Starting phenix.real_space_refine on Sun Aug 24 17:19:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tm5_41379/08_2025/8tm5_41379.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tm5_41379/08_2025/8tm5_41379.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/8tm5_41379/08_2025/8tm5_41379.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tm5_41379/08_2025/8tm5_41379.map" model { file = "/net/cci-nas-00/data/ceres_data/8tm5_41379/08_2025/8tm5_41379.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tm5_41379/08_2025/8tm5_41379.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 133 5.16 5 C 13829 2.51 5 N 3712 2.21 5 O 4015 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21689 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1800 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 222} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 4} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 1933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1933 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 245} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1792 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 6, 'TRANS': 231} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 4, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 55 Chain: "D" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1708 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 7, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 34 Chain: "E" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1816 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "F" Number of atoms: 1832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1832 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 233} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "G" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1873 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 236} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "H" Number of atoms: 1596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1596 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 10, 'TRANS': 208} Chain breaks: 3 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "I" Number of atoms: 1331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1331 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 9, 'TRANS': 165} Chain breaks: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "J" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1222 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 6, 'TRANS': 161} Chain breaks: 3 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 8, 'ARG:plan': 6, 'HIS:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 100 Chain: "c" Number of atoms: 2092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2092 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 13, 'TRANS': 265} Chain breaks: 1 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 14, 'ASP:plan': 3, 'ARG:plan': 6, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 106 Chain: "d" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1907 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 231} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "e" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 787 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 92} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.75, per 1000 atoms: 0.22 Number of scatterers: 21689 At special positions: 0 Unit cell: (130.38, 137.8, 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 4015 8.00 N 3712 7.00 C 13829 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=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 791.5 milliseconds Enol-peptide restraints added in 1.4 microseconds 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5342 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 25 sheets defined 41.8% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 3 through 9 Processing helix chain 'A' and resid 19 through 31 Processing helix chain 'A' and resid 79 through 102 Processing helix chain 'A' and resid 106 through 124 removed outlier: 3.626A pdb=" N TYR A 121 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 178 Processing helix chain 'A' and resid 186 through 198 Processing helix chain 'A' and resid 222 through 234 Processing helix chain 'B' and resid 18 through 30 removed outlier: 3.556A pdb=" N GLU B 22 " --> pdb=" O LEU B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 102 removed outlier: 3.684A pdb=" N VAL B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 124 Processing helix chain 'B' and resid 167 through 178 Processing helix chain 'B' and resid 185 through 201 Processing helix chain 'B' and resid 229 through 252 Processing helix chain 'C' and resid 16 through 29 Processing helix chain 'C' and resid 76 through 99 Processing helix chain 'C' and resid 103 through 119 Processing helix chain 'C' and resid 164 through 176 Processing helix chain 'C' and resid 183 through 199 Processing helix chain 'C' and resid 221 through 239 Processing helix chain 'D' and resid 21 through 33 removed outlier: 3.529A pdb=" N GLU D 25 " --> pdb=" O LEU D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 103 removed outlier: 3.778A pdb=" N THR D 87 " --> pdb=" O ALA D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 121 Processing helix chain 'D' and resid 173 through 185 Processing helix chain 'D' and resid 190 through 206 Processing helix chain 'D' and resid 230 through 239 removed outlier: 3.724A pdb=" N VAL D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 32 removed outlier: 3.686A pdb=" N GLU E 23 " --> pdb=" O ILE E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 98 Processing helix chain 'E' and resid 104 through 122 Proline residue: E 119 - end of helix Processing helix chain 'E' and resid 164 through 175 removed outlier: 4.358A pdb=" N ALA E 168 " --> pdb=" O ARG E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 182 Processing helix chain 'E' and resid 183 through 199 removed outlier: 3.611A pdb=" N THR E 198 " --> pdb=" O ALA E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 234 Proline residue: E 231 - end of helix Processing helix chain 'F' and resid 21 through 33 Processing helix chain 'F' and resid 81 through 104 Processing helix chain 'F' and resid 108 through 126 removed outlier: 3.849A pdb=" N TYR F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 180 Processing helix chain 'F' and resid 186 through 202 removed outlier: 4.662A pdb=" N LYS F 192 " --> pdb=" O ARG F 188 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU F 193 " --> pdb=" O ASP F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 222 No H-bonds generated for 'chain 'F' and resid 220 through 222' Processing helix chain 'F' and resid 229 through 243 Processing helix chain 'G' and resid 22 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 231 through 245 Processing helix chain 'H' and resid -26 through -12 removed outlier: 3.800A pdb=" N LYS H -13 " --> pdb=" O ALA H -17 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 71 Processing helix chain 'H' and resid 75 through 90 Processing helix chain 'H' and resid 130 through 142 Processing helix chain 'H' and resid 147 through 164 Processing helix chain 'I' and resid 56 through 79 Processing helix chain 'I' and resid 83 through 98 removed outlier: 3.938A pdb=" N LYS I 98 " --> pdb=" O LEU I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 154 Processing helix chain 'I' and resid 159 through 173 Processing helix chain 'J' and resid 49 through 72 removed outlier: 3.544A pdb=" N VAL J 54 " --> pdb=" O ALA J 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 95 Processing helix chain 'J' and resid 138 through 146 Processing helix chain 'J' and resid 152 through 170 Processing helix chain 'c' and resid 17 through 25 Processing helix chain 'c' and resid 26 through 30 removed outlier: 4.043A pdb=" N ARG c 29 " --> pdb=" O GLU c 26 " (cutoff:3.500A) Processing helix chain 'c' and resid 31 through 45 Processing helix chain 'c' and resid 61 through 66 Processing helix chain 'c' and resid 76 through 87 Processing helix chain 'c' and resid 142 through 154 removed outlier: 4.359A pdb=" N TYR c 147 " --> pdb=" O GLU c 143 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLN c 148 " --> pdb=" O ASP c 144 " (cutoff:3.500A) Processing helix chain 'c' and resid 214 through 226 Processing helix chain 'c' and resid 243 through 249 Processing helix chain 'c' and resid 250 through 255 Processing helix chain 'c' and resid 265 through 279 removed outlier: 3.950A pdb=" N LYS c 275 " --> pdb=" O GLU c 271 " (cutoff:3.500A) Processing helix chain 'd' and resid 26 through 40 Processing helix chain 'd' and resid 66 through 69 removed outlier: 3.573A pdb=" N THR d 69 " --> pdb=" O GLY d 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 66 through 69' Processing helix chain 'd' and resid 98 through 114 Processing helix chain 'd' and resid 130 through 137 removed outlier: 3.798A pdb=" N THR d 137 " --> pdb=" O GLN d 133 " (cutoff:3.500A) Processing helix chain 'd' and resid 148 through 159 Processing helix chain 'd' and resid 185 through 198 removed outlier: 3.631A pdb=" N THR d 189 " --> pdb=" O GLY d 185 " (cutoff:3.500A) Processing helix chain 'd' and resid 213 through 229 removed outlier: 3.804A pdb=" N TRP d 227 " --> pdb=" O TYR d 223 " (cutoff:3.500A) Processing helix chain 'e' and resid 46 through 54 removed outlier: 4.386A pdb=" N LEU e 50 " --> pdb=" O HIS e 46 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER e 51 " --> pdb=" O PRO e 47 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 71 Processing helix chain 'e' and resid 73 through 89 removed outlier: 3.948A pdb=" N VAL e 89 " --> pdb=" O ALA e 85 " (cutoff:3.500A) Processing helix chain 'e' and resid 99 through 107 Processing helix chain 'e' and resid 113 through 118 removed outlier: 3.657A 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 69 removed outlier: 6.604A pdb=" N ILE A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A 133 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 161 through 164 Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.504A pdb=" N GLY B 138 " --> pdb=" O GLN B 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 158 through 161 Processing sheet with id=AA6, first strand: chain 'C' and resid 158 through 161 Processing sheet with id=AA7, first strand: chain 'C' and resid 62 through 66 removed outlier: 6.575A pdb=" N VAL C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER C 130 " --> pdb=" O ALA C 74 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA C 131 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU C 144 " --> pdb=" O TRP C 156 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 167 through 170 Processing sheet with id=AA9, first strand: chain 'D' and resid 67 through 71 removed outlier: 3.557A pdb=" N CYS D 76 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE D 70 " --> pdb=" O ILE D 74 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 145 through 147 Processing sheet with id=AB2, first strand: chain 'E' and resid 158 through 161 removed outlier: 3.612A pdb=" N ILE E 212 " --> pdb=" O TYR E 224 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 63 through 64 removed outlier: 3.567A pdb=" N LEU E 132 " --> pdb=" O THR E 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 163 through 166 removed outlier: 3.736A pdb=" N GLU F 213 " --> pdb=" O VAL F 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 67 through 68 removed outlier: 3.685A pdb=" N GLY F 139 " --> pdb=" O GLY F 75 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR F 159 " --> pdb=" O MET F 151 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 165 through 169 removed outlier: 5.385A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN G 53 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 69 through 71 removed outlier: 4.033A pdb=" N VAL G 151 " --> pdb=" O PHE G 163 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 124 through 127 removed outlier: 3.696A pdb=" N GLY H 11 " --> pdb=" O TYR H 8 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 35 through 38 removed outlier: 5.330A pdb=" N PHE H 36 " --> pdb=" O CYS H 43 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N CYS H 43 " --> pdb=" O PHE H 36 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL H 99 " --> pdb=" O CYS H 44 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 215 through 218 removed outlier: 3.601A pdb=" N LYS H 215 " --> pdb=" O THR I 197 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR I 197 " --> pdb=" O LYS H 215 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR H 217 " --> pdb=" O ILE I 195 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE I 195 " --> pdb=" O THR H 217 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU I 191 " --> pdb=" O LYS I 194 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP I 25 " --> pdb=" O ALA I 10 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ALA I 10 " --> pdb=" O ASP I 25 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 42 through 44 removed outlier: 3.712A pdb=" N PHE I 43 " --> pdb=" O ILE I 51 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE I 121 " --> pdb=" O THR I 133 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR I 133 " --> pdb=" O ILE I 121 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 129 through 130 removed outlier: 3.929A pdb=" N VAL J 13 " --> pdb=" O ILE J 183 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE J 183 " --> pdb=" O VAL J 13 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG J 181 " --> pdb=" O VAL J 15 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 35 through 37 removed outlier: 3.643A pdb=" N MET J 118 " --> pdb=" O LEU J 102 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'c' and resid 56 through 57 removed outlier: 5.281A pdb=" N GLU c 95 " --> pdb=" O HIS c 125 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N HIS c 125 " --> pdb=" O GLU c 95 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY c 97 " --> pdb=" O PHE c 123 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N CYS c 121 " --> pdb=" O ALA c 99 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS c 70 " --> pdb=" O PHE c 133 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N CYS c 135 " --> pdb=" O LYS c 70 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE c 72 " --> pdb=" O CYS c 135 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N CYS c 137 " --> pdb=" O ILE c 72 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ALA c 74 " --> pdb=" O CYS c 137 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N CYS c 169 " --> pdb=" O ILE c 75 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'c' and resid 212 through 213 removed outlier: 3.510A pdb=" N SER d 72 " --> pdb=" O GLY d 57 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'd' and resid 3 through 4 removed outlier: 3.516A pdb=" N SER d 42 " --> pdb=" O SER d 79 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL d 77 " --> pdb=" O ILE d 44 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N TYR d 46 " --> pdb=" O ALA d 75 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ALA d 75 " --> pdb=" O TYR d 46 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU d 88 " --> pdb=" O LEU d 18 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU d 90 " --> pdb=" O PRO d 20 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N LEU d 121 " --> pdb=" O LEU d 17 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N MET d 19 " --> pdb=" O LEU d 121 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N SER d 123 " --> pdb=" O MET d 19 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS d 206 " --> pdb=" O SER d 122 " (cutoff:3.500A) 1209 hydrogen bonds defined for protein. 3474 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.36 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7082 1.34 - 1.46: 3909 1.46 - 1.58: 10886 1.58 - 1.70: 1 1.70 - 1.81: 206 Bond restraints: 22084 Sorted by residual: bond pdb=" CB PRO e 44 " pdb=" CG PRO e 44 " ideal model delta sigma weight residual 1.492 1.676 -0.184 5.00e-02 4.00e+02 1.35e+01 bond pdb=" CG PRO e 44 " pdb=" CD PRO e 44 " ideal model delta sigma weight residual 1.503 1.390 0.113 3.40e-02 8.65e+02 1.10e+01 bond pdb=" N LEU e 43 " pdb=" CA LEU e 43 " ideal model delta sigma weight residual 1.458 1.507 -0.049 1.90e-02 2.77e+03 6.76e+00 bond pdb=" N GLY F 5 " pdb=" CA GLY F 5 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.13e+00 bond pdb=" N SER B 2 " pdb=" CA SER B 2 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.12e+00 ... (remaining 22079 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 29810 3.22 - 6.44: 114 6.44 - 9.66: 3 9.66 - 12.88: 1 12.88 - 16.11: 1 Bond angle restraints: 29929 Sorted by residual: angle pdb=" CA PRO e 44 " pdb=" N PRO e 44 " pdb=" CD PRO e 44 " ideal model delta sigma weight residual 112.00 95.89 16.11 1.40e+00 5.10e-01 1.32e+02 angle pdb=" N PRO e 44 " pdb=" CD PRO e 44 " pdb=" CG PRO e 44 " ideal model delta sigma weight residual 103.20 96.09 7.11 1.50e+00 4.44e-01 2.25e+01 angle pdb=" C TYR H -10 " pdb=" CA TYR H -10 " pdb=" CB TYR H -10 " ideal model delta sigma weight residual 115.79 110.55 5.24 1.19e+00 7.06e-01 1.94e+01 angle pdb=" N ILE C 181 " pdb=" CA ILE C 181 " pdb=" C ILE C 181 " ideal model delta sigma weight residual 112.43 108.92 3.51 9.20e-01 1.18e+00 1.46e+01 angle pdb=" N SER c 128 " pdb=" CA SER c 128 " pdb=" C SER c 128 " ideal model delta sigma weight residual 113.41 109.06 4.35 1.22e+00 6.72e-01 1.27e+01 ... (remaining 29924 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 11825 17.97 - 35.94: 1154 35.94 - 53.91: 245 53.91 - 71.88: 51 71.88 - 89.84: 23 Dihedral angle restraints: 13298 sinusoidal: 5009 harmonic: 8289 Sorted by residual: dihedral pdb=" CA CYS G 154 " pdb=" C CYS G 154 " pdb=" N ASP G 155 " pdb=" CA ASP G 155 " ideal model delta harmonic sigma weight residual -180.00 -159.21 -20.79 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA PHE G 210 " pdb=" C PHE G 210 " pdb=" N LYS G 211 " pdb=" CA LYS G 211 " ideal model delta harmonic sigma weight residual 180.00 159.83 20.17 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA MET I 158 " pdb=" C MET I 158 " pdb=" N ASP I 159 " pdb=" CA ASP I 159 " ideal model delta harmonic sigma weight residual 180.00 160.44 19.56 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 13295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2381 0.032 - 0.063: 688 0.063 - 0.095: 245 0.095 - 0.126: 151 0.126 - 0.157: 7 Chirality restraints: 3472 Sorted by residual: chirality pdb=" CA ILE J 183 " pdb=" N ILE J 183 " pdb=" C ILE J 183 " pdb=" CB ILE J 183 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.20e-01 chirality pdb=" CA VAL D 50 " pdb=" N VAL D 50 " pdb=" C VAL D 50 " pdb=" CB VAL D 50 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CA ILE D 74 " pdb=" N ILE D 74 " pdb=" C ILE D 74 " pdb=" CB ILE D 74 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 3469 not shown) Planarity restraints: 3821 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU e 43 " -0.067 5.00e-02 4.00e+02 9.10e-02 1.33e+01 pdb=" N PRO e 44 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO e 44 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO e 44 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA c 12 " 0.054 5.00e-02 4.00e+02 8.08e-02 1.05e+01 pdb=" N PRO c 13 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO c 13 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO c 13 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA d 9 " -0.036 5.00e-02 4.00e+02 5.42e-02 4.70e+00 pdb=" N PRO d 10 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO d 10 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO d 10 " -0.030 5.00e-02 4.00e+02 ... (remaining 3818 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 212 2.60 - 3.18: 19407 3.18 - 3.75: 36119 3.75 - 4.33: 50410 4.33 - 4.90: 82782 Nonbonded interactions: 188930 Sorted by model distance: nonbonded pdb=" OG1 THR C 8 " pdb=" OD1 ASN C 122 " model vdw 2.026 3.040 nonbonded pdb=" OE1 GLN A 202 " pdb=" OG1 THR A 204 " model vdw 2.026 3.040 nonbonded pdb=" OD1 ASP J 184 " pdb=" N LYS J 185 " model vdw 2.063 3.120 nonbonded pdb=" OD1 ASP B 71 " pdb=" OG1 THR B 223 " model vdw 2.113 3.040 nonbonded pdb=" OE2 GLU C 170 " pdb=" NZ LYS C 174 " model vdw 2.134 3.120 ... (remaining 188925 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: 5.710 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: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.460 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 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:8.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 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 : 0.003 0.184 22085 Z= 0.148 Angle : 0.614 16.106 29931 Z= 0.363 Chirality : 0.039 0.157 3472 Planarity : 0.004 0.091 3821 Dihedral : 15.368 89.845 7953 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.06 % Favored : 96.87 % Rotamer: Outliers : 0.09 % Allowed : 18.30 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.16), residues: 2808 helix: 1.79 (0.16), residues: 1124 sheet: -1.97 (0.20), residues: 592 loop : -1.41 (0.17), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 93 TYR 0.014 0.001 TYR H 90 PHE 0.013 0.001 PHE J 36 TRP 0.006 0.001 TRP I 154 HIS 0.006 0.001 HIS D 155 Details of bonding type rmsd covalent geometry : bond 0.00310 (22084) covalent geometry : angle 0.61206 (29929) SS BOND : bond 0.00583 ( 1) SS BOND : angle 6.37740 ( 2) hydrogen bonds : bond 0.17272 ( 1201) hydrogen bonds : angle 7.76707 ( 3474) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 493 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 MET cc_start: 0.8489 (mmt) cc_final: 0.8216 (mtt) REVERT: A 233 ILE cc_start: 0.8725 (mm) cc_final: 0.8509 (mm) REVERT: B 116 ASP cc_start: 0.8503 (m-30) cc_final: 0.8297 (m-30) REVERT: B 174 MET cc_start: 0.8273 (ttm) cc_final: 0.7840 (ttm) REVERT: C 23 GLN cc_start: 0.8642 (tp-100) cc_final: 0.8379 (mm-40) REVERT: C 71 MET cc_start: 0.8685 (ptm) cc_final: 0.8377 (ptm) REVERT: D 66 LYS cc_start: 0.8600 (mmmt) cc_final: 0.8287 (mmmm) REVERT: D 114 GLN cc_start: 0.8611 (tt0) cc_final: 0.8140 (tm-30) REVERT: F 68 PHE cc_start: 0.7729 (m-80) cc_final: 0.7513 (m-80) REVERT: F 203 ASP cc_start: 0.7630 (t0) cc_final: 0.7364 (t0) REVERT: G 3 ARG cc_start: 0.8234 (mpp80) cc_final: 0.7028 (mmm160) REVERT: G 131 MET cc_start: 0.8541 (mpp) cc_final: 0.8255 (mtm) REVERT: H 135 MET cc_start: 0.8451 (tpp) cc_final: 0.8115 (tpp) REVERT: I 90 MET cc_start: 0.8902 (mtp) cc_final: 0.8650 (mtm) REVERT: I 106 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8577 (mt-10) REVERT: I 131 MET cc_start: 0.8807 (tmm) cc_final: 0.8578 (tmm) REVERT: I 146 MET cc_start: 0.6507 (mmt) cc_final: 0.6173 (mmt) REVERT: c 78 ASN cc_start: 0.8342 (m110) cc_final: 0.8068 (m-40) REVERT: d 32 MET cc_start: 0.9048 (mmm) cc_final: 0.8494 (mmm) REVERT: d 179 ILE cc_start: 0.8091 (mm) cc_final: 0.7385 (pp) REVERT: d 210 GLU cc_start: 0.7357 (mt-10) cc_final: 0.6988 (tt0) REVERT: e 49 GLU cc_start: 0.8653 (tp30) cc_final: 0.8373 (tp30) REVERT: e 56 GLN cc_start: 0.7912 (tp-100) cc_final: 0.7063 (tm-30) REVERT: e 108 ASN cc_start: 0.8485 (p0) cc_final: 0.8259 (p0) REVERT: e 137 LYS cc_start: 0.9299 (tttm) cc_final: 0.9026 (ttmt) outliers start: 2 outliers final: 2 residues processed: 493 average time/residue: 0.5545 time to fit residues: 313.2026 Evaluate side-chains 387 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 385 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 HIS Chi-restraints excluded: chain G residue 209 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.0980 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 102 GLN B 88 ASN B 155 ASN C 154 HIS ** D 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN D 178 GLN ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 238 HIS H -22 ASN H 57 GLN H 62 ASN J 63 ASN J 65 GLN J 87 ASN J 99 HIS c 78 ASN c 145 GLN c 268 GLN d 133 GLN e 99 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.083932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.070128 restraints weight = 57661.417| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 3.01 r_work: 0.2962 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 22085 Z= 0.189 Angle : 0.640 7.840 29931 Z= 0.334 Chirality : 0.044 0.177 3472 Planarity : 0.005 0.056 3821 Dihedral : 4.712 37.389 3079 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.13 % Favored : 96.79 % Rotamer: Outliers : 2.86 % Allowed : 18.57 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.16), residues: 2808 helix: 1.81 (0.15), residues: 1134 sheet: -1.44 (0.20), residues: 599 loop : -1.21 (0.18), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 93 TYR 0.024 0.002 TYR H 90 PHE 0.021 0.002 PHE G 210 TRP 0.021 0.002 TRP G 189 HIS 0.010 0.001 HIS D 155 Details of bonding type rmsd covalent geometry : bond 0.00428 (22084) covalent geometry : angle 0.63931 (29929) SS BOND : bond 0.00630 ( 1) SS BOND : angle 2.99079 ( 2) hydrogen bonds : bond 0.04249 ( 1201) hydrogen bonds : angle 5.42767 ( 3474) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 432 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8572 (mp0) REVERT: A 103 GLU cc_start: 0.8786 (tp30) cc_final: 0.8356 (tt0) REVERT: A 150 ASP cc_start: 0.8843 (m-30) cc_final: 0.8591 (m-30) REVERT: A 212 ILE cc_start: 0.9442 (pt) cc_final: 0.9219 (pp) REVERT: A 233 ILE cc_start: 0.8892 (mm) cc_final: 0.8615 (mm) REVERT: B 41 ASP cc_start: 0.8588 (m-30) cc_final: 0.8327 (m-30) REVERT: C 16 LEU cc_start: 0.8869 (mp) cc_final: 0.8506 (mt) REVERT: C 20 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8470 (mp0) REVERT: C 71 MET cc_start: 0.9004 (ptm) cc_final: 0.8698 (ptm) REVERT: D 5 ARG cc_start: 0.8821 (mpt-90) cc_final: 0.8606 (mpt90) REVERT: D 7 GLU cc_start: 0.7812 (tp30) cc_final: 0.7436 (tp30) REVERT: D 8 TYR cc_start: 0.9086 (m-80) cc_final: 0.8854 (m-80) REVERT: D 91 LYS cc_start: 0.8994 (tptp) cc_final: 0.8743 (tptp) REVERT: D 104 ASN cc_start: 0.8092 (m-40) cc_final: 0.7796 (m110) REVERT: D 114 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.7793 (tm-30) REVERT: E 72 ILE cc_start: 0.9449 (pt) cc_final: 0.9138 (pp) REVERT: E 125 ARG cc_start: 0.8163 (mmt180) cc_final: 0.7626 (mtp85) REVERT: G 3 ARG cc_start: 0.8188 (mpp80) cc_final: 0.6941 (mmm160) REVERT: G 83 MET cc_start: 0.9177 (OUTLIER) cc_final: 0.8708 (mmt) REVERT: G 179 LEU cc_start: 0.9424 (mt) cc_final: 0.9195 (mp) REVERT: H -18 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8419 (mp0) REVERT: H 12 ILE cc_start: 0.9493 (OUTLIER) cc_final: 0.9244 (mm) REVERT: I 80 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8518 (ptt-90) REVERT: I 90 MET cc_start: 0.9368 (mtp) cc_final: 0.9122 (mtm) REVERT: I 189 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8409 (pp) REVERT: I 198 ARG cc_start: 0.8119 (mtm-85) cc_final: 0.7763 (mtm-85) REVERT: J 53 THR cc_start: 0.8910 (p) cc_final: 0.8687 (p) REVERT: J 74 GLU cc_start: 0.8519 (pm20) cc_final: 0.8071 (mt-10) REVERT: d 55 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8501 (ppp) REVERT: d 229 GLN cc_start: 0.9395 (mt0) cc_final: 0.8958 (mp10) REVERT: e 49 GLU cc_start: 0.9105 (tp30) cc_final: 0.8891 (tp30) REVERT: e 56 GLN cc_start: 0.8233 (tp-100) cc_final: 0.7837 (tm-30) REVERT: e 58 ASN cc_start: 0.9226 (m-40) cc_final: 0.8977 (m110) REVERT: e 60 ASP cc_start: 0.8912 (m-30) cc_final: 0.8006 (m-30) REVERT: e 66 THR cc_start: 0.9231 (OUTLIER) cc_final: 0.8930 (t) REVERT: e 106 ARG cc_start: 0.8990 (ttm-80) cc_final: 0.8372 (mtt-85) REVERT: e 110 GLU cc_start: 0.8133 (pp20) cc_final: 0.7824 (pt0) REVERT: e 137 LYS cc_start: 0.9337 (tttm) cc_final: 0.9084 (ttmt) outliers start: 64 outliers final: 21 residues processed: 467 average time/residue: 0.5701 time to fit residues: 303.0600 Evaluate side-chains 406 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 376 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 114 GLN Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 123 TYR Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 140 ASP Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 80 ARG Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 91 CYS Chi-restraints excluded: chain J residue 144 ASP Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain c residue 168 THR Chi-restraints excluded: chain c residue 253 ILE Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 55 MET Chi-restraints excluded: chain d residue 93 ILE Chi-restraints excluded: chain d residue 186 ILE Chi-restraints excluded: chain e residue 66 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 71 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 155 optimal weight: 0.9990 chunk 150 optimal weight: 0.6980 chunk 61 optimal weight: 0.0030 chunk 198 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 112 GLN C 159 ASN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN G 53 GLN J 61 GLN J 65 GLN J 189 HIS d 29 GLN e 88 GLN e 123 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.083318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.069567 restraints weight = 57841.838| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.03 r_work: 0.2953 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22085 Z= 0.139 Angle : 0.579 8.062 29931 Z= 0.300 Chirality : 0.042 0.207 3472 Planarity : 0.004 0.058 3821 Dihedral : 4.383 22.134 3075 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.67 % Favored : 97.26 % Rotamer: Outliers : 2.81 % Allowed : 20.98 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.16), residues: 2808 helix: 2.06 (0.15), residues: 1135 sheet: -1.14 (0.20), residues: 616 loop : -1.08 (0.18), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 168 TYR 0.022 0.001 TYR H 90 PHE 0.018 0.001 PHE G 210 TRP 0.015 0.001 TRP D 100 HIS 0.007 0.001 HIS D 155 Details of bonding type rmsd covalent geometry : bond 0.00318 (22084) covalent geometry : angle 0.57838 (29929) SS BOND : bond 0.00370 ( 1) SS BOND : angle 4.26300 ( 2) hydrogen bonds : bond 0.03875 ( 1201) hydrogen bonds : angle 5.08122 ( 3474) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 418 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8554 (mp0) REVERT: A 57 TYR cc_start: 0.8038 (m-80) cc_final: 0.7597 (m-80) REVERT: A 79 MET cc_start: 0.8699 (mmt) cc_final: 0.8200 (mtt) REVERT: A 103 GLU cc_start: 0.8799 (tp30) cc_final: 0.8394 (tt0) REVERT: A 212 ILE cc_start: 0.9457 (pt) cc_final: 0.9228 (pp) REVERT: A 233 ILE cc_start: 0.8910 (mm) cc_final: 0.8634 (mm) REVERT: B 41 ASP cc_start: 0.8650 (m-30) cc_final: 0.8443 (m-30) REVERT: B 174 MET cc_start: 0.8886 (ttm) cc_final: 0.8242 (ttp) REVERT: C 16 LEU cc_start: 0.8807 (mp) cc_final: 0.8497 (mm) REVERT: C 20 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.8502 (mp0) REVERT: C 120 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8088 (mm-40) REVERT: D 7 GLU cc_start: 0.7986 (tp30) cc_final: 0.7623 (tp30) REVERT: D 8 TYR cc_start: 0.9138 (m-80) cc_final: 0.8930 (m-80) REVERT: D 84 ASP cc_start: 0.8936 (m-30) cc_final: 0.8679 (p0) REVERT: D 91 LYS cc_start: 0.9063 (tptp) cc_final: 0.8832 (tptp) REVERT: D 114 GLN cc_start: 0.8850 (tt0) cc_final: 0.8170 (tm-30) REVERT: D 168 ARG cc_start: 0.8849 (tpt-90) cc_final: 0.8622 (tpt-90) REVERT: D 191 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.6982 (mt) REVERT: E 9 ASP cc_start: 0.8727 (t0) cc_final: 0.8506 (t0) REVERT: E 72 ILE cc_start: 0.9432 (pt) cc_final: 0.9154 (pp) REVERT: E 125 ARG cc_start: 0.8076 (mmt180) cc_final: 0.7571 (mtp85) REVERT: F 94 GLU cc_start: 0.8866 (mp0) cc_final: 0.8662 (mp0) REVERT: F 151 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8207 (tmm) REVERT: F 203 ASP cc_start: 0.7863 (t0) cc_final: 0.7493 (t0) REVERT: G 83 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8862 (mtt) REVERT: G 209 ASP cc_start: 0.8728 (OUTLIER) cc_final: 0.8291 (m-30) REVERT: H -22 ASN cc_start: 0.8862 (t0) cc_final: 0.7319 (t0) REVERT: H -18 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8453 (mp0) REVERT: H -3 LYS cc_start: 0.8960 (mtpt) cc_final: 0.8677 (mtpm) REVERT: I 75 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8806 (mt-10) REVERT: I 90 MET cc_start: 0.9334 (mtp) cc_final: 0.9106 (mtm) REVERT: I 198 ARG cc_start: 0.8253 (mtm-85) cc_final: 0.7883 (mtm-85) REVERT: J 37 LYS cc_start: 0.8742 (ptmm) cc_final: 0.8515 (tttm) REVERT: J 91 CYS cc_start: 0.8487 (OUTLIER) cc_final: 0.7740 (t) REVERT: J 93 ARG cc_start: 0.8769 (mtm110) cc_final: 0.8506 (mtm-85) REVERT: d 32 MET cc_start: 0.9192 (mmm) cc_final: 0.8652 (mmm) REVERT: d 229 GLN cc_start: 0.9382 (mt0) cc_final: 0.8983 (mp10) REVERT: e 49 GLU cc_start: 0.9111 (tp30) cc_final: 0.8688 (tp30) REVERT: e 56 GLN cc_start: 0.8299 (tp-100) cc_final: 0.7967 (tm-30) REVERT: e 58 ASN cc_start: 0.9258 (m-40) cc_final: 0.8998 (m110) REVERT: e 60 ASP cc_start: 0.8900 (m-30) cc_final: 0.8107 (m-30) REVERT: e 66 THR cc_start: 0.9242 (m) cc_final: 0.8956 (t) REVERT: e 106 ARG cc_start: 0.9002 (ttm-80) cc_final: 0.8433 (mtt-85) REVERT: e 110 GLU cc_start: 0.8278 (pp20) cc_final: 0.7946 (pt0) REVERT: e 137 LYS cc_start: 0.9415 (tttm) cc_final: 0.9178 (ttmt) outliers start: 63 outliers final: 20 residues processed: 456 average time/residue: 0.5918 time to fit residues: 308.2059 Evaluate side-chains 400 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 372 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 123 TYR Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain H residue -5 VAL Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 91 CYS Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain c residue 77 ASN Chi-restraints excluded: chain c residue 253 ILE Chi-restraints excluded: chain c residue 262 LEU Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 186 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 253 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 222 optimal weight: 6.9990 chunk 160 optimal weight: 0.0370 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN B 84 ASN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 GLN ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 GLN J 61 GLN J 63 ASN J 65 GLN e 63 ASN e 87 GLN e 88 GLN e 123 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.081841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.067997 restraints weight = 58007.889| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 3.02 r_work: 0.2912 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 22085 Z= 0.153 Angle : 0.590 8.864 29931 Z= 0.304 Chirality : 0.042 0.223 3472 Planarity : 0.004 0.055 3821 Dihedral : 4.338 22.453 3075 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.92 % Favored : 97.01 % Rotamer: Outliers : 4.29 % Allowed : 20.58 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.16), residues: 2808 helix: 2.10 (0.15), residues: 1130 sheet: -0.93 (0.20), residues: 605 loop : -0.97 (0.18), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 168 TYR 0.026 0.001 TYR H 90 PHE 0.015 0.001 PHE G 210 TRP 0.017 0.001 TRP D 100 HIS 0.006 0.001 HIS D 155 Details of bonding type rmsd covalent geometry : bond 0.00356 (22084) covalent geometry : angle 0.58921 (29929) SS BOND : bond 0.01641 ( 1) SS BOND : angle 4.80642 ( 2) hydrogen bonds : bond 0.03804 ( 1201) hydrogen bonds : angle 4.93362 ( 3474) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 434 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 MET cc_start: 0.8786 (mmt) cc_final: 0.8484 (mtt) REVERT: A 103 GLU cc_start: 0.8835 (tp30) cc_final: 0.8400 (tt0) REVERT: A 212 ILE cc_start: 0.9471 (pt) cc_final: 0.9224 (pp) REVERT: A 233 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8722 (mm) REVERT: B 41 ASP cc_start: 0.8764 (m-30) cc_final: 0.8491 (m-30) REVERT: C 16 LEU cc_start: 0.8833 (mp) cc_final: 0.8528 (mm) REVERT: C 20 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8539 (mp0) REVERT: C 39 ASP cc_start: 0.8809 (m-30) cc_final: 0.8497 (m-30) REVERT: C 120 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8071 (mm-40) REVERT: C 178 ASP cc_start: 0.8368 (p0) cc_final: 0.7789 (t0) REVERT: D 7 GLU cc_start: 0.8041 (tp30) cc_final: 0.7671 (tp30) REVERT: D 8 TYR cc_start: 0.9221 (m-80) cc_final: 0.9015 (m-80) REVERT: D 51 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7297 (pp20) REVERT: D 86 LYS cc_start: 0.8826 (mmtt) cc_final: 0.8522 (mmmt) REVERT: D 168 ARG cc_start: 0.8919 (tpt-90) cc_final: 0.8686 (tpt-90) REVERT: E 27 GLU cc_start: 0.9268 (mm-30) cc_final: 0.8726 (mm-30) REVERT: E 72 ILE cc_start: 0.9417 (pt) cc_final: 0.9143 (pp) REVERT: E 125 ARG cc_start: 0.8126 (mmt180) cc_final: 0.7640 (mtp85) REVERT: F 94 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8660 (mp0) REVERT: G 3 ARG cc_start: 0.8358 (mpp80) cc_final: 0.7049 (mmm160) REVERT: G 112 ASP cc_start: 0.8870 (p0) cc_final: 0.8614 (p0) REVERT: G 209 ASP cc_start: 0.8797 (OUTLIER) cc_final: 0.8446 (m-30) REVERT: H -22 ASN cc_start: 0.8911 (t0) cc_final: 0.7596 (m-40) REVERT: H -18 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8471 (mp0) REVERT: H -3 LYS cc_start: 0.9131 (mtpt) cc_final: 0.8653 (mtpm) REVERT: H 215 LYS cc_start: 0.9076 (pptt) cc_final: 0.8633 (pptt) REVERT: I 78 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8683 (mt-10) REVERT: I 80 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8405 (ptt-90) REVERT: I 90 MET cc_start: 0.9340 (mtp) cc_final: 0.9088 (mtm) REVERT: I 104 TYR cc_start: 0.8284 (m-80) cc_final: 0.7905 (m-80) REVERT: I 131 MET cc_start: 0.8692 (tmm) cc_final: 0.8441 (tpp) REVERT: I 189 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8468 (pp) REVERT: J 15 VAL cc_start: 0.9029 (m) cc_final: 0.8736 (m) REVERT: J 37 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8592 (tttm) REVERT: J 65 GLN cc_start: 0.9189 (tp40) cc_final: 0.8974 (tm-30) REVERT: J 74 GLU cc_start: 0.8640 (pm20) cc_final: 0.8344 (mt-10) REVERT: J 90 ASP cc_start: 0.9448 (t0) cc_final: 0.8993 (t0) REVERT: J 93 ARG cc_start: 0.8850 (mtm110) cc_final: 0.8116 (mtm-85) REVERT: c 8 GLU cc_start: 0.8703 (tp30) cc_final: 0.8406 (tp30) REVERT: c 143 GLU cc_start: 0.8942 (pm20) cc_final: 0.8588 (pm20) REVERT: d 229 GLN cc_start: 0.9390 (mt0) cc_final: 0.9013 (mp10) REVERT: e 56 GLN cc_start: 0.8301 (tp-100) cc_final: 0.7934 (tm-30) REVERT: e 60 ASP cc_start: 0.8927 (m-30) cc_final: 0.8102 (m-30) REVERT: e 66 THR cc_start: 0.9268 (m) cc_final: 0.8980 (t) REVERT: e 106 ARG cc_start: 0.9005 (ttm-80) cc_final: 0.8377 (mtt-85) REVERT: e 110 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8163 (pt0) REVERT: e 129 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8589 (tm-30) REVERT: e 137 LYS cc_start: 0.9470 (tttm) cc_final: 0.9259 (tttt) outliers start: 96 outliers final: 27 residues processed: 486 average time/residue: 0.5801 time to fit residues: 320.3855 Evaluate side-chains 416 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 379 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 123 TYR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain H residue -39 SER Chi-restraints excluded: chain H residue -5 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 80 ARG Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 37 LYS Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain c residue 83 LEU Chi-restraints excluded: chain c residue 168 THR Chi-restraints excluded: chain c residue 253 ILE Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 93 ILE Chi-restraints excluded: chain d residue 131 ASP Chi-restraints excluded: chain e residue 54 ASN Chi-restraints excluded: chain e residue 65 SER Chi-restraints excluded: chain e residue 68 ARG Chi-restraints excluded: chain e residue 110 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 230 optimal weight: 1.9990 chunk 203 optimal weight: 4.9990 chunk 136 optimal weight: 0.7980 chunk 168 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 241 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 226 optimal weight: 0.8980 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 148 GLN B 220 ASN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 ASN G 33 ASN I 93 ASN J 61 GLN c 195 GLN c 268 GLN d 29 GLN e 63 ASN e 87 GLN e 123 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.080092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.066366 restraints weight = 58184.121| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.00 r_work: 0.2888 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 22085 Z= 0.166 Angle : 0.598 9.637 29931 Z= 0.309 Chirality : 0.042 0.185 3472 Planarity : 0.004 0.053 3821 Dihedral : 4.384 23.476 3075 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.13 % Favored : 96.79 % Rotamer: Outliers : 3.44 % Allowed : 22.72 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.16), residues: 2808 helix: 2.20 (0.15), residues: 1125 sheet: -0.79 (0.20), residues: 616 loop : -0.90 (0.19), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 198 TYR 0.028 0.001 TYR C 153 PHE 0.012 0.001 PHE I 69 TRP 0.011 0.001 TRP G 189 HIS 0.006 0.001 HIS D 155 Details of bonding type rmsd covalent geometry : bond 0.00391 (22084) covalent geometry : angle 0.59663 (29929) SS BOND : bond 0.00619 ( 1) SS BOND : angle 5.53103 ( 2) hydrogen bonds : bond 0.03820 ( 1201) hydrogen bonds : angle 4.90393 ( 3474) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 414 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 MET cc_start: 0.8819 (mmt) cc_final: 0.8542 (mtt) REVERT: A 103 GLU cc_start: 0.8827 (tp30) cc_final: 0.8419 (tt0) REVERT: A 212 ILE cc_start: 0.9480 (pt) cc_final: 0.9244 (pp) REVERT: A 233 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8730 (mm) REVERT: B 41 ASP cc_start: 0.8779 (m-30) cc_final: 0.8530 (m-30) REVERT: B 178 ASP cc_start: 0.8799 (m-30) cc_final: 0.8367 (m-30) REVERT: B 199 LYS cc_start: 0.9386 (tmtt) cc_final: 0.9139 (tmmt) REVERT: C 16 LEU cc_start: 0.8924 (mp) cc_final: 0.8621 (mm) REVERT: C 20 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8577 (mp0) REVERT: C 120 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8127 (mm-40) REVERT: C 219 ILE cc_start: 0.9286 (pp) cc_final: 0.9079 (mm) REVERT: D 7 GLU cc_start: 0.8065 (tp30) cc_final: 0.7788 (tp30) REVERT: D 51 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7229 (pp20) REVERT: D 107 MET cc_start: 0.8469 (tpt) cc_final: 0.8255 (mmt) REVERT: D 117 SER cc_start: 0.8855 (OUTLIER) cc_final: 0.8545 (t) REVERT: D 182 GLN cc_start: 0.8879 (pp30) cc_final: 0.8629 (pp30) REVERT: D 191 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7368 (tp) REVERT: E 27 GLU cc_start: 0.9263 (mm-30) cc_final: 0.8746 (mm-30) REVERT: E 72 ILE cc_start: 0.9426 (pt) cc_final: 0.9167 (pp) REVERT: E 125 ARG cc_start: 0.8140 (mmt180) cc_final: 0.7684 (mtp85) REVERT: F 29 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8904 (ttpt) REVERT: F 94 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8642 (mp0) REVERT: F 151 MET cc_start: 0.8934 (tmm) cc_final: 0.8668 (tmt) REVERT: F 153 ASP cc_start: 0.8668 (m-30) cc_final: 0.8460 (m-30) REVERT: F 203 ASP cc_start: 0.7933 (t0) cc_final: 0.7539 (t0) REVERT: G 3 ARG cc_start: 0.8481 (mpp80) cc_final: 0.7142 (mmm160) REVERT: G 58 ASP cc_start: 0.7705 (p0) cc_final: 0.7316 (p0) REVERT: G 209 ASP cc_start: 0.8812 (OUTLIER) cc_final: 0.8485 (m-30) REVERT: H -27 ASP cc_start: 0.9099 (p0) cc_final: 0.8877 (p0) REVERT: H -22 ASN cc_start: 0.8913 (t0) cc_final: 0.7258 (t0) REVERT: H -18 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8348 (mp0) REVERT: H -3 LYS cc_start: 0.9220 (mtpt) cc_final: 0.8943 (mtmm) REVERT: H 146 MET cc_start: 0.6805 (mmp) cc_final: 0.6518 (tpp) REVERT: H 215 LYS cc_start: 0.8866 (pptt) cc_final: 0.8606 (pptt) REVERT: I 80 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8407 (ptt-90) REVERT: I 90 MET cc_start: 0.9350 (mtp) cc_final: 0.9086 (mtm) REVERT: I 131 MET cc_start: 0.8717 (tmm) cc_final: 0.8496 (tpp) REVERT: I 189 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8490 (pp) REVERT: J 12 TYR cc_start: 0.8146 (p90) cc_final: 0.7879 (p90) REVERT: J 37 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8759 (tttm) REVERT: J 74 GLU cc_start: 0.8649 (pm20) cc_final: 0.8406 (mt-10) REVERT: c 8 GLU cc_start: 0.8690 (tp30) cc_final: 0.8399 (tp30) REVERT: c 36 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8166 (tm-30) REVERT: c 40 GLN cc_start: 0.8710 (mm110) cc_final: 0.8428 (mm110) REVERT: c 52 ARG cc_start: 0.7081 (tpt-90) cc_final: 0.6865 (tpp80) REVERT: c 148 GLN cc_start: 0.8797 (mt0) cc_final: 0.8434 (mt0) REVERT: d 229 GLN cc_start: 0.9379 (mt0) cc_final: 0.8950 (mp10) REVERT: e 56 GLN cc_start: 0.8382 (tp-100) cc_final: 0.7939 (tm-30) REVERT: e 60 ASP cc_start: 0.8939 (m-30) cc_final: 0.8055 (m-30) REVERT: e 66 THR cc_start: 0.9315 (OUTLIER) cc_final: 0.9036 (t) REVERT: e 106 ARG cc_start: 0.9033 (ttm-80) cc_final: 0.8418 (mtt-85) REVERT: e 129 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8632 (tm-30) REVERT: e 137 LYS cc_start: 0.9475 (tttm) cc_final: 0.9252 (tttt) outliers start: 77 outliers final: 34 residues processed: 456 average time/residue: 0.5588 time to fit residues: 290.0320 Evaluate side-chains 424 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 377 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 123 TYR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain H residue -39 SER Chi-restraints excluded: chain H residue -5 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 80 ARG Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 37 LYS Chi-restraints excluded: chain c residue 49 LEU Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain c residue 77 ASN Chi-restraints excluded: chain c residue 132 VAL Chi-restraints excluded: chain c residue 168 THR Chi-restraints excluded: chain c residue 238 ASP Chi-restraints excluded: chain c residue 253 ILE Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 63 THR Chi-restraints excluded: chain d residue 93 ILE Chi-restraints excluded: chain d residue 131 ASP Chi-restraints excluded: chain d residue 186 ILE Chi-restraints excluded: chain e residue 54 ASN Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 97 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 189 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 267 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 GLN G 33 ASN J 61 GLN J 63 ASN J 65 GLN ** c 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 63 ASN e 87 GLN e 88 GLN e 123 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.079436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.065753 restraints weight = 58413.203| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 3.01 r_work: 0.2876 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 22085 Z= 0.171 Angle : 0.599 10.506 29931 Z= 0.309 Chirality : 0.042 0.199 3472 Planarity : 0.004 0.054 3821 Dihedral : 4.390 24.668 3075 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.10 % Favored : 96.83 % Rotamer: Outliers : 3.48 % Allowed : 23.57 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.16), residues: 2808 helix: 2.20 (0.15), residues: 1126 sheet: -0.76 (0.20), residues: 617 loop : -0.84 (0.18), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 168 TYR 0.029 0.001 TYR C 153 PHE 0.021 0.001 PHE J 36 TRP 0.013 0.001 TRP G 189 HIS 0.007 0.001 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.00400 (22084) covalent geometry : angle 0.59785 (29929) SS BOND : bond 0.00600 ( 1) SS BOND : angle 5.26378 ( 2) hydrogen bonds : bond 0.03827 ( 1201) hydrogen bonds : angle 4.87069 ( 3474) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 388 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 MET cc_start: 0.8827 (mmt) cc_final: 0.8559 (mtt) REVERT: A 103 GLU cc_start: 0.8834 (tp30) cc_final: 0.8409 (tt0) REVERT: A 212 ILE cc_start: 0.9477 (pt) cc_final: 0.9240 (pp) REVERT: A 233 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8734 (mm) REVERT: B 41 ASP cc_start: 0.8804 (m-30) cc_final: 0.8559 (m-30) REVERT: B 178 ASP cc_start: 0.8697 (m-30) cc_final: 0.8374 (m-30) REVERT: B 199 LYS cc_start: 0.9358 (tmtt) cc_final: 0.9069 (tmmt) REVERT: B 236 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9202 (mm) REVERT: C 8 THR cc_start: 0.9146 (m) cc_final: 0.8865 (p) REVERT: C 39 ASP cc_start: 0.8803 (m-30) cc_final: 0.8495 (m-30) REVERT: C 120 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8007 (mm-40) REVERT: C 178 ASP cc_start: 0.8406 (p0) cc_final: 0.7940 (t0) REVERT: D 7 GLU cc_start: 0.8071 (tp30) cc_final: 0.7805 (tp30) REVERT: D 86 LYS cc_start: 0.8867 (mmtt) cc_final: 0.8653 (mmmt) REVERT: D 117 SER cc_start: 0.8832 (OUTLIER) cc_final: 0.8609 (t) REVERT: D 182 GLN cc_start: 0.8876 (pp30) cc_final: 0.8527 (pp30) REVERT: E 27 GLU cc_start: 0.9253 (mm-30) cc_final: 0.8753 (mm-30) REVERT: E 72 ILE cc_start: 0.9414 (pt) cc_final: 0.9133 (pp) REVERT: E 125 ARG cc_start: 0.8111 (mmt180) cc_final: 0.7610 (mtp85) REVERT: F 71 ASP cc_start: 0.8635 (t0) cc_final: 0.8375 (t0) REVERT: F 94 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8623 (mp0) REVERT: F 151 MET cc_start: 0.8927 (tmm) cc_final: 0.8450 (tmt) REVERT: F 203 ASP cc_start: 0.7950 (t0) cc_final: 0.7557 (t0) REVERT: G 3 ARG cc_start: 0.8493 (mpp80) cc_final: 0.7167 (mmm160) REVERT: G 209 ASP cc_start: 0.8893 (OUTLIER) cc_final: 0.8608 (m-30) REVERT: H -27 ASP cc_start: 0.9106 (p0) cc_final: 0.8876 (p0) REVERT: H -22 ASN cc_start: 0.8924 (OUTLIER) cc_final: 0.7216 (t0) REVERT: H -18 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8223 (mp0) REVERT: H -3 LYS cc_start: 0.9270 (mtpt) cc_final: 0.8991 (mtmm) REVERT: H 146 MET cc_start: 0.6797 (mmp) cc_final: 0.6589 (mmp) REVERT: H 215 LYS cc_start: 0.8799 (pptt) cc_final: 0.8466 (pptt) REVERT: I 75 GLU cc_start: 0.9105 (mt-10) cc_final: 0.8894 (mt-10) REVERT: I 80 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8285 (ptt-90) REVERT: I 90 MET cc_start: 0.9330 (mtp) cc_final: 0.9118 (mtm) REVERT: I 189 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8498 (pp) REVERT: J 12 TYR cc_start: 0.8191 (p90) cc_final: 0.7819 (p90) REVERT: J 37 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8753 (tttm) REVERT: J 74 GLU cc_start: 0.8635 (pm20) cc_final: 0.8364 (mt-10) REVERT: J 86 ARG cc_start: 0.9171 (OUTLIER) cc_final: 0.8232 (ttm170) REVERT: J 142 ILE cc_start: 0.8789 (mp) cc_final: 0.8256 (tt) REVERT: c 40 GLN cc_start: 0.8733 (mm110) cc_final: 0.8503 (mm110) REVERT: c 77 ASN cc_start: 0.8896 (OUTLIER) cc_final: 0.8603 (p0) REVERT: c 240 MET cc_start: 0.8729 (mtp) cc_final: 0.8248 (mmm) REVERT: d 229 GLN cc_start: 0.9373 (mt0) cc_final: 0.8958 (mp10) REVERT: e 56 GLN cc_start: 0.8396 (tp-100) cc_final: 0.7940 (tm-30) REVERT: e 60 ASP cc_start: 0.8960 (m-30) cc_final: 0.8036 (m-30) REVERT: e 66 THR cc_start: 0.9304 (OUTLIER) cc_final: 0.9026 (t) REVERT: e 106 ARG cc_start: 0.8995 (ttm-80) cc_final: 0.8406 (mtt-85) REVERT: e 129 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8587 (tm-30) REVERT: e 137 LYS cc_start: 0.9485 (tttm) cc_final: 0.9273 (tttt) outliers start: 78 outliers final: 36 residues processed: 433 average time/residue: 0.5258 time to fit residues: 260.4790 Evaluate side-chains 407 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 358 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 123 TYR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain H residue -39 SER Chi-restraints excluded: chain H residue -22 ASN Chi-restraints excluded: chain H residue -5 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 80 ARG Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain I residue 142 CYS Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 37 LYS Chi-restraints excluded: chain J residue 86 ARG Chi-restraints excluded: chain c residue 49 LEU Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain c residue 77 ASN Chi-restraints excluded: chain c residue 83 LEU Chi-restraints excluded: chain c residue 132 VAL Chi-restraints excluded: chain c residue 168 THR Chi-restraints excluded: chain c residue 253 ILE Chi-restraints excluded: chain d residue 63 THR Chi-restraints excluded: chain d residue 93 ILE Chi-restraints excluded: chain d residue 123 SER Chi-restraints excluded: chain d residue 131 ASP Chi-restraints excluded: chain d residue 186 ILE Chi-restraints excluded: chain d residue 201 MET Chi-restraints excluded: chain e residue 54 ASN Chi-restraints excluded: chain e residue 65 SER Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 97 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 144 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 228 optimal weight: 0.9990 chunk 154 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 260 optimal weight: 0.8980 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 96 GLN A 148 GLN B 220 ASN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 GLN G 33 ASN G 75 ASN H 91 GLN J 61 GLN J 65 GLN c 78 ASN ** c 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 195 GLN e 63 ASN e 87 GLN e 123 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.079999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.066406 restraints weight = 58531.899| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.02 r_work: 0.2889 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22085 Z= 0.139 Angle : 0.592 11.143 29931 Z= 0.303 Chirality : 0.042 0.170 3472 Planarity : 0.004 0.055 3821 Dihedral : 4.337 26.601 3075 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.96 % Favored : 96.97 % Rotamer: Outliers : 3.66 % Allowed : 23.93 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.16), residues: 2808 helix: 2.26 (0.15), residues: 1125 sheet: -0.73 (0.20), residues: 626 loop : -0.76 (0.19), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 168 TYR 0.030 0.001 TYR C 153 PHE 0.017 0.001 PHE c 71 TRP 0.011 0.001 TRP G 189 HIS 0.007 0.001 HIS D 155 Details of bonding type rmsd covalent geometry : bond 0.00326 (22084) covalent geometry : angle 0.59073 (29929) SS BOND : bond 0.00176 ( 1) SS BOND : angle 5.34438 ( 2) hydrogen bonds : bond 0.03604 ( 1201) hydrogen bonds : angle 4.76923 ( 3474) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 399 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8810 (tp30) cc_final: 0.8316 (tt0) REVERT: A 212 ILE cc_start: 0.9459 (pt) cc_final: 0.9213 (pp) REVERT: A 233 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8741 (mm) REVERT: B 41 ASP cc_start: 0.8802 (m-30) cc_final: 0.8558 (m-30) REVERT: B 199 LYS cc_start: 0.9380 (tmtt) cc_final: 0.9162 (tmmt) REVERT: C 175 ASN cc_start: 0.9194 (m-40) cc_final: 0.8933 (m-40) REVERT: D 7 GLU cc_start: 0.8104 (tp30) cc_final: 0.7852 (tp30) REVERT: D 117 SER cc_start: 0.8845 (OUTLIER) cc_final: 0.8636 (t) REVERT: D 191 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7400 (tp) REVERT: E 27 GLU cc_start: 0.9250 (mm-30) cc_final: 0.8788 (mm-30) REVERT: E 72 ILE cc_start: 0.9400 (pt) cc_final: 0.9086 (pp) REVERT: E 125 ARG cc_start: 0.8088 (mmt180) cc_final: 0.7590 (mtp85) REVERT: F 29 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8871 (ttpt) REVERT: F 94 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8639 (mp0) REVERT: F 151 MET cc_start: 0.8912 (tmm) cc_final: 0.8651 (tmt) REVERT: F 153 ASP cc_start: 0.8776 (m-30) cc_final: 0.8422 (m-30) REVERT: G 3 ARG cc_start: 0.8409 (mpp80) cc_final: 0.7090 (mmm160) REVERT: G 209 ASP cc_start: 0.8912 (OUTLIER) cc_final: 0.8649 (m-30) REVERT: H -27 ASP cc_start: 0.9109 (p0) cc_final: 0.8865 (p0) REVERT: H -22 ASN cc_start: 0.8901 (OUTLIER) cc_final: 0.7534 (t0) REVERT: H -18 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8363 (mp0) REVERT: H -3 LYS cc_start: 0.9343 (mtpt) cc_final: 0.9045 (mtmm) REVERT: H 215 LYS cc_start: 0.8684 (pptt) cc_final: 0.8304 (pptt) REVERT: I 80 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8159 (ptt-90) REVERT: I 90 MET cc_start: 0.9340 (mtp) cc_final: 0.9056 (mtm) REVERT: I 189 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8442 (pp) REVERT: I 198 ARG cc_start: 0.8470 (mtm-85) cc_final: 0.8187 (mtm-85) REVERT: J 12 TYR cc_start: 0.8163 (p90) cc_final: 0.7729 (p90) REVERT: J 17 SER cc_start: 0.8890 (p) cc_final: 0.8675 (t) REVERT: J 37 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8575 (tttm) REVERT: J 74 GLU cc_start: 0.8673 (pm20) cc_final: 0.8410 (mt-10) REVERT: J 142 ILE cc_start: 0.8710 (mp) cc_final: 0.8230 (tt) REVERT: J 159 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8570 (tp) REVERT: c 52 ARG cc_start: 0.7040 (tpp80) cc_final: 0.6757 (tpp80) REVERT: c 77 ASN cc_start: 0.8871 (OUTLIER) cc_final: 0.8663 (p0) REVERT: d 43 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8743 (ttmt) REVERT: d 229 GLN cc_start: 0.9379 (mt0) cc_final: 0.8953 (mp10) REVERT: e 56 GLN cc_start: 0.8323 (tp-100) cc_final: 0.7838 (tm-30) REVERT: e 60 ASP cc_start: 0.8960 (m-30) cc_final: 0.8087 (m-30) REVERT: e 66 THR cc_start: 0.9295 (m) cc_final: 0.9030 (t) REVERT: e 106 ARG cc_start: 0.8977 (ttm-80) cc_final: 0.8418 (mtt-85) REVERT: e 129 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8550 (tm-30) outliers start: 82 outliers final: 35 residues processed: 451 average time/residue: 0.5217 time to fit residues: 269.0693 Evaluate side-chains 416 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 368 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain E residue 123 TYR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain H residue -39 SER Chi-restraints excluded: chain H residue -22 ASN Chi-restraints excluded: chain H residue -5 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 80 ARG Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain I residue 142 CYS Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 37 LYS Chi-restraints excluded: chain J residue 55 GLN Chi-restraints excluded: chain J residue 159 LEU Chi-restraints excluded: chain c residue 49 LEU Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain c residue 77 ASN Chi-restraints excluded: chain c residue 83 LEU Chi-restraints excluded: chain c residue 132 VAL Chi-restraints excluded: chain c residue 168 THR Chi-restraints excluded: chain c residue 253 ILE Chi-restraints excluded: chain c residue 263 VAL Chi-restraints excluded: chain d residue 43 LYS Chi-restraints excluded: chain d residue 63 THR Chi-restraints excluded: chain d residue 93 ILE Chi-restraints excluded: chain d residue 123 SER Chi-restraints excluded: chain d residue 201 MET Chi-restraints excluded: chain e residue 50 LEU Chi-restraints excluded: chain e residue 54 ASN Chi-restraints excluded: chain e residue 65 SER Chi-restraints excluded: chain e residue 97 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 204 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 192 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 243 optimal weight: 0.9990 chunk 239 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 148 GLN B 220 ASN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 GLN E 69 HIS E 175 HIS G 33 ASN H 85 GLN H 91 GLN J 61 GLN c 148 GLN e 63 ASN e 87 GLN e 88 GLN e 123 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.079432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.065922 restraints weight = 58434.447| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.01 r_work: 0.2880 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22085 Z= 0.152 Angle : 0.617 11.384 29931 Z= 0.313 Chirality : 0.042 0.312 3472 Planarity : 0.004 0.056 3821 Dihedral : 4.349 23.843 3075 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.13 % Favored : 96.79 % Rotamer: Outliers : 3.21 % Allowed : 24.91 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.16), residues: 2808 helix: 2.24 (0.15), residues: 1126 sheet: -0.69 (0.20), residues: 640 loop : -0.70 (0.19), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 168 TYR 0.031 0.001 TYR C 153 PHE 0.019 0.001 PHE c 71 TRP 0.012 0.001 TRP D 100 HIS 0.008 0.001 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.00356 (22084) covalent geometry : angle 0.61627 (29929) SS BOND : bond 0.00904 ( 1) SS BOND : angle 4.07969 ( 2) hydrogen bonds : bond 0.03660 ( 1201) hydrogen bonds : angle 4.77826 ( 3474) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 398 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8766 (tp30) cc_final: 0.8300 (tt0) REVERT: A 212 ILE cc_start: 0.9451 (pt) cc_final: 0.9219 (pp) REVERT: A 233 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8755 (mm) REVERT: B 41 ASP cc_start: 0.8824 (m-30) cc_final: 0.8600 (m-30) REVERT: B 72 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8701 (mtm) REVERT: B 199 LYS cc_start: 0.9369 (tmtt) cc_final: 0.9127 (tmmt) REVERT: C 39 ASP cc_start: 0.8808 (m-30) cc_final: 0.8504 (m-30) REVERT: C 175 ASN cc_start: 0.9244 (m-40) cc_final: 0.9005 (m-40) REVERT: C 178 ASP cc_start: 0.8447 (p0) cc_final: 0.8180 (t0) REVERT: D 7 GLU cc_start: 0.8110 (tp30) cc_final: 0.7858 (tp30) REVERT: D 53 ARG cc_start: 0.9100 (mmm-85) cc_final: 0.8750 (mpp80) REVERT: D 117 SER cc_start: 0.8822 (OUTLIER) cc_final: 0.8605 (t) REVERT: D 182 GLN cc_start: 0.8885 (pp30) cc_final: 0.8574 (pp30) REVERT: D 191 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7510 (tp) REVERT: E 8 ASN cc_start: 0.9234 (p0) cc_final: 0.8787 (m-40) REVERT: E 27 GLU cc_start: 0.9248 (mm-30) cc_final: 0.8766 (mm-30) REVERT: E 72 ILE cc_start: 0.9384 (pt) cc_final: 0.9093 (pp) REVERT: E 125 ARG cc_start: 0.8042 (mmt180) cc_final: 0.7571 (mtp85) REVERT: F 29 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8891 (ttpt) REVERT: F 94 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8595 (mp0) REVERT: F 151 MET cc_start: 0.8898 (tmm) cc_final: 0.8500 (tmt) REVERT: F 203 ASP cc_start: 0.8020 (t0) cc_final: 0.7624 (t0) REVERT: G 3 ARG cc_start: 0.8432 (mpp80) cc_final: 0.7126 (mmm160) REVERT: G 209 ASP cc_start: 0.8904 (OUTLIER) cc_final: 0.8676 (m-30) REVERT: H -39 SER cc_start: 0.5905 (OUTLIER) cc_final: 0.5229 (p) REVERT: H -27 ASP cc_start: 0.9094 (p0) cc_final: 0.8855 (p0) REVERT: H -22 ASN cc_start: 0.8879 (OUTLIER) cc_final: 0.7215 (t0) REVERT: H -18 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8254 (mp0) REVERT: H -3 LYS cc_start: 0.9348 (mtpt) cc_final: 0.9075 (mtmm) REVERT: H 12 ILE cc_start: 0.9539 (OUTLIER) cc_final: 0.9309 (mm) REVERT: H 149 GLU cc_start: 0.8779 (pm20) cc_final: 0.8477 (pm20) REVERT: H 215 LYS cc_start: 0.8646 (pptt) cc_final: 0.8244 (pptt) REVERT: I 75 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8839 (mm-30) REVERT: I 80 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8136 (ptt-90) REVERT: I 90 MET cc_start: 0.9386 (mtp) cc_final: 0.9186 (mtm) REVERT: I 189 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8510 (pp) REVERT: I 198 ARG cc_start: 0.8527 (mtm-85) cc_final: 0.8255 (mtm-85) REVERT: J 12 TYR cc_start: 0.8213 (p90) cc_final: 0.7702 (p90) REVERT: J 17 SER cc_start: 0.8942 (p) cc_final: 0.8688 (t) REVERT: J 37 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8614 (tttp) REVERT: J 69 MET cc_start: 0.8962 (ttp) cc_final: 0.8721 (ttm) REVERT: J 74 GLU cc_start: 0.8655 (pm20) cc_final: 0.8451 (mt-10) REVERT: c 40 GLN cc_start: 0.8058 (mm110) cc_final: 0.7812 (mm-40) REVERT: c 52 ARG cc_start: 0.7039 (tpp80) cc_final: 0.6801 (tpp80) REVERT: c 77 ASN cc_start: 0.8902 (OUTLIER) cc_final: 0.8653 (p0) REVERT: d 43 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8764 (ttmt) REVERT: d 229 GLN cc_start: 0.9366 (mt0) cc_final: 0.8969 (mp10) REVERT: e 56 GLN cc_start: 0.8356 (tp-100) cc_final: 0.7867 (tm-30) REVERT: e 60 ASP cc_start: 0.8958 (m-30) cc_final: 0.8105 (m-30) REVERT: e 66 THR cc_start: 0.9327 (m) cc_final: 0.9051 (t) REVERT: e 106 ARG cc_start: 0.9010 (ttm-80) cc_final: 0.8475 (mtt-85) REVERT: e 129 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8609 (tm-30) outliers start: 72 outliers final: 35 residues processed: 440 average time/residue: 0.5023 time to fit residues: 252.6144 Evaluate side-chains 424 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 374 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain E residue 123 TYR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain H residue -39 SER Chi-restraints excluded: chain H residue -22 ASN Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 80 ARG Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 37 LYS Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain c residue 49 LEU Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain c residue 77 ASN Chi-restraints excluded: chain c residue 83 LEU Chi-restraints excluded: chain c residue 132 VAL Chi-restraints excluded: chain c residue 199 ASP Chi-restraints excluded: chain c residue 253 ILE Chi-restraints excluded: chain c residue 263 VAL Chi-restraints excluded: chain d residue 43 LYS Chi-restraints excluded: chain d residue 63 THR Chi-restraints excluded: chain d residue 93 ILE Chi-restraints excluded: chain d residue 123 SER Chi-restraints excluded: chain d residue 131 ASP Chi-restraints excluded: chain d residue 186 ILE Chi-restraints excluded: chain d residue 201 MET Chi-restraints excluded: chain e residue 50 LEU Chi-restraints excluded: chain e residue 54 ASN Chi-restraints excluded: chain e residue 65 SER Chi-restraints excluded: chain e residue 97 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 61 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 210 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 chunk 270 optimal weight: 1.9990 chunk 231 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 230 optimal weight: 0.5980 chunk 173 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 125 optimal weight: 4.9990 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 96 GLN A 148 GLN B 220 ASN D 97 GLN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 GLN G 33 ASN H 85 GLN J 61 GLN c 78 ASN c 195 GLN e 63 ASN e 87 GLN e 123 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.079748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.066146 restraints weight = 58496.839| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.07 r_work: 0.2880 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22085 Z= 0.135 Angle : 0.632 13.417 29931 Z= 0.322 Chirality : 0.042 0.234 3472 Planarity : 0.004 0.055 3821 Dihedral : 4.352 25.522 3075 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.85 % Favored : 97.08 % Rotamer: Outliers : 2.72 % Allowed : 25.76 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.16), residues: 2808 helix: 2.22 (0.15), residues: 1130 sheet: -0.64 (0.20), residues: 632 loop : -0.70 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 168 TYR 0.031 0.001 TYR A 83 PHE 0.025 0.001 PHE c 71 TRP 0.013 0.001 TRP D 100 HIS 0.008 0.001 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.00313 (22084) covalent geometry : angle 0.63038 (29929) SS BOND : bond 0.01093 ( 1) SS BOND : angle 6.23969 ( 2) hydrogen bonds : bond 0.03556 ( 1201) hydrogen bonds : angle 4.77018 ( 3474) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 403 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8772 (tp30) cc_final: 0.8318 (tt0) REVERT: A 212 ILE cc_start: 0.9434 (pt) cc_final: 0.9190 (pp) REVERT: A 233 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8763 (mm) REVERT: B 41 ASP cc_start: 0.8840 (m-30) cc_final: 0.8607 (m-30) REVERT: B 199 LYS cc_start: 0.9401 (tmtt) cc_final: 0.9170 (tmmt) REVERT: C 20 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8614 (mp0) REVERT: C 39 ASP cc_start: 0.8811 (m-30) cc_final: 0.8497 (m-30) REVERT: C 175 ASN cc_start: 0.9235 (m-40) cc_final: 0.8992 (m-40) REVERT: C 178 ASP cc_start: 0.8463 (p0) cc_final: 0.8158 (t0) REVERT: D 7 GLU cc_start: 0.8155 (tp30) cc_final: 0.7878 (tp30) REVERT: D 10 ARG cc_start: 0.8477 (mmt180) cc_final: 0.8250 (mmt180) REVERT: D 53 ARG cc_start: 0.9113 (mmm-85) cc_final: 0.8832 (mpp80) REVERT: D 182 GLN cc_start: 0.8866 (pp30) cc_final: 0.8528 (pp30) REVERT: D 191 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7678 (tp) REVERT: E 8 ASN cc_start: 0.9224 (p0) cc_final: 0.8752 (m110) REVERT: E 27 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8759 (mm-30) REVERT: E 72 ILE cc_start: 0.9395 (pt) cc_final: 0.9083 (pp) REVERT: E 125 ARG cc_start: 0.8047 (mmt180) cc_final: 0.7530 (mtp85) REVERT: F 29 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8866 (ttpt) REVERT: F 151 MET cc_start: 0.8978 (tmm) cc_final: 0.8707 (tmt) REVERT: F 203 ASP cc_start: 0.7998 (t0) cc_final: 0.7597 (t0) REVERT: G 3 ARG cc_start: 0.8408 (mpp80) cc_final: 0.7078 (mmm160) REVERT: G 147 GLN cc_start: 0.9316 (mp10) cc_final: 0.8581 (mp10) REVERT: G 209 ASP cc_start: 0.8907 (OUTLIER) cc_final: 0.8702 (m-30) REVERT: H -39 SER cc_start: 0.5914 (OUTLIER) cc_final: 0.5259 (p) REVERT: H -27 ASP cc_start: 0.9067 (p0) cc_final: 0.8843 (p0) REVERT: H -22 ASN cc_start: 0.8856 (OUTLIER) cc_final: 0.7131 (t0) REVERT: H -18 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8214 (mp0) REVERT: H -3 LYS cc_start: 0.9351 (mtpt) cc_final: 0.9055 (mtmt) REVERT: H 12 ILE cc_start: 0.9538 (OUTLIER) cc_final: 0.9329 (mm) REVERT: H 215 LYS cc_start: 0.8650 (pptt) cc_final: 0.8249 (pptt) REVERT: I 75 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8865 (mm-30) REVERT: I 80 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8439 (ptt180) REVERT: I 81 GLN cc_start: 0.9208 (mt0) cc_final: 0.8735 (mp10) REVERT: I 90 MET cc_start: 0.9407 (mtp) cc_final: 0.9145 (mtm) REVERT: I 142 CYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7811 (p) REVERT: I 189 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8450 (pp) REVERT: I 198 ARG cc_start: 0.8464 (mtm-85) cc_final: 0.8192 (mtm-85) REVERT: J 12 TYR cc_start: 0.8320 (p90) cc_final: 0.7755 (p90) REVERT: J 17 SER cc_start: 0.8793 (p) cc_final: 0.8530 (t) REVERT: J 37 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8482 (tttm) REVERT: J 74 GLU cc_start: 0.8631 (pm20) cc_final: 0.8399 (mt-10) REVERT: c 40 GLN cc_start: 0.8025 (mm110) cc_final: 0.7786 (mm110) REVERT: c 52 ARG cc_start: 0.7053 (tpp80) cc_final: 0.6794 (tpp80) REVERT: c 77 ASN cc_start: 0.8872 (OUTLIER) cc_final: 0.8623 (p0) REVERT: d 43 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8769 (ttmt) REVERT: d 229 GLN cc_start: 0.9373 (mt0) cc_final: 0.8951 (mp10) REVERT: e 56 GLN cc_start: 0.8294 (tp-100) cc_final: 0.7810 (tm-30) REVERT: e 60 ASP cc_start: 0.8923 (m-30) cc_final: 0.8040 (m-30) REVERT: e 66 THR cc_start: 0.9275 (m) cc_final: 0.8999 (t) REVERT: e 106 ARG cc_start: 0.8983 (ttm-80) cc_final: 0.8321 (mtt-85) REVERT: e 129 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8571 (tm-30) outliers start: 61 outliers final: 32 residues processed: 434 average time/residue: 0.4879 time to fit residues: 242.3184 Evaluate side-chains 422 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 376 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain E residue 123 TYR Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain H residue -39 SER Chi-restraints excluded: chain H residue -22 ASN Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 80 ARG Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain I residue 142 CYS Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 37 LYS Chi-restraints excluded: chain c residue 49 LEU Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain c residue 77 ASN Chi-restraints excluded: chain c residue 83 LEU Chi-restraints excluded: chain c residue 132 VAL Chi-restraints excluded: chain c residue 253 ILE Chi-restraints excluded: chain c residue 263 VAL Chi-restraints excluded: chain d residue 35 ILE Chi-restraints excluded: chain d residue 43 LYS Chi-restraints excluded: chain d residue 63 THR Chi-restraints excluded: chain d residue 93 ILE Chi-restraints excluded: chain d residue 123 SER Chi-restraints excluded: chain d residue 186 ILE Chi-restraints excluded: chain e residue 54 ASN Chi-restraints excluded: chain e residue 65 SER Chi-restraints excluded: chain e residue 97 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 120 optimal weight: 2.9990 chunk 178 optimal weight: 0.9980 chunk 270 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 247 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN A 169 ASN B 220 ASN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 GLN G 33 ASN ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 GLN I 40 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.078502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.064964 restraints weight = 58789.011| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 3.07 r_work: 0.2852 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 22085 Z= 0.174 Angle : 0.651 11.725 29931 Z= 0.333 Chirality : 0.043 0.241 3472 Planarity : 0.004 0.056 3821 Dihedral : 4.410 26.185 3075 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.10 % Favored : 96.83 % Rotamer: Outliers : 2.46 % Allowed : 26.38 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.16), residues: 2808 helix: 2.09 (0.15), residues: 1137 sheet: -0.63 (0.20), residues: 627 loop : -0.69 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 168 TYR 0.040 0.002 TYR A 83 PHE 0.033 0.001 PHE c 71 TRP 0.014 0.001 TRP D 100 HIS 0.009 0.001 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.00410 (22084) covalent geometry : angle 0.64879 (29929) SS BOND : bond 0.00965 ( 1) SS BOND : angle 6.00005 ( 2) hydrogen bonds : bond 0.03792 ( 1201) hydrogen bonds : angle 4.81847 ( 3474) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 387 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8776 (tp30) cc_final: 0.8305 (tt0) REVERT: A 212 ILE cc_start: 0.9444 (pt) cc_final: 0.9212 (pp) REVERT: A 233 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8775 (mm) REVERT: B 41 ASP cc_start: 0.8851 (m-30) cc_final: 0.8628 (m-30) REVERT: B 72 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8711 (mtm) REVERT: C 39 ASP cc_start: 0.8829 (m-30) cc_final: 0.8515 (m-30) REVERT: C 120 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8057 (mm-40) REVERT: C 175 ASN cc_start: 0.9263 (m-40) cc_final: 0.9046 (m-40) REVERT: C 178 ASP cc_start: 0.8465 (p0) cc_final: 0.8197 (t0) REVERT: D 53 ARG cc_start: 0.9117 (mmm-85) cc_final: 0.8854 (mpp80) REVERT: D 182 GLN cc_start: 0.8873 (pp30) cc_final: 0.8532 (pp30) REVERT: E 8 ASN cc_start: 0.9226 (p0) cc_final: 0.8814 (m110) REVERT: E 27 GLU cc_start: 0.9250 (mm-30) cc_final: 0.8785 (mm-30) REVERT: E 72 ILE cc_start: 0.9421 (pt) cc_final: 0.9121 (pp) REVERT: E 125 ARG cc_start: 0.8053 (mmt180) cc_final: 0.7499 (mtp85) REVERT: F 29 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8870 (ttpt) REVERT: F 94 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8643 (mp0) REVERT: F 151 MET cc_start: 0.9026 (tmm) cc_final: 0.8661 (tmt) REVERT: F 203 ASP cc_start: 0.8058 (t0) cc_final: 0.7653 (t0) REVERT: G 3 ARG cc_start: 0.8453 (mpp80) cc_final: 0.7158 (mmm160) REVERT: G 209 ASP cc_start: 0.8914 (OUTLIER) cc_final: 0.8697 (m-30) REVERT: H -39 SER cc_start: 0.5956 (OUTLIER) cc_final: 0.5278 (p) REVERT: H -22 ASN cc_start: 0.8850 (OUTLIER) cc_final: 0.7511 (m-40) REVERT: H -18 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8356 (mp0) REVERT: H -3 LYS cc_start: 0.9357 (mtpt) cc_final: 0.9066 (mtmt) REVERT: H 12 ILE cc_start: 0.9546 (OUTLIER) cc_final: 0.9313 (mm) REVERT: H 215 LYS cc_start: 0.8696 (pptt) cc_final: 0.8350 (pptt) REVERT: I 75 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8899 (mm-30) REVERT: I 80 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8473 (ptt180) REVERT: I 81 GLN cc_start: 0.9215 (mt0) cc_final: 0.8747 (mp10) REVERT: I 90 MET cc_start: 0.9411 (mtp) cc_final: 0.9150 (mtm) REVERT: I 189 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8508 (pp) REVERT: I 198 ARG cc_start: 0.8485 (mtm-85) cc_final: 0.8207 (mtm-85) REVERT: J 12 TYR cc_start: 0.8417 (p90) cc_final: 0.8097 (p90) REVERT: J 37 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8930 (tttm) REVERT: c 40 GLN cc_start: 0.8052 (mm110) cc_final: 0.7796 (mm110) REVERT: c 52 ARG cc_start: 0.7031 (tpp80) cc_final: 0.6784 (tpp80) REVERT: c 77 ASN cc_start: 0.8893 (OUTLIER) cc_final: 0.8634 (p0) REVERT: d 229 GLN cc_start: 0.9373 (mt0) cc_final: 0.8972 (mp10) REVERT: e 51 SER cc_start: 0.9073 (t) cc_final: 0.8857 (m) REVERT: e 56 GLN cc_start: 0.8351 (tp-100) cc_final: 0.7874 (tm-30) REVERT: e 60 ASP cc_start: 0.8922 (m-30) cc_final: 0.8021 (m-30) REVERT: e 66 THR cc_start: 0.9271 (m) cc_final: 0.9001 (t) REVERT: e 106 ARG cc_start: 0.9034 (ttm-80) cc_final: 0.8415 (mtt-85) REVERT: e 129 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8561 (tm-30) outliers start: 55 outliers final: 27 residues processed: 418 average time/residue: 0.5152 time to fit residues: 245.9594 Evaluate side-chains 411 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 371 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain H residue -39 SER Chi-restraints excluded: chain H residue -22 ASN Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 80 ARG Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 37 LYS Chi-restraints excluded: chain c residue 49 LEU Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain c residue 77 ASN Chi-restraints excluded: chain c residue 83 LEU Chi-restraints excluded: chain c residue 132 VAL Chi-restraints excluded: chain c residue 253 ILE Chi-restraints excluded: chain c residue 263 VAL Chi-restraints excluded: chain d residue 35 ILE Chi-restraints excluded: chain d residue 63 THR Chi-restraints excluded: chain d residue 93 ILE Chi-restraints excluded: chain d residue 123 SER Chi-restraints excluded: chain d residue 132 LEU Chi-restraints excluded: chain e residue 54 ASN Chi-restraints excluded: chain e residue 65 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 158 optimal weight: 2.9990 chunk 227 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 chunk 140 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 258 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN B 220 ASN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 GLN ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN H 62 ASN H 85 GLN I 40 GLN J 61 GLN c 148 GLN e 63 ASN e 87 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.078906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.065428 restraints weight = 58687.250| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.05 r_work: 0.2857 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 22085 Z= 0.158 Angle : 0.656 14.173 29931 Z= 0.335 Chirality : 0.043 0.219 3472 Planarity : 0.004 0.056 3821 Dihedral : 4.414 26.202 3075 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.06 % Favored : 96.87 % Rotamer: Outliers : 2.28 % Allowed : 26.65 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.16), residues: 2808 helix: 2.08 (0.15), residues: 1136 sheet: -0.63 (0.20), residues: 629 loop : -0.68 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 168 TYR 0.041 0.002 TYR A 83 PHE 0.031 0.001 PHE c 71 TRP 0.014 0.001 TRP D 100 HIS 0.010 0.001 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.00373 (22084) covalent geometry : angle 0.65464 (29929) SS BOND : bond 0.00928 ( 1) SS BOND : angle 5.33210 ( 2) hydrogen bonds : bond 0.03765 ( 1201) hydrogen bonds : angle 4.79771 ( 3474) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5838.25 seconds wall clock time: 100 minutes 43.16 seconds (6043.16 seconds total)