) cc_final: 0.7315 (p90) REVERT: J 189 HIS cc_start: 0.7125 (m-70) cc_final: 0.6832 (m90) REVERT: c 41 LEU cc_start: 0.8839 (tp) cc_final: 0.8631 (tt) REVERT: c 44 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8457 (tttm) REVERT: c 179 GLU cc_start: 0.8790 (mp0) cc_final: 0.8506 (pm20) REVERT: c 184 LEU cc_start: 0.9178 (mm) cc_final: 0.8963 (mt) REVERT: c 243 ASP cc_start: 0.8606 (t0) cc_final: 0.8078 (t0) REVERT: d 148 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.8829 (tm-30) REVERT: d 153 ASN cc_start: 0.9174 (OUTLIER) cc_final: 0.8942 (m110) REVERT: d 200 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8259 (mt0) REVERT: e 90 GLN cc_start: 0.8871 (pm20) cc_final: 0.8038 (pm20) REVERT: e 124 SER cc_start: 0.8927 (t) cc_final: 0.8561 (t) outliers start: 62 outliers final: 42 residues processed: 408 average time/residue: 1.1666 time to fit residues: 549.2265 Evaluate side-chains 405 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 349 time to evaluate : 2.441 ------------------------------------------------------------------------------- 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 182 LEU Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 34 CYS 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 117 ARG Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 134 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 78 MET 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 50 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain H residue 0 THR Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 78 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 104 LEU Chi-restraints excluded: chain c residue 44 LYS 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 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 189 THR Chi-restraints excluded: chain d residue 199 ILE Chi-restraints excluded: chain d residue 200 GLN Chi-restraints excluded: chain d residue 208 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 175 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 260 optimal weight: 3.9990 chunk 220 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 193 optimal weight: 0.0060 chunk 209 optimal weight: 6.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN C 116 GLN C 120 GLN ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 108 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.082871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.069110 restraints weight = 57814.651| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.19 r_work: 0.2975 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.6600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21760 Z= 0.139 Angle : 0.690 12.784 29470 Z= 0.341 Chirality : 0.043 0.213 3387 Planarity : 0.004 0.073 3773 Dihedral : 4.567 55.179 3016 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.42 % Favored : 96.54 % Rotamer: Outliers : 3.28 % Allowed : 28.41 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.16), residues: 2746 helix: 1.82 (0.16), residues: 1089 sheet: -0.96 (0.20), residues: 601 loop : -0.70 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP c 105 HIS 0.007 0.001 HIS D 186 PHE 0.015 0.001 PHE e 55 TYR 0.032 0.001 TYR H 7 ARG 0.021 0.000 ARG G 3 Details of bonding type rmsd hydrogen bonds : bond 0.03647 ( 1038) hydrogen bonds : angle 4.38780 ( 2970) SS BOND : bond 0.00140 ( 1) SS BOND : angle 3.23766 ( 2) covalent geometry : bond 0.00329 (21759) covalent geometry : angle 0.68933 (29468) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14715.53 seconds wall clock time: 254 minutes 42.52 seconds (15282.52 seconds total)