Starting phenix.real_space_refine on Wed May 21 11:09:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tm4_41378/05_2025/8tm4_41378.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tm4_41378/05_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_41378/05_2025/8tm4_41378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tm4_41378/05_2025/8tm4_41378.map" model { file = "/net/cci-nas-00/data/ceres_data/8tm4_41378/05_2025/8tm4_41378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tm4_41378/05_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-5687/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: 12.07, per 1000 atoms: 0.56 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: 4.44 Conformation dependent library (CDL) restraints added in 2.7 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: 2.22 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: 7.60 Time building geometry restraints manager: 5.30 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: 4.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.720 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 46.390 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.100 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:14.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.680 ------------------------------------------------------------------------------- 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 : 2.416 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: 1.1317 time to fit residues: 1035.5398 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 : 2.594 ------------------------------------------------------------------------------- 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 = 0.082558 restraints weight = 54186.615| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 3.28 r_work: 0.3240 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- 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 5.83540 ( 2970) SS BOND : bond 0.01099 ( 1) SS BOND : angle 1.08963 ( 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 : 2.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8207 (mmm) REVERT: A 150 ASP cc_start: 0.8497 (m-30) cc_final: 0.8261 (m-30) REVERT: A 166 ASN cc_start: 0.8442 (m-40) cc_final: 0.8108 (t0) REVERT: B 146 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7282 (mp10) REVERT: B 230 GLN cc_start: 0.6974 (tp40) cc_final: 0.6623 (tp40) REVERT: C 211 MET cc_start: 0.8124 (tpp) cc_final: 0.7894 (tpt) REVERT: D 25 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8134 (mt-10) REVERT: D 178 GLN cc_start: 0.8827 (tp40) cc_final: 0.7987 (tp40) REVERT: D 202 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8246 (mt) REVERT: D 215 ILE cc_start: 0.8594 (tt) cc_final: 0.8134 (tp) REVERT: D 229 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.7887 (t80) REVERT: D 231 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.8052 (tppt) REVERT: F 94 GLU cc_start: 0.9078 (tp30) cc_final: 0.8685 (tm-30) REVERT: F 118 MET cc_start: 0.9221 (mmp) cc_final: 0.8917 (mmt) REVERT: F 181 GLN cc_start: 0.7410 (OUTLIER) cc_final: 0.7196 (pp30) REVERT: G 101 TRP cc_start: 0.9392 (t-100) cc_final: 0.8638 (t-100) REVERT: G 107 TYR cc_start: 0.8468 (p90) cc_final: 0.7930 (p90) REVERT: G 123 GLN cc_start: 0.9488 (OUTLIER) cc_final: 0.9213 (tm-30) REVERT: G 128 ASN cc_start: 0.8813 (t0) cc_final: 0.8487 (t0) REVERT: H 63 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8238 (mm-30) REVERT: H 79 ASN cc_start: 0.9142 (t0) cc_final: 0.8756 (t0) REVERT: H 126 MET cc_start: 0.7686 (mtp) cc_final: 0.7469 (mtp) REVERT: H 175 CYS cc_start: 0.8429 (m) cc_final: 0.7815 (t) REVERT: H 180 ASN cc_start: 0.7901 (p0) cc_final: 0.7680 (p0) REVERT: I 104 TYR cc_start: 0.7935 (m-80) cc_final: 0.7626 (m-80) REVERT: I 131 MET cc_start: 0.6399 (ppp) cc_final: 0.6029 (pp-130) REVERT: I 146 MET cc_start: 0.7969 (pmm) cc_final: 0.7724 (pmm) REVERT: I 149 MET cc_start: 0.8159 (tpt) cc_final: 0.7633 (tpp) REVERT: I 169 GLN cc_start: 0.8253 (mm110) cc_final: 0.7936 (tp40) REVERT: J 118 MET cc_start: 0.7812 (ttm) cc_final: 0.7540 (ttp) REVERT: c 210 ASN cc_start: 0.8487 (m-40) cc_final: 0.8264 (m-40) REVERT: c 236 TYR cc_start: 0.8885 (m-80) cc_final: 0.8552 (m-80) REVERT: c 243 ASP cc_start: 0.8103 (t0) cc_final: 0.7607 (t0) REVERT: c 256 THR cc_start: 0.8190 (p) cc_final: 0.7807 (p) REVERT: d 83 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8607 (mmm160) REVERT: d 200 GLN cc_start: 0.8213 (mt0) cc_final: 0.7972 (mt0) REVERT: d 264 PHE cc_start: 0.8377 (m-80) cc_final: 0.8127 (m-80) REVERT: e 57 LEU cc_start: 0.8864 (mm) cc_final: 0.8396 (tm) REVERT: e 58 ASN cc_start: 0.9132 (m-40) cc_final: 0.8868 (m-40) REVERT: e 59 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8405 (mm110) REVERT: e 90 GLN cc_start: 0.8771 (pm20) cc_final: 0.8391 (pm20) REVERT: e 119 ASN cc_start: 0.7672 (t0) cc_final: 0.7383 (t0) outliers start: 128 outliers final: 39 residues processed: 531 average time/residue: 1.0359 time to fit residues: 643.9637 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 : 2.514 ------------------------------------------------------------------------------- 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: 7.9990 chunk 33 optimal weight: 0.7980 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: 0.0270 chunk 63 optimal weight: 0.9980 overall best weight: 0.9640 ------------------------------------------------------------------------------- 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 175 HIS ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 238 HIS ** I 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 HIS ** 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 = 0.3496 r_free = 0.3496 target = 0.089402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.075113 restraints weight = 56070.733| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 3.24 r_work: 0.3096 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 21760 Z= 0.163 Angle : 0.712 15.456 29470 Z= 0.359 Chirality : 0.044 0.190 3387 Planarity : 0.005 0.057 3773 Dihedral : 5.697 58.680 3027 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.42 % Favored : 96.43 % Rotamer: Outliers : 5.61 % Allowed : 21.05 % Favored : 73.34 % 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: -1.33 (0.15), residues: 2746 helix: 0.57 (0.15), residues: 1101 sheet: -2.08 (0.19), residues: 599 loop : -1.59 (0.17), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 100 HIS 0.009 0.001 HIS F 73 PHE 0.019 0.002 PHE d 102 TYR 0.021 0.002 TYR A 83 ARG 0.010 0.001 ARG G 3 Details of bonding type rmsd hydrogen bonds : bond 0.04276 ( 1038) hydrogen bonds : angle 5.14629 ( 2970) SS BOND : bond 0.00163 ( 1) SS BOND : angle 1.87700 ( 2) covalent geometry : bond 0.00377 (21759) covalent geometry : angle 0.71168 (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 531 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 406 time to evaluate : 2.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8451 (mmm) REVERT: A 166 ASN cc_start: 0.8724 (m-40) cc_final: 0.8446 (t0) REVERT: B 51 ASN cc_start: 0.8397 (m-40) cc_final: 0.7851 (p0) REVERT: C 211 MET cc_start: 0.8411 (tpp) cc_final: 0.8122 (ttt) REVERT: C 225 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8802 (pp) REVERT: D 25 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8260 (mt-10) REVERT: D 229 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.8091 (t80) REVERT: E 3 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.8013 (ptp-170) REVERT: E 85 CYS cc_start: 0.9398 (OUTLIER) cc_final: 0.9182 (t) REVERT: E 178 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7564 (mp0) REVERT: E 184 LEU cc_start: 0.7912 (pt) cc_final: 0.7700 (tm) REVERT: F 94 GLU cc_start: 0.9130 (tp30) cc_final: 0.8864 (tm-30) REVERT: F 98 ASN cc_start: 0.9130 (t0) cc_final: 0.8413 (t0) REVERT: F 118 MET cc_start: 0.9356 (mmp) cc_final: 0.9118 (mmt) REVERT: G 83 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8727 (mtp) REVERT: G 101 TRP cc_start: 0.9443 (t-100) cc_final: 0.8760 (t-100) REVERT: G 107 TYR cc_start: 0.8635 (p90) cc_final: 0.8063 (p90) REVERT: G 123 GLN cc_start: 0.9486 (OUTLIER) cc_final: 0.9209 (tm-30) REVERT: H 56 GLN cc_start: 0.9018 (tt0) cc_final: 0.8585 (tp40) REVERT: H 63 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8395 (mm-30) REVERT: H 79 ASN cc_start: 0.9181 (t0) cc_final: 0.8801 (t0) REVERT: H 84 GLN cc_start: 0.8715 (mt0) cc_final: 0.8340 (mm-40) REVERT: H 123 TYR cc_start: 0.8584 (p90) cc_final: 0.7981 (p90) REVERT: H 126 MET cc_start: 0.7826 (mtp) cc_final: 0.7620 (mtp) REVERT: H 137 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.7696 (t80) REVERT: H 139 ASP cc_start: 0.8840 (t0) cc_final: 0.8616 (t0) REVERT: H 145 MET cc_start: 0.7939 (tpp) cc_final: 0.7722 (tpp) REVERT: H 146 GLU cc_start: 0.7974 (pm20) cc_final: 0.7658 (pm20) REVERT: H 175 CYS cc_start: 0.8354 (m) cc_final: 0.7694 (t) REVERT: I 75 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8144 (tp30) REVERT: I 80 ARG cc_start: 0.8784 (ptt90) cc_final: 0.8501 (ptp90) REVERT: I 131 MET cc_start: 0.6512 (ppp) cc_final: 0.6101 (pp-130) REVERT: I 149 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7783 (tpp) REVERT: I 169 GLN cc_start: 0.8184 (mm110) cc_final: 0.7915 (tp40) REVERT: I 171 MET cc_start: 0.7965 (mmm) cc_final: 0.7702 (mmm) REVERT: J 11 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7248 (m-30) REVERT: J 65 GLN cc_start: 0.7650 (tm-30) cc_final: 0.7003 (tm-30) REVERT: J 70 ARG cc_start: 0.8244 (ttm-80) cc_final: 0.7975 (ttp80) REVERT: J 118 MET cc_start: 0.8047 (ttm) cc_final: 0.7620 (mtp) REVERT: c 176 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8753 (mmtp) REVERT: c 210 ASN cc_start: 0.8571 (m-40) cc_final: 0.8338 (m-40) REVERT: c 236 TYR cc_start: 0.8990 (m-80) cc_final: 0.8556 (m-80) REVERT: d 83 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8702 (mmm160) REVERT: d 200 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8301 (mt0) REVERT: e 68 ARG cc_start: 0.8646 (tpt90) cc_final: 0.7856 (tpt90) REVERT: e 90 GLN cc_start: 0.8722 (pm20) cc_final: 0.7964 (pm20) outliers start: 125 outliers final: 36 residues processed: 478 average time/residue: 1.1218 time to fit residues: 623.6596 Evaluate side-chains 405 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 354 time to evaluate : 2.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 25 GLU 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 139 ASP Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 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 39 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 200 GLN 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: 0.0980 chunk 56 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 146 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 76 optimal weight: 0.0570 chunk 124 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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** C 23 GLN ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN D 104 ASN D 178 GLN F 98 ASN I 162 HIS I 173 ASN J 110 HIS c 136 GLN d 67 ASN ** d 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 88 GLN e 108 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.089076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.074743 restraints weight = 57190.007| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.27 r_work: 0.3092 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21760 Z= 0.128 Angle : 0.664 12.396 29470 Z= 0.328 Chirality : 0.042 0.294 3387 Planarity : 0.004 0.052 3773 Dihedral : 5.139 56.661 3023 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.06 % Favored : 96.83 % Rotamer: Outliers : 4.35 % Allowed : 23.29 % Favored : 72.35 % 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: -0.62 (0.16), residues: 2746 helix: 1.14 (0.15), residues: 1091 sheet: -1.64 (0.20), residues: 584 loop : -1.22 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 100 HIS 0.006 0.001 HIS E 65 PHE 0.015 0.001 PHE I 69 TYR 0.019 0.001 TYR G 103 ARG 0.010 0.000 ARG G 3 Details of bonding type rmsd hydrogen bonds : bond 0.03731 ( 1038) hydrogen bonds : angle 4.77905 ( 2970) SS BOND : bond 0.01180 ( 1) SS BOND : angle 2.43170 ( 2) covalent geometry : bond 0.00293 (21759) covalent geometry : angle 0.66362 (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 503 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 406 time to evaluate : 2.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8743 (mt-10) REVERT: A 83 TYR cc_start: 0.8970 (t80) cc_final: 0.8457 (t80) REVERT: A 166 ASN cc_start: 0.8846 (m-40) cc_final: 0.8604 (t0) REVERT: B 45 LEU cc_start: 0.9025 (mt) cc_final: 0.8792 (mt) REVERT: B 51 ASN cc_start: 0.8367 (m-40) cc_final: 0.7877 (p0) REVERT: C 129 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.8951 (pp) REVERT: C 211 MET cc_start: 0.8427 (tpp) cc_final: 0.8224 (ttt) REVERT: C 225 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8805 (pp) REVERT: D 107 MET cc_start: 0.7903 (ttp) cc_final: 0.7170 (ttp) REVERT: D 215 ILE cc_start: 0.8949 (tt) cc_final: 0.8721 (tp) REVERT: D 229 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.8474 (t80) REVERT: E 3 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7934 (ptp-170) REVERT: E 91 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8419 (mp0) REVERT: E 184 LEU cc_start: 0.7918 (pt) cc_final: 0.7715 (tm) REVERT: F 94 GLU cc_start: 0.9161 (tp30) cc_final: 0.8949 (tm-30) REVERT: F 98 ASN cc_start: 0.9101 (t0) cc_final: 0.8609 (t0) REVERT: G 83 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8588 (mtp) REVERT: G 101 TRP cc_start: 0.9447 (t-100) cc_final: 0.8797 (t-100) REVERT: G 107 TYR cc_start: 0.8717 (p90) cc_final: 0.8172 (p90) REVERT: G 138 MET cc_start: 0.8967 (ttm) cc_final: 0.8592 (ttp) REVERT: H 56 GLN cc_start: 0.8947 (tt0) cc_final: 0.8569 (tp40) REVERT: H 63 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8227 (mm-30) REVERT: H 79 ASN cc_start: 0.9166 (t0) cc_final: 0.8793 (t0) REVERT: H 84 GLN cc_start: 0.8600 (mt0) cc_final: 0.8208 (mm-40) REVERT: H 123 TYR cc_start: 0.8607 (p90) cc_final: 0.8067 (p90) REVERT: H 137 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.7727 (t80) REVERT: H 175 CYS cc_start: 0.8381 (m) cc_final: 0.7703 (t) REVERT: I 12 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7238 (mtm) REVERT: I 68 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8907 (tmtm) REVERT: I 75 GLU cc_start: 0.8451 (tp30) cc_final: 0.8159 (tp30) REVERT: I 146 MET cc_start: 0.8391 (pmm) cc_final: 0.8091 (pmm) REVERT: I 149 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7840 (tpp) REVERT: I 169 GLN cc_start: 0.8046 (mm110) cc_final: 0.7780 (tp40) REVERT: I 193 ASP cc_start: 0.8722 (m-30) cc_final: 0.8430 (m-30) REVERT: J 118 MET cc_start: 0.8020 (ttm) cc_final: 0.7712 (mtp) REVERT: J 121 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8400 (mt) REVERT: c 210 ASN cc_start: 0.8582 (m-40) cc_final: 0.8320 (m-40) REVERT: c 236 TYR cc_start: 0.8981 (m-80) cc_final: 0.8689 (m-80) REVERT: c 273 LEU cc_start: 0.9475 (tp) cc_final: 0.9247 (tm) REVERT: d 83 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8722 (mmm160) REVERT: d 148 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8583 (tm-30) REVERT: e 68 ARG cc_start: 0.8714 (tpt90) cc_final: 0.8061 (tpm170) REVERT: e 90 GLN cc_start: 0.8717 (pm20) cc_final: 0.7939 (pm20) outliers start: 97 outliers final: 27 residues processed: 469 average time/residue: 1.0672 time to fit residues: 580.8334 Evaluate side-chains 395 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 356 time to evaluate : 2.227 ------------------------------------------------------------------------------- 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 C residue 45 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 225 ILE 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 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 42 ILE Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain c residue 153 VAL Chi-restraints excluded: chain c residue 212 VAL 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 148 GLN Chi-restraints excluded: chain d residue 187 THR Chi-restraints excluded: chain d residue 189 THR Chi-restraints excluded: chain d residue 228 LEU Chi-restraints excluded: chain e residue 122 SER Chi-restraints excluded: chain e residue 124 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 123 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 269 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 chunk 157 optimal weight: 3.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN C 23 GLN ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN D 104 ASN E 16 GLN ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H -22 ASN J 110 HIS ** 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 = 0.3458 r_free = 0.3458 target = 0.086843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.072568 restraints weight = 57266.980| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 3.26 r_work: 0.3051 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.5173 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= 0.141 Angle : 0.649 13.102 29470 Z= 0.322 Chirality : 0.042 0.240 3387 Planarity : 0.004 0.057 3773 Dihedral : 4.872 57.623 3018 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.28 % Favored : 96.61 % Rotamer: Outliers : 4.17 % Allowed : 24.96 % Favored : 70.87 % 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: -0.25 (0.16), residues: 2746 helix: 1.42 (0.16), residues: 1091 sheet: -1.44 (0.20), residues: 599 loop : -0.99 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 100 HIS 0.007 0.001 HIS E 65 PHE 0.015 0.001 PHE I 69 TYR 0.021 0.001 TYR C 153 ARG 0.014 0.001 ARG G 3 Details of bonding type rmsd hydrogen bonds : bond 0.03739 ( 1038) hydrogen bonds : angle 4.63652 ( 2970) SS BOND : bond 0.00164 ( 1) SS BOND : angle 2.74097 ( 2) covalent geometry : bond 0.00324 (21759) covalent geometry : angle 0.64824 (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 485 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 392 time to evaluate : 2.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8751 (mt-10) REVERT: A 83 TYR cc_start: 0.8976 (t80) cc_final: 0.8395 (t80) REVERT: A 166 ASN cc_start: 0.8883 (m-40) cc_final: 0.8652 (t0) REVERT: B 51 ASN cc_start: 0.8274 (m-40) cc_final: 0.7896 (p0) REVERT: C 225 ILE cc_start: 0.9087 (pt) cc_final: 0.8827 (pp) REVERT: D 107 MET cc_start: 0.8094 (ttp) cc_final: 0.7632 (ttp) REVERT: D 229 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.8246 (t80) REVERT: E 3 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7992 (ptp-170) REVERT: E 16 GLN cc_start: 0.9404 (OUTLIER) cc_final: 0.9154 (mm-40) REVERT: E 88 MET cc_start: 0.9352 (mtm) cc_final: 0.8603 (mtm) REVERT: E 91 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8702 (mm-30) REVERT: E 184 LEU cc_start: 0.7974 (pt) cc_final: 0.7755 (tm) REVERT: F 28 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.7813 (mpt) REVERT: F 94 GLU cc_start: 0.9158 (tp30) cc_final: 0.8893 (tm-30) REVERT: F 98 ASN cc_start: 0.9110 (t0) cc_final: 0.8275 (t0) REVERT: F 137 MET cc_start: 0.8525 (mtm) cc_final: 0.8273 (mtm) REVERT: G 83 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8658 (mtp) REVERT: G 101 TRP cc_start: 0.9465 (t-100) cc_final: 0.8876 (t-100) REVERT: G 107 TYR cc_start: 0.8816 (p90) cc_final: 0.8275 (p90) REVERT: G 138 MET cc_start: 0.8971 (ttm) cc_final: 0.8634 (ttp) REVERT: H 56 GLN cc_start: 0.9009 (tt0) cc_final: 0.8646 (tp-100) REVERT: H 79 ASN cc_start: 0.9188 (t0) cc_final: 0.8814 (t0) REVERT: H 84 GLN cc_start: 0.8619 (mt0) cc_final: 0.8253 (mm-40) REVERT: H 123 TYR cc_start: 0.8687 (p90) cc_final: 0.8445 (p90) REVERT: H 146 GLU cc_start: 0.7983 (pm20) cc_final: 0.7589 (pm20) REVERT: H 175 CYS cc_start: 0.8462 (m) cc_final: 0.7654 (t) REVERT: I 12 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7351 (mtm) REVERT: I 65 GLN cc_start: 0.8528 (mt0) cc_final: 0.8257 (mt0) REVERT: I 68 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.8919 (tmtm) REVERT: I 75 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8198 (tp30) REVERT: I 80 ARG cc_start: 0.9132 (ptp90) cc_final: 0.8711 (ptp90) REVERT: I 149 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7904 (tpp) REVERT: I 153 LEU cc_start: 0.9116 (mt) cc_final: 0.8765 (pp) REVERT: I 165 GLU cc_start: 0.8333 (mp0) cc_final: 0.7804 (mp0) REVERT: I 169 GLN cc_start: 0.8012 (mm110) cc_final: 0.7684 (tp40) REVERT: I 193 ASP cc_start: 0.8712 (m-30) cc_final: 0.8438 (m-30) REVERT: J 189 HIS cc_start: 0.5709 (m170) cc_final: 0.5454 (m170) REVERT: c 184 LEU cc_start: 0.8890 (mm) cc_final: 0.8558 (mm) REVERT: c 210 ASN cc_start: 0.8654 (m-40) cc_final: 0.8427 (m-40) REVERT: c 236 TYR cc_start: 0.9050 (m-80) cc_final: 0.8753 (m-80) REVERT: c 243 ASP cc_start: 0.8524 (t0) cc_final: 0.7886 (t0) REVERT: d 83 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8692 (mmm160) REVERT: d 148 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8634 (tm-30) REVERT: d 153 ASN cc_start: 0.9256 (OUTLIER) cc_final: 0.9047 (m110) REVERT: d 200 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8230 (mt0) REVERT: e 68 ARG cc_start: 0.8791 (tpt90) cc_final: 0.7868 (tpt170) REVERT: e 90 GLN cc_start: 0.8780 (pm20) cc_final: 0.7957 (pm20) outliers start: 93 outliers final: 28 residues processed: 452 average time/residue: 1.1027 time to fit residues: 578.4405 Evaluate side-chains 382 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 341 time to evaluate : 2.463 ------------------------------------------------------------------------------- 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 C residue 45 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 4 ASN Chi-restraints excluded: chain E residue 16 GLN Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain F residue 28 MET 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 75 VAL Chi-restraints excluded: chain I residue 12 MET Chi-restraints excluded: chain I residue 22 ILE 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 17 SER Chi-restraints excluded: chain c residue 77 ASN 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 201 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 245 optimal weight: 0.9980 chunk 191 optimal weight: 0.6980 chunk 194 optimal weight: 2.9990 chunk 240 optimal weight: 5.9990 chunk 190 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 259 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 164 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 C 92 GLN C 116 GLN D 104 ASN E 21 GLN E 59 HIS G 172 GLN H 56 GLN I 93 ASN I 173 ASN J 110 HIS ** d 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 108 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.084920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.070824 restraints weight = 57561.459| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.23 r_work: 0.3015 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.5551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21760 Z= 0.144 Angle : 0.657 12.122 29470 Z= 0.325 Chirality : 0.042 0.298 3387 Planarity : 0.004 0.062 3773 Dihedral : 4.752 57.733 3017 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.50 % Favored : 96.47 % Rotamer: Outliers : 4.53 % Allowed : 25.31 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1091 sheet: -1.26 (0.20), residues: 597 loop : -0.91 (0.18), residues: 1058 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 69 TYR 0.029 0.001 TYR H 7 ARG 0.017 0.001 ARG G 3 Details of bonding type rmsd hydrogen bonds : bond 0.03719 ( 1038) hydrogen bonds : angle 4.53629 ( 2970) SS BOND : bond 0.00280 ( 1) SS BOND : angle 3.04902 ( 2) covalent geometry : bond 0.00334 (21759) covalent geometry : angle 0.65633 (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 469 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 368 time to evaluate : 2.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8795 (mt-10) REVERT: A 83 TYR cc_start: 0.8963 (t80) cc_final: 0.8360 (t80) REVERT: A 103 GLU cc_start: 0.7790 (tp30) cc_final: 0.7588 (tm-30) REVERT: A 166 ASN cc_start: 0.8933 (m-40) cc_final: 0.8716 (t0) REVERT: B 51 ASN cc_start: 0.8252 (m-40) cc_final: 0.7930 (p0) REVERT: B 114 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9089 (tp) REVERT: B 151 ASP cc_start: 0.8533 (m-30) cc_final: 0.8294 (m-30) REVERT: C 66 ASP cc_start: 0.7443 (t0) cc_final: 0.6756 (t0) REVERT: C 129 ILE cc_start: 0.9336 (OUTLIER) cc_final: 0.8979 (pp) REVERT: C 146 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8512 (tm-30) REVERT: D 20 ARG cc_start: 0.8677 (mtp85) cc_final: 0.8457 (mtm110) REVERT: D 107 MET cc_start: 0.8286 (ttp) cc_final: 0.7983 (ttp) REVERT: E 3 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8007 (ptp-170) REVERT: E 91 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8695 (mm-30) REVERT: F 94 GLU cc_start: 0.9169 (tp30) cc_final: 0.8920 (tm-30) REVERT: F 98 ASN cc_start: 0.9123 (t0) cc_final: 0.8284 (t0) REVERT: F 137 MET cc_start: 0.8585 (mtm) cc_final: 0.8333 (mtm) REVERT: G 83 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8637 (mtp) REVERT: G 123 GLN cc_start: 0.9510 (OUTLIER) cc_final: 0.9215 (tm-30) REVERT: G 138 MET cc_start: 0.8953 (ttm) cc_final: 0.8487 (ttp) REVERT: H 56 GLN cc_start: 0.8985 (tt0) cc_final: 0.8675 (tp-100) REVERT: H 79 ASN cc_start: 0.9187 (t0) cc_final: 0.8768 (t0) REVERT: H 84 GLN cc_start: 0.8606 (mt0) cc_final: 0.8253 (mm-40) REVERT: H 145 MET cc_start: 0.8178 (tpp) cc_final: 0.7825 (mmm) REVERT: H 146 GLU cc_start: 0.8100 (pm20) cc_final: 0.7672 (pm20) REVERT: H 175 CYS cc_start: 0.8451 (m) cc_final: 0.7698 (t) REVERT: I 12 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7623 (mtm) REVERT: I 25 ASP cc_start: 0.7907 (p0) cc_final: 0.7661 (p0) REVERT: I 65 GLN cc_start: 0.8628 (mt0) cc_final: 0.8341 (mt0) REVERT: I 68 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.8907 (tmtm) REVERT: I 75 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8168 (tp30) REVERT: I 80 ARG cc_start: 0.9103 (ptp90) cc_final: 0.8617 (ptp90) REVERT: I 149 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7916 (tpp) REVERT: I 153 LEU cc_start: 0.9089 (mt) cc_final: 0.8813 (pp) REVERT: I 165 GLU cc_start: 0.8383 (mp0) cc_final: 0.7822 (mp0) REVERT: I 169 GLN cc_start: 0.8087 (mm110) cc_final: 0.7778 (tp40) REVERT: I 171 MET cc_start: 0.7812 (mmm) cc_final: 0.7527 (mmm) REVERT: J 17 SER cc_start: 0.4483 (OUTLIER) cc_final: 0.4149 (t) REVERT: J 65 GLN cc_start: 0.7761 (tt0) cc_final: 0.7112 (tm-30) REVERT: J 73 TYR cc_start: 0.7335 (p90) cc_final: 0.7010 (p90) REVERT: J 189 HIS cc_start: 0.5905 (m170) cc_final: 0.5615 (m170) REVERT: c 236 TYR cc_start: 0.9078 (m-80) cc_final: 0.8845 (m-80) REVERT: c 243 ASP cc_start: 0.8538 (t0) cc_final: 0.7958 (t0) REVERT: d 83 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8680 (mmm160) REVERT: d 127 TYR cc_start: 0.9316 (p90) cc_final: 0.9077 (p90) REVERT: d 148 GLN cc_start: 0.9068 (OUTLIER) cc_final: 0.8650 (tm-30) REVERT: d 200 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8185 (mt0) REVERT: e 68 ARG cc_start: 0.8898 (tpt90) cc_final: 0.7971 (tpt170) REVERT: e 90 GLN cc_start: 0.8804 (pm20) cc_final: 0.7988 (pm20) outliers start: 101 outliers final: 38 residues processed: 435 average time/residue: 1.1229 time to fit residues: 567.7647 Evaluate side-chains 394 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 342 time to evaluate : 2.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 114 LEU 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 146 GLN Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain D residue 114 GLN Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain E residue 3 ARG 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 64 ASN 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 22 ILE 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 17 SER Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain J residue 104 LEU 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 187 THR Chi-restraints excluded: chain d residue 189 THR Chi-restraints excluded: chain d residue 199 ILE Chi-restraints excluded: chain d residue 200 GLN Chi-restraints excluded: chain d residue 209 SER Chi-restraints excluded: chain e residue 50 LEU Chi-restraints excluded: chain e residue 99 ASN 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: 4.9990 chunk 2 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 208 optimal weight: 0.9990 chunk 185 optimal weight: 0.8980 chunk 253 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 127 optimal weight: 4.9990 chunk 38 optimal weight: 0.0270 chunk 27 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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 G 172 GLN H 56 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.084885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.070977 restraints weight = 57161.345| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.20 r_work: 0.3017 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.5787 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= 0.131 Angle : 0.657 12.409 29470 Z= 0.324 Chirality : 0.042 0.282 3387 Planarity : 0.004 0.066 3773 Dihedral : 4.695 59.015 3017 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.31 % Favored : 96.65 % Rotamer: Outliers : 3.90 % Allowed : 25.81 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.11 (0.16), residues: 2746 helix: 1.69 (0.16), residues: 1095 sheet: -1.16 (0.20), residues: 605 loop : -0.81 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 100 HIS 0.007 0.001 HIS E 65 PHE 0.018 0.001 PHE H 87 TYR 0.031 0.001 TYR C 153 ARG 0.018 0.000 ARG G 3 Details of bonding type rmsd hydrogen bonds : bond 0.03633 ( 1038) hydrogen bonds : angle 4.46198 ( 2970) SS BOND : bond 0.00129 ( 1) SS BOND : angle 2.95313 ( 2) covalent geometry : bond 0.00305 (21759) covalent geometry : angle 0.65608 (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 462 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 375 time to evaluate : 2.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8824 (mt-10) REVERT: A 83 TYR cc_start: 0.8940 (t80) cc_final: 0.8361 (t80) REVERT: A 150 ASP cc_start: 0.8439 (m-30) cc_final: 0.8209 (m-30) REVERT: A 166 ASN cc_start: 0.8919 (m-40) cc_final: 0.8708 (t0) REVERT: A 182 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7727 (tm) REVERT: B 51 ASN cc_start: 0.8219 (m-40) cc_final: 0.7969 (p0) REVERT: B 114 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9057 (tp) REVERT: B 151 ASP cc_start: 0.8572 (m-30) cc_final: 0.8344 (m-30) REVERT: C 129 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.8984 (pp) REVERT: C 146 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8532 (tm-30) REVERT: D 107 MET cc_start: 0.8364 (ttp) cc_final: 0.8144 (ttp) REVERT: D 141 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8751 (mt) REVERT: E 3 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7958 (ptp-170) REVERT: E 88 MET cc_start: 0.9253 (mtm) cc_final: 0.8617 (mtm) REVERT: E 91 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8668 (mm-30) REVERT: E 197 GLU cc_start: 0.8761 (tt0) cc_final: 0.8541 (tt0) REVERT: F 28 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.7712 (mpt) REVERT: F 94 GLU cc_start: 0.9164 (tp30) cc_final: 0.8954 (tm-30) REVERT: F 98 ASN cc_start: 0.9148 (t0) cc_final: 0.8755 (t0) REVERT: F 137 MET cc_start: 0.8648 (mtm) cc_final: 0.8410 (mtm) REVERT: G 83 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8623 (mtp) REVERT: G 138 MET cc_start: 0.8920 (ttm) cc_final: 0.8558 (ttp) REVERT: H -18 GLU cc_start: 0.8952 (tt0) cc_final: 0.8694 (mt-10) REVERT: H 79 ASN cc_start: 0.9171 (t0) cc_final: 0.8751 (t0) REVERT: H 84 GLN cc_start: 0.8534 (mt0) cc_final: 0.8176 (mm110) REVERT: H 123 TYR cc_start: 0.8854 (p90) cc_final: 0.8585 (p90) REVERT: H 146 GLU cc_start: 0.8076 (pm20) cc_final: 0.7734 (pm20) REVERT: H 175 CYS cc_start: 0.8431 (m) cc_final: 0.7778 (t) REVERT: I 12 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7443 (mtm) REVERT: I 15 LYS cc_start: 0.7571 (mmtt) cc_final: 0.7312 (mmmt) REVERT: I 25 ASP cc_start: 0.8055 (p0) cc_final: 0.7851 (p0) REVERT: I 68 LYS cc_start: 0.9371 (OUTLIER) cc_final: 0.9007 (tmtm) REVERT: I 75 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8212 (tp30) REVERT: I 80 ARG cc_start: 0.9140 (ptp90) cc_final: 0.8332 (ptp90) REVERT: I 88 MET cc_start: 0.9007 (ttp) cc_final: 0.8609 (ttt) REVERT: I 131 MET cc_start: 0.7239 (ptt) cc_final: 0.6645 (pp-130) REVERT: I 146 MET cc_start: 0.8505 (pmm) cc_final: 0.8167 (pmm) REVERT: I 149 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.7967 (tpp) REVERT: I 165 GLU cc_start: 0.8483 (mp0) cc_final: 0.7876 (mp0) REVERT: I 169 GLN cc_start: 0.7866 (mm110) cc_final: 0.7605 (tp40) REVERT: J 17 SER cc_start: 0.5223 (OUTLIER) cc_final: 0.4984 (t) REVERT: J 69 MET cc_start: 0.8059 (ptm) cc_final: 0.7726 (ptm) REVERT: J 73 TYR cc_start: 0.7468 (p90) cc_final: 0.7148 (p90) REVERT: J 189 HIS cc_start: 0.6956 (m-70) cc_final: 0.6662 (m170) REVERT: c 236 TYR cc_start: 0.9090 (m-80) cc_final: 0.8804 (m-80) REVERT: c 243 ASP cc_start: 0.8549 (t0) cc_final: 0.7965 (t0) REVERT: d 127 TYR cc_start: 0.9328 (p90) cc_final: 0.9120 (p90) REVERT: d 148 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.8662 (tm-30) REVERT: d 200 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8220 (mt0) REVERT: e 68 ARG cc_start: 0.8926 (tpt90) cc_final: 0.8586 (tpt90) REVERT: e 90 GLN cc_start: 0.8833 (pm20) cc_final: 0.7997 (pm20) outliers start: 87 outliers final: 38 residues processed: 432 average time/residue: 1.1050 time to fit residues: 553.5221 Evaluate side-chains 393 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 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 156 PHE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 186 ASP 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 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 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 104 ASN Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 4 ASN Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain F residue 28 MET 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 H residue 0 THR Chi-restraints excluded: chain H residue 61 ASN Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain I residue 12 MET Chi-restraints excluded: chain I residue 22 ILE 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 17 SER Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain J residue 104 LEU 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 151 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 191 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 172 optimal weight: 8.9990 chunk 156 optimal weight: 0.6980 chunk 176 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 237 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 E 16 GLN G 172 GLN I 72 ASN I 157 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.081674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.067837 restraints weight = 58303.903| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 3.15 r_work: 0.2954 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.6140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21760 Z= 0.179 Angle : 0.697 11.603 29470 Z= 0.346 Chirality : 0.044 0.305 3387 Planarity : 0.005 0.097 3773 Dihedral : 4.751 57.755 3017 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.71 % Favored : 96.25 % Rotamer: Outliers : 3.86 % Allowed : 26.48 % Favored : 69.66 % 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: 0.18 (0.16), residues: 2746 helix: 1.75 (0.16), residues: 1088 sheet: -1.03 (0.20), residues: 599 loop : -0.84 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 162 HIS 0.007 0.001 HIS E 65 PHE 0.020 0.002 PHE J 36 TYR 0.029 0.002 TYR C 153 ARG 0.018 0.001 ARG G 3 Details of bonding type rmsd hydrogen bonds : bond 0.04010 ( 1038) hydrogen bonds : angle 4.52113 ( 2970) SS BOND : bond 0.00547 ( 1) SS BOND : angle 2.89044 ( 2) covalent geometry : bond 0.00419 (21759) covalent geometry : angle 0.69689 (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 448 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 362 time to evaluate : 2.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.9088 (mm-30) cc_final: 0.8856 (mt-10) REVERT: A 83 TYR cc_start: 0.8989 (t80) cc_final: 0.8414 (t80) REVERT: A 150 ASP cc_start: 0.8457 (m-30) cc_final: 0.8245 (m-30) REVERT: A 166 ASN cc_start: 0.8947 (m-40) cc_final: 0.8741 (t0) REVERT: A 182 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7947 (tm) REVERT: B 51 ASN cc_start: 0.8195 (m-40) cc_final: 0.7947 (p0) REVERT: B 114 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9131 (tp) REVERT: C 23 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8568 (mp10) REVERT: C 129 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.9045 (pp) REVERT: C 146 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8652 (tm-30) REVERT: D 114 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8487 (mt0) REVERT: D 141 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8810 (mt) REVERT: E 3 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8235 (ptp-170) REVERT: E 88 MET cc_start: 0.9230 (mtm) cc_final: 0.8961 (mtm) REVERT: E 91 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8707 (mm-30) REVERT: E 197 GLU cc_start: 0.8808 (tt0) cc_final: 0.8550 (tt0) REVERT: F 72 ARG cc_start: 0.8668 (mtm110) cc_final: 0.8286 (ptp-170) REVERT: F 94 GLU cc_start: 0.9151 (tp30) cc_final: 0.8925 (tm-30) REVERT: F 98 ASN cc_start: 0.9182 (t0) cc_final: 0.8785 (t0) REVERT: F 185 MET cc_start: 0.9334 (OUTLIER) cc_final: 0.9101 (mtm) REVERT: G 83 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8680 (mtp) REVERT: G 123 GLN cc_start: 0.9549 (OUTLIER) cc_final: 0.9317 (tm-30) REVERT: G 138 MET cc_start: 0.8850 (ttm) cc_final: 0.8473 (ttp) REVERT: H 79 ASN cc_start: 0.9191 (t0) cc_final: 0.8785 (t0) REVERT: H 84 GLN cc_start: 0.8699 (mt0) cc_final: 0.8332 (mm-40) REVERT: H 123 TYR cc_start: 0.8942 (p90) cc_final: 0.8683 (p90) REVERT: H 140 LYS cc_start: 0.8165 (mtmm) cc_final: 0.7913 (mtmm) REVERT: H 146 GLU cc_start: 0.8193 (pm20) cc_final: 0.7874 (pm20) REVERT: H 175 CYS cc_start: 0.8490 (m) cc_final: 0.7867 (t) REVERT: I 12 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7661 (mtm) REVERT: I 15 LYS cc_start: 0.7569 (mmtt) cc_final: 0.6979 (mmpt) REVERT: I 68 LYS cc_start: 0.9401 (OUTLIER) cc_final: 0.8847 (tmtm) REVERT: I 75 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8287 (tp30) REVERT: I 80 ARG cc_start: 0.9004 (ptp90) cc_final: 0.8570 (ptp90) REVERT: I 134 ASP cc_start: 0.8484 (t0) cc_final: 0.8090 (t0) REVERT: I 146 MET cc_start: 0.8637 (pmm) cc_final: 0.8399 (pmm) REVERT: I 149 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8064 (tpp) REVERT: I 165 GLU cc_start: 0.8526 (mp0) cc_final: 0.7900 (mp0) REVERT: I 169 GLN cc_start: 0.7899 (mm110) cc_final: 0.7670 (tp40) REVERT: J 69 MET cc_start: 0.8237 (ptm) cc_final: 0.7985 (ptm) REVERT: J 73 TYR cc_start: 0.7811 (p90) cc_final: 0.7467 (p90) REVERT: J 78 THR cc_start: 0.9123 (OUTLIER) cc_final: 0.8890 (m) REVERT: J 189 HIS cc_start: 0.7005 (m-70) cc_final: 0.6664 (m170) REVERT: c 41 LEU cc_start: 0.8783 (tp) cc_final: 0.8563 (tt) REVERT: c 66 TYR cc_start: 0.8377 (m-80) cc_final: 0.8114 (m-10) REVERT: c 236 TYR cc_start: 0.9142 (m-80) cc_final: 0.8906 (m-80) REVERT: c 243 ASP cc_start: 0.8597 (t0) cc_final: 0.7949 (t0) REVERT: d 148 GLN cc_start: 0.9088 (OUTLIER) cc_final: 0.8678 (tm-30) REVERT: e 90 GLN cc_start: 0.8960 (pm20) cc_final: 0.8136 (pm20) REVERT: e 124 SER cc_start: 0.9023 (t) cc_final: 0.8692 (t) outliers start: 86 outliers final: 41 residues processed: 421 average time/residue: 1.2094 time to fit residues: 584.5327 Evaluate side-chains 385 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 327 time to evaluate : 2.301 ------------------------------------------------------------------------------- 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 81 SER Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 65 LEU 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 114 GLN Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain E residue 3 ARG 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 185 MET 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 72 LEU Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 180 ASN Chi-restraints excluded: chain I residue 12 MET Chi-restraints excluded: chain I residue 22 ILE 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 158 MET Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain c residue 77 ASN 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 77 VAL Chi-restraints excluded: chain d residue 148 GLN Chi-restraints excluded: chain d residue 151 VAL 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 209 SER 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: 2.9990 chunk 150 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 152 optimal weight: 0.4980 chunk 228 optimal weight: 0.9990 chunk 203 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 3 optimal weight: 0.2980 chunk 95 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 E 16 GLN H 65 HIS d 153 ASN ** d 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 108 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.081321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.067571 restraints weight = 58049.542| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 3.17 r_work: 0.2938 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.6327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21760 Z= 0.179 Angle : 0.710 12.181 29470 Z= 0.354 Chirality : 0.044 0.299 3387 Planarity : 0.005 0.078 3773 Dihedral : 4.736 56.975 3015 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.50 % Favored : 96.47 % Rotamer: Outliers : 3.86 % Allowed : 27.47 % 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: 0.17 (0.16), residues: 2746 helix: 1.69 (0.16), residues: 1088 sheet: -1.00 (0.21), residues: 596 loop : -0.82 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP c 105 HIS 0.007 0.001 HIS E 65 PHE 0.022 0.002 PHE G 187 TYR 0.033 0.002 TYR H 7 ARG 0.020 0.001 ARG G 3 Details of bonding type rmsd hydrogen bonds : bond 0.04035 ( 1038) hydrogen bonds : angle 4.54190 ( 2970) SS BOND : bond 0.00142 ( 1) SS BOND : angle 3.13961 ( 2) covalent geometry : bond 0.00421 (21759) covalent geometry : angle 0.70917 (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 438 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 352 time to evaluate : 2.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8807 (mt-10) REVERT: A 83 TYR cc_start: 0.8984 (t80) cc_final: 0.8408 (t80) REVERT: A 103 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7885 (tp30) REVERT: A 150 ASP cc_start: 0.8482 (m-30) cc_final: 0.8239 (m-30) REVERT: A 166 ASN cc_start: 0.8948 (m-40) cc_final: 0.8717 (t0) REVERT: A 182 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7841 (tm) REVERT: A 183 GLU cc_start: 0.8214 (pt0) cc_final: 0.7837 (pm20) REVERT: B 51 ASN cc_start: 0.8205 (m-40) cc_final: 0.7859 (p0) REVERT: B 114 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9086 (tp) REVERT: C 129 ILE cc_start: 0.9327 (OUTLIER) cc_final: 0.8986 (pp) REVERT: D 114 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8382 (mt0) REVERT: D 141 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8802 (mt) REVERT: E 88 MET cc_start: 0.9264 (mtm) cc_final: 0.9034 (mtm) REVERT: E 91 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8713 (mm-30) REVERT: E 176 MET cc_start: 0.7449 (ttp) cc_final: 0.7191 (mtp) REVERT: E 197 GLU cc_start: 0.8843 (tt0) cc_final: 0.8578 (tt0) REVERT: F 94 GLU cc_start: 0.9231 (tp30) cc_final: 0.8876 (tp30) REVERT: F 98 ASN cc_start: 0.9123 (t0) cc_final: 0.8826 (t0) REVERT: G 83 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8789 (mtp) REVERT: G 121 ILE cc_start: 0.8406 (mp) cc_final: 0.8112 (mt) REVERT: G 123 GLN cc_start: 0.9531 (OUTLIER) cc_final: 0.9303 (tm-30) REVERT: H -10 TYR cc_start: 0.6943 (m-10) cc_final: 0.6734 (m-10) REVERT: H 79 ASN cc_start: 0.9195 (t0) cc_final: 0.8784 (t0) REVERT: H 84 GLN cc_start: 0.8633 (mt0) cc_final: 0.8295 (mm-40) REVERT: H 123 TYR cc_start: 0.8981 (p90) cc_final: 0.8747 (p90) REVERT: H 146 GLU cc_start: 0.8185 (pm20) cc_final: 0.7883 (pm20) REVERT: H 175 CYS cc_start: 0.8547 (m) cc_final: 0.7880 (t) REVERT: I 12 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7601 (mtm) REVERT: I 15 LYS cc_start: 0.7498 (mmtt) cc_final: 0.6946 (mmpt) REVERT: I 75 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8267 (tp30) REVERT: I 78 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8121 (mt-10) REVERT: I 80 ARG cc_start: 0.8962 (ptp90) cc_final: 0.8408 (ptp90) REVERT: I 134 ASP cc_start: 0.8518 (t0) cc_final: 0.8123 (t0) REVERT: I 135 ASP cc_start: 0.8497 (p0) cc_final: 0.8283 (p0) REVERT: I 165 GLU cc_start: 0.8512 (mp0) cc_final: 0.8107 (mp0) REVERT: I 169 GLN cc_start: 0.7888 (mm110) cc_final: 0.7678 (tm-30) REVERT: J 69 MET cc_start: 0.8292 (ptm) cc_final: 0.8055 (ptm) REVERT: J 73 TYR cc_start: 0.7859 (p90) cc_final: 0.7483 (p90) REVERT: J 78 THR cc_start: 0.9068 (OUTLIER) cc_final: 0.8848 (m) REVERT: J 121 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8401 (mt) REVERT: J 189 HIS cc_start: 0.7146 (m-70) cc_final: 0.6817 (m90) REVERT: c 236 TYR cc_start: 0.9139 (m-80) cc_final: 0.8919 (m-80) REVERT: d 148 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8720 (tm-30) REVERT: e 59 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.8698 (mm110) REVERT: e 90 GLN cc_start: 0.8942 (pm20) cc_final: 0.8098 (pm20) REVERT: e 124 SER cc_start: 0.9003 (t) cc_final: 0.8655 (t) outliers start: 86 outliers final: 44 residues processed: 411 average time/residue: 1.1680 time to fit residues: 557.1715 Evaluate side-chains 388 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 330 time to evaluate : 2.258 ------------------------------------------------------------------------------- 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 103 GLU 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 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 134 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain D residue 114 GLN 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 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 72 LEU Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain H residue 180 ASN Chi-restraints excluded: chain I residue 12 MET Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 158 MET Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 42 ILE Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain c residue 77 ASN 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 77 VAL Chi-restraints excluded: chain d residue 148 GLN Chi-restraints excluded: chain d residue 151 VAL 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 209 SER Chi-restraints excluded: chain d residue 228 LEU Chi-restraints excluded: chain e residue 59 GLN Chi-restraints excluded: chain e residue 122 SER Chi-restraints excluded: chain e residue 140 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 23 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 270 optimal weight: 3.9990 chunk 120 optimal weight: 0.1980 chunk 201 optimal weight: 0.9980 chunk 185 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 D 104 ASN E 16 GLN G 100 ASN ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 80 GLN e 108 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.081683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.067749 restraints weight = 58142.305| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 3.21 r_work: 0.2946 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.6523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21760 Z= 0.153 Angle : 0.706 12.813 29470 Z= 0.350 Chirality : 0.043 0.293 3387 Planarity : 0.004 0.070 3773 Dihedral : 4.690 56.287 3015 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.79 % Favored : 96.18 % Rotamer: Outliers : 3.28 % Allowed : 27.96 % Favored : 68.76 % 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: 0.22 (0.16), residues: 2746 helix: 1.75 (0.16), residues: 1084 sheet: -1.00 (0.20), residues: 597 loop : -0.78 (0.18), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP c 105 HIS 0.007 0.001 HIS E 65 PHE 0.014 0.001 PHE I 69 TYR 0.027 0.001 TYR G 160 ARG 0.016 0.001 ARG E 107 Details of bonding type rmsd hydrogen bonds : bond 0.03853 ( 1038) hydrogen bonds : angle 4.49093 ( 2970) SS BOND : bond 0.00045 ( 1) SS BOND : angle 3.04284 ( 2) covalent geometry : bond 0.00358 (21759) covalent geometry : angle 0.70605 (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 432 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 359 time to evaluate : 2.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.9088 (mm-30) cc_final: 0.8849 (mt-10) REVERT: A 83 TYR cc_start: 0.8959 (t80) cc_final: 0.8367 (t80) REVERT: A 150 ASP cc_start: 0.8471 (m-30) cc_final: 0.8208 (m-30) REVERT: A 166 ASN cc_start: 0.8928 (m-40) cc_final: 0.8667 (t0) REVERT: A 182 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7873 (tm) REVERT: A 183 GLU cc_start: 0.8219 (pt0) cc_final: 0.7818 (pm20) REVERT: B 51 ASN cc_start: 0.8204 (m-40) cc_final: 0.7862 (p0) REVERT: B 114 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9098 (tp) REVERT: B 151 ASP cc_start: 0.8592 (m-30) cc_final: 0.8116 (p0) REVERT: C 23 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8377 (mm110) REVERT: C 129 ILE cc_start: 0.9336 (OUTLIER) cc_final: 0.9009 (pp) REVERT: C 159 ASN cc_start: 0.9155 (t0) cc_final: 0.8905 (t160) REVERT: D 114 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8346 (mt0) REVERT: E 88 MET cc_start: 0.9248 (mtm) cc_final: 0.9030 (mtm) REVERT: E 91 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8711 (mm-30) REVERT: E 176 MET cc_start: 0.7470 (ttp) cc_final: 0.7213 (mtp) REVERT: E 197 GLU cc_start: 0.8829 (tt0) cc_final: 0.8556 (tt0) REVERT: F 72 ARG cc_start: 0.8757 (mtm110) cc_final: 0.8321 (ptp-170) REVERT: F 94 GLU cc_start: 0.9192 (tp30) cc_final: 0.8938 (tp30) REVERT: F 98 ASN cc_start: 0.9119 (t0) cc_final: 0.8782 (t0) REVERT: F 176 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8566 (mp0) REVERT: G 83 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8752 (mtp) REVERT: G 121 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8087 (mt) REVERT: H 79 ASN cc_start: 0.9192 (t0) cc_final: 0.8762 (t0) REVERT: H 84 GLN cc_start: 0.8637 (mt0) cc_final: 0.8311 (mm-40) REVERT: H 123 TYR cc_start: 0.9018 (p90) cc_final: 0.8732 (p90) REVERT: H 175 CYS cc_start: 0.8609 (m) cc_final: 0.7936 (t) REVERT: I 12 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7626 (mtm) REVERT: I 15 LYS cc_start: 0.7581 (mmtt) cc_final: 0.7181 (mmmt) REVERT: I 75 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8272 (tp30) REVERT: I 78 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8063 (mt-10) REVERT: I 80 ARG cc_start: 0.8998 (ptp90) cc_final: 0.8483 (ptp90) REVERT: I 134 ASP cc_start: 0.8512 (t0) cc_final: 0.8136 (t0) REVERT: I 135 ASP cc_start: 0.8496 (p0) cc_final: 0.8278 (p0) REVERT: I 165 GLU cc_start: 0.8506 (mp0) cc_final: 0.8096 (mp0) REVERT: J 59 TYR cc_start: 0.8147 (t80) cc_final: 0.7861 (t80) REVERT: J 69 MET cc_start: 0.8282 (ptm) cc_final: 0.8030 (ptm) REVERT: J 73 TYR cc_start: 0.7819 (p90) cc_final: 0.7430 (p90) REVERT: J 78 THR cc_start: 0.9085 (OUTLIER) cc_final: 0.8849 (m) REVERT: J 121 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8388 (mt) REVERT: J 189 HIS cc_start: 0.7187 (m-70) cc_final: 0.6869 (m90) REVERT: c 236 TYR cc_start: 0.9141 (m-80) cc_final: 0.8915 (m-80) REVERT: c 243 ASP cc_start: 0.8613 (t0) cc_final: 0.8018 (t0) REVERT: d 148 GLN cc_start: 0.9155 (OUTLIER) cc_final: 0.8770 (tm-30) REVERT: e 90 GLN cc_start: 0.8925 (pm20) cc_final: 0.8102 (pm20) REVERT: e 124 SER cc_start: 0.8983 (t) cc_final: 0.8621 (t) outliers start: 73 outliers final: 42 residues processed: 407 average time/residue: 1.1662 time to fit residues: 546.0172 Evaluate side-chains 390 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 335 time to evaluate : 2.487 ------------------------------------------------------------------------------- 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 114 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain D residue 114 GLN 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 186 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 121 ILE 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 12 MET Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 78 GLU Chi-restraints excluded: chain I residue 158 MET Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 42 ILE Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain c residue 77 ASN 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 77 VAL Chi-restraints excluded: chain d residue 148 GLN Chi-restraints excluded: chain d residue 151 VAL 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 209 SER Chi-restraints excluded: chain d residue 228 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: 0.6980 chunk 79 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 111 optimal weight: 0.5980 chunk 260 optimal weight: 3.9990 chunk 220 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 163 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 193 optimal weight: 0.9980 chunk 209 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 E 16 GLN F 222 ASN G 100 ASN ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 108 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.081840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.068224 restraints weight = 57859.369| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 3.16 r_work: 0.2958 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.6613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21760 Z= 0.146 Angle : 0.709 12.948 29470 Z= 0.351 Chirality : 0.043 0.285 3387 Planarity : 0.004 0.068 3773 Dihedral : 4.685 55.843 3015 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.57 % Favored : 96.39 % Rotamer: Outliers : 2.92 % Allowed : 28.68 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.76 (0.16), residues: 1083 sheet: -0.98 (0.20), residues: 597 loop : -0.76 (0.18), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP c 105 HIS 0.007 0.001 HIS E 65 PHE 0.018 0.001 PHE H 87 TYR 0.032 0.002 TYR H 7 ARG 0.015 0.001 ARG E 107 Details of bonding type rmsd hydrogen bonds : bond 0.03815 ( 1038) hydrogen bonds : angle 4.48299 ( 2970) SS BOND : bond 0.00170 ( 1) SS BOND : angle 2.93313 ( 2) covalent geometry : bond 0.00343 (21759) covalent geometry : angle 0.70851 (29468) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13590.72 seconds wall clock time: 235 minutes 20.18 seconds (14120.18 seconds total)