Starting phenix.real_space_refine on Wed Jan 14 06:13:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m6j_23698/01_2026/7m6j_23698.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m6j_23698/01_2026/7m6j_23698.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7m6j_23698/01_2026/7m6j_23698.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m6j_23698/01_2026/7m6j_23698.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m6j_23698/01_2026/7m6j_23698.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m6j_23698/01_2026/7m6j_23698.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.071 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: 6 Type Number sf(0) Gaussians P 14 5.49 5 Mg 1 5.21 5 S 64 5.16 5 C 8177 2.51 5 N 2213 2.21 5 O 2432 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12901 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1810 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 9, 'TRANS': 224} Chain breaks: 2 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 66 Chain: "B" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2260 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 277} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 2150 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 270, 2134 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 255} Chain breaks: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 30 Conformer: "B" Number of residues, atoms: 270, 2134 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 255} Chain breaks: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 30 bond proxies already assigned to first conformer: 2159 Chain: "D" Number of atoms: 2149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2149 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 258} Chain breaks: 2 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "E" Number of atoms: 2349 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 296, 2338 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 285} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 296, 2338 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 285} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 2368 Chain: "F" Number of atoms: 2006 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 1983 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 243} Chain breaks: 2 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 62 Conformer: "B" Number of residues, atoms: 254, 1983 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 243} Chain breaks: 2 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 62 bond proxies already assigned to first conformer: 1995 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N AASN C 302 " occ=0.56 ... (14 atoms not shown) pdb=" ND2BASN C 302 " occ=0.44 residue: pdb=" N AGLY E 78 " occ=0.46 ... (6 atoms not shown) pdb=" O BGLY E 78 " occ=0.54 residue: pdb=" N ACYS F 111 " occ=0.57 ... (10 atoms not shown) pdb=" SG BCYS F 111 " occ=0.43 residue: pdb=" N AARG F 112 " occ=0.57 ... (20 atoms not shown) pdb=" NH2BARG F 112 " occ=0.43 residue: pdb=" N ACYS F 114 " occ=0.57 ... (10 atoms not shown) pdb=" SG BCYS F 114 " occ=0.43 Time building chain proxies: 4.18, per 1000 atoms: 0.32 Number of scatterers: 12901 At special positions: 0 Unit cell: (66.22, 74.82, 260.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 64 16.00 P 14 15.00 Mg 1 11.99 O 2432 8.00 N 2213 7.00 C 8177 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 111 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG ACYS F 111 " - pdb=" SG ACYS F 114 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 835.9 milliseconds 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3056 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 14 sheets defined 41.0% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 49 through 59 Processing helix chain 'A' and resid 70 through 74 removed outlier: 3.559A pdb=" N LYS A 74 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 128 removed outlier: 3.828A pdb=" N ILE A 119 " --> pdb=" O PHE A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 172 removed outlier: 3.565A pdb=" N PHE A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 187 removed outlier: 3.606A pdb=" N THR A 186 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 187 " --> pdb=" O ALA A 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 183 through 187' Processing helix chain 'A' and resid 188 through 206 Processing helix chain 'A' and resid 225 through 234 Processing helix chain 'A' and resid 272 through 283 Processing helix chain 'A' and resid 283 through 300 removed outlier: 4.254A pdb=" N HIS A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TYR A 296 " --> pdb=" O GLN A 292 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU A 297 " --> pdb=" O ASP A 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 40 removed outlier: 4.021A pdb=" N LEU B 32 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL B 33 " --> pdb=" O PRO B 29 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LYS B 35 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL B 37 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N SER B 38 " --> pdb=" O ASN B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 63 Processing helix chain 'B' and resid 115 through 118 Processing helix chain 'B' and resid 119 through 134 removed outlier: 3.631A pdb=" N ALA B 128 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N TYR B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 172 removed outlier: 3.522A pdb=" N LYS B 172 " --> pdb=" O VAL B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 208 removed outlier: 5.115A pdb=" N LYS B 196 " --> pdb=" O SER B 192 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLU B 204 " --> pdb=" O LYS B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 removed outlier: 3.506A pdb=" N HIS B 232 " --> pdb=" O THR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 275 Processing helix chain 'B' and resid 283 through 294 removed outlier: 3.547A pdb=" N HIS B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 48 removed outlier: 4.547A pdb=" N ASN C 38 " --> pdb=" O ALA C 34 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS C 46 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG C 47 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY C 48 " --> pdb=" O SER C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 71 removed outlier: 3.594A pdb=" N PHE C 71 " --> pdb=" O ILE C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 85 removed outlier: 3.944A pdb=" N SER C 84 " --> pdb=" O PRO C 81 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N HIS C 85 " --> pdb=" O GLY C 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 81 through 85' Processing helix chain 'C' and resid 127 through 145 Processing helix chain 'C' and resid 173 through 183 Processing helix chain 'C' and resid 196 through 199 removed outlier: 3.664A pdb=" N LEU C 199 " --> pdb=" O ALA C 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 196 through 199' Processing helix chain 'C' and resid 200 through 218 removed outlier: 4.375A pdb=" N GLN C 216 " --> pdb=" O MET C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 244 removed outlier: 3.932A pdb=" N ARG C 243 " --> pdb=" O ILE C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 293 through 304 Processing helix chain 'C' and resid 304 through 314 removed outlier: 3.507A pdb=" N LEU C 314 " --> pdb=" O ARG C 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 48 Processing helix chain 'D' and resid 63 through 71 Processing helix chain 'D' and resid 127 through 145 Processing helix chain 'D' and resid 173 through 180 Processing helix chain 'D' and resid 182 through 186 removed outlier: 4.211A pdb=" N GLU D 185 " --> pdb=" O ARG D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 199 removed outlier: 3.578A pdb=" N THR D 198 " --> pdb=" O LYS D 195 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU D 199 " --> pdb=" O ALA D 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 195 through 199' Processing helix chain 'D' and resid 200 through 216 Processing helix chain 'D' and resid 281 through 288 Processing helix chain 'D' and resid 293 through 305 Processing helix chain 'D' and resid 305 through 317 removed outlier: 3.972A pdb=" N ALA D 315 " --> pdb=" O SER D 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 38 removed outlier: 5.051A pdb=" N VAL E 33 " --> pdb=" O PRO E 29 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN E 34 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER E 38 " --> pdb=" O ASN E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 63 Processing helix chain 'E' and resid 110 through 114 removed outlier: 4.120A pdb=" N ASP E 113 " --> pdb=" O ASN E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 134 removed outlier: 4.028A pdb=" N PHE E 121 " --> pdb=" O PRO E 117 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA E 128 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR E 129 " --> pdb=" O GLN E 125 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU E 134 " --> pdb=" O LEU E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 172 Processing helix chain 'E' and resid 190 through 208 removed outlier: 3.773A pdb=" N THR E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LYS E 196 " --> pdb=" O SER E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 231 removed outlier: 3.993A pdb=" N ALA E 231 " --> pdb=" O GLY E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 276 Processing helix chain 'E' and resid 282 through 293 Processing helix chain 'E' and resid 294 through 303 Processing helix chain 'F' and resid 50 through 59 removed outlier: 3.787A pdb=" N PHE F 58 " --> pdb=" O ILE F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 77 removed outlier: 4.367A pdb=" N GLU F 76 " --> pdb=" O GLU F 73 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG F 77 " --> pdb=" O LYS F 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 73 through 77' Processing helix chain 'F' and resid 115 through 130 Processing helix chain 'F' and resid 161 through 171 removed outlier: 3.526A pdb=" N VAL F 165 " --> pdb=" O LYS F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 187 removed outlier: 3.959A pdb=" N LEU F 187 " --> pdb=" O ALA F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 207 removed outlier: 3.551A pdb=" N HIS F 206 " --> pdb=" O GLU F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 235 Processing helix chain 'F' and resid 272 through 283 Processing helix chain 'F' and resid 283 through 294 Processing helix chain 'F' and resid 295 through 302 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 removed outlier: 7.267A pdb=" N VAL A 43 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE A 237 " --> pdb=" O PRO A 179 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 255 through 258 Processing sheet with id=AA3, first strand: chain 'B' and resid 41 through 42 removed outlier: 7.244A pdb=" N PHE B 41 " --> pdb=" O LYS B 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA5, first strand: chain 'B' and resid 80 through 81 removed outlier: 5.971A pdb=" N ILE B 45 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N THR B 102 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N CYS B 47 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU B 46 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE B 154 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL B 48 " --> pdb=" O PHE B 154 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N CYS B 151 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ILE B 182 " --> pdb=" O CYS B 151 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYR B 153 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 10.180A pdb=" N PHE B 235 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 253 through 256 Processing sheet with id=AA7, first strand: chain 'C' and resid 98 through 102 removed outlier: 9.912A pdb=" N CYS C 160 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N THR C 52 " --> pdb=" O CYS C 160 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N LEU C 162 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N MET C 54 " --> pdb=" O LEU C 162 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N PHE C 164 " --> pdb=" O MET C 54 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N VAL C 56 " --> pdb=" O PHE C 164 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N VAL C 248 " --> pdb=" O PRO C 191 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ILE C 193 " --> pdb=" O VAL C 248 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 265 through 267 Processing sheet with id=AA9, first strand: chain 'D' and resid 94 through 100 removed outlier: 3.664A pdb=" N CYS D 160 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N CYS D 161 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LEU D 192 " --> pdb=" O CYS D 161 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N TYR D 163 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 264 through 267 Processing sheet with id=AB2, first strand: chain 'E' and resid 80 through 86 removed outlier: 7.067A pdb=" N PHE E 41 " --> pdb=" O LYS E 96 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N THR E 98 " --> pdb=" O PHE E 41 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N PHE E 43 " --> pdb=" O THR E 98 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N VAL E 100 " --> pdb=" O PHE E 43 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE E 45 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N THR E 102 " --> pdb=" O ILE E 45 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N CYS E 47 " --> pdb=" O THR E 102 " (cutoff:3.500A) removed outlier: 9.125A pdb=" N VAL E 150 " --> pdb=" O CYS E 42 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASN E 44 " --> pdb=" O VAL E 150 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N LEU E 152 " --> pdb=" O ASN E 44 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU E 46 " --> pdb=" O LEU E 152 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N PHE E 154 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL E 48 " --> pdb=" O PHE E 154 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N CYS E 151 " --> pdb=" O ILE E 180 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ILE E 182 " --> pdb=" O CYS E 151 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N TYR E 153 " --> pdb=" O ILE E 182 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE E 235 " --> pdb=" O PRO E 181 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 242 through 243 removed outlier: 4.283A pdb=" N GLU E 242 " --> pdb=" O ALA E 253 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA E 253 " --> pdb=" O GLU E 242 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 82 through 85 removed outlier: 6.251A pdb=" N LEU F 40 " --> pdb=" O VAL F 100 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR F 39 " --> pdb=" O CYS F 148 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N PHE F 150 " --> pdb=" O THR F 39 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N MET F 41 " --> pdb=" O PHE F 150 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N PHE F 152 " --> pdb=" O MET F 41 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL F 43 " --> pdb=" O PHE F 152 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N CYS F 149 " --> pdb=" O VAL F 178 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL F 180 " --> pdb=" O CYS F 149 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N TYR F 151 " --> pdb=" O VAL F 180 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE F 237 " --> pdb=" O PRO F 179 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 245 through 246 472 hydrogen bonds defined for protein. 1342 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: 1.86 Time building geometry restraints manager: 1.46 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: 4090 1.34 - 1.46: 1953 1.46 - 1.58: 7001 1.58 - 1.70: 22 1.70 - 1.82: 98 Bond restraints: 13164 Sorted by residual: bond pdb=" C TYR B 298 " pdb=" N ARG B 299 " ideal model delta sigma weight residual 1.329 1.215 0.113 1.79e-02 3.12e+03 4.01e+01 bond pdb=" C ARG B 299 " pdb=" N ARG B 300 " ideal model delta sigma weight residual 1.335 1.407 -0.072 1.34e-02 5.57e+03 2.85e+01 bond pdb=" C5 GDP F 401 " pdb=" C4 GDP F 401 " ideal model delta sigma weight residual 1.490 1.462 0.028 2.00e-02 2.50e+03 1.98e+00 bond pdb=" C5 GDP D 501 " pdb=" C4 GDP D 501 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.49e+00 bond pdb=" C5 GDP A 401 " pdb=" C4 GDP A 401 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.47e+00 ... (remaining 13159 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.45: 17846 5.45 - 10.91: 20 10.91 - 16.36: 2 16.36 - 21.81: 1 21.81 - 27.26: 1 Bond angle restraints: 17870 Sorted by residual: angle pdb=" N GLY E 21 " pdb=" CA GLY E 21 " pdb=" C GLY E 21 " ideal model delta sigma weight residual 112.64 85.38 27.26 1.74e+00 3.30e-01 2.46e+02 angle pdb=" N HIS E 22 " pdb=" CA HIS E 22 " pdb=" CB HIS E 22 " ideal model delta sigma weight residual 110.39 93.63 16.76 1.65e+00 3.67e-01 1.03e+02 angle pdb=" N HIS E 22 " pdb=" CA HIS E 22 " pdb=" C HIS E 22 " ideal model delta sigma weight residual 107.75 96.25 11.50 1.86e+00 2.89e-01 3.82e+01 angle pdb=" CA GLY E 21 " pdb=" C GLY E 21 " pdb=" N HIS E 22 " ideal model delta sigma weight residual 114.30 118.51 -4.21 1.20e+00 6.94e-01 1.23e+01 angle pdb=" C ASN E 282 " pdb=" N MET E 283 " pdb=" CA MET E 283 " ideal model delta sigma weight residual 121.52 115.18 6.34 1.84e+00 2.95e-01 1.19e+01 ... (remaining 17865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.35: 7733 35.35 - 70.70: 174 70.70 - 106.05: 21 106.05 - 141.39: 3 141.39 - 176.74: 3 Dihedral angle restraints: 7934 sinusoidal: 3208 harmonic: 4726 Sorted by residual: dihedral pdb=" N HIS E 22 " pdb=" C HIS E 22 " pdb=" CA HIS E 22 " pdb=" CB HIS E 22 " ideal model delta harmonic sigma weight residual 122.80 96.34 26.46 0 2.50e+00 1.60e-01 1.12e+02 dihedral pdb=" CB CYS A 111 " pdb=" SG CYS A 111 " pdb=" SG CYS A 114 " pdb=" CB CYS A 114 " ideal model delta sinusoidal sigma weight residual 93.00 15.32 77.68 1 1.00e+01 1.00e-02 7.55e+01 dihedral pdb=" C8 GTP B 501 " pdb=" C1' GTP B 501 " pdb=" N9 GTP B 501 " pdb=" O4' GTP B 501 " ideal model delta sinusoidal sigma weight residual 104.59 -72.15 176.74 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 7931 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 2029 0.132 - 0.265: 9 0.265 - 0.397: 0 0.397 - 0.529: 0 0.529 - 0.662: 1 Chirality restraints: 2039 Sorted by residual: chirality pdb=" CA HIS E 22 " pdb=" N HIS E 22 " pdb=" C HIS E 22 " pdb=" CB HIS E 22 " both_signs ideal model delta sigma weight residual False 2.51 3.17 -0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" CB ILE B 136 " pdb=" CA ILE B 136 " pdb=" CG1 ILE B 136 " pdb=" CG2 ILE B 136 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA MET C 212 " pdb=" N MET C 212 " pdb=" C MET C 212 " pdb=" CB MET C 212 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.11e-01 ... (remaining 2036 not shown) Planarity restraints: 2266 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 77 " -0.036 5.00e-02 4.00e+02 5.42e-02 4.70e+00 pdb=" N PRO D 78 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 78 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 78 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 199 " 0.010 2.00e-02 2.50e+03 2.00e-02 4.00e+00 pdb=" C ILE B 199 " -0.035 2.00e-02 2.50e+03 pdb=" O ILE B 199 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS B 200 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 200 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO C 201 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 201 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 201 " -0.026 5.00e-02 4.00e+02 ... (remaining 2263 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 166 2.57 - 3.15: 11004 3.15 - 3.74: 19449 3.74 - 4.32: 25719 4.32 - 4.90: 43129 Nonbonded interactions: 99467 Sorted by model distance: nonbonded pdb=" OE2 GLU D 307 " pdb=" NH2 ARG E 138 " model vdw 1.991 3.120 nonbonded pdb="MG MG E 501 " pdb=" O1G GTP E 502 " model vdw 2.010 2.170 nonbonded pdb=" N GLY E 21 " pdb=" O GLY E 21 " model vdw 2.035 2.496 nonbonded pdb="MG MG E 501 " pdb=" O1B GTP E 502 " model vdw 2.055 2.170 nonbonded pdb="MG MG E 501 " pdb=" O3G GTP E 502 " model vdw 2.113 2.170 ... (remaining 99462 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 38 through 93 or (resid 94 through 96 and (name N or name \ CA or name C or name O or name CB )) or resid 97 through 110 or resid 113 or res \ id 115 through 127 or (resid 128 and (name N or name CA or name C or name O or n \ ame CB )) or resid 129 through 224 or (resid 225 through 226 and (name N or name \ CA or name C or name O or name CB )) or resid 227 through 228 or (resid 229 and \ (name N or name CA or name C or name O or name CB )) or resid 230 through 286 o \ r (resid 287 through 289 and (name N or name CA or name C or name O or name CB ) \ ) or resid 290 through 295 or (resid 296 through 298 and (name N or name CA or n \ ame C or name O or name CB )) or resid 299 through 401)) selection = (chain 'F' and (resid 38 through 44 or (resid 45 and (name N or name CA or name \ C or name O or name CB )) or resid 46 through 64 or (resid 65 and (name N or nam \ e CA or name C or name O or name CB )) or resid 66 through 75 or (resid 76 and ( \ name N or name CA or name C or name O or name CB )) or resid 77 through 89 or (r \ esid 90 through 91 and (name N or name CA or name C or name O or name CB )) or r \ esid 92 through 94 or (resid 95 through 96 and (name N or name CA or name C or n \ ame O or name CB )) or resid 97 through 110 or resid 113 or resid 115 through 13 \ 0 or resid 149 through 167 or (resid 168 and (name N or name CA or name C or nam \ e O or name CB )) or resid 169 through 192 or (resid 193 and (name N or name CA \ or name C or name O or name CB )) or resid 194 through 196 or (resid 197 and (na \ me N or name CA or name C or name O or name CB )) or resid 198 through 201 or (r \ esid 202 and (name N or name CA or name C or name O or name CB )) or resid 203 t \ hrough 212 or resid 224 through 225 or (resid 226 and (name N or name CA or name \ C or name O or name CB )) or resid 227 through 250 or (resid 251 through 252 an \ d (name N or name CA or name C or name O or name CB )) or resid 253 through 287 \ or (resid 288 through 289 and (name N or name CA or name C or name O or name CB \ )) or resid 290 through 291 or (resid 292 and (name N or name CA or name C or na \ me O or name CB )) or resid 293 through 297 or (resid 298 and (name N or name CA \ or name C or name O or name CB )) or resid 299 or (resid 300 and (name N or nam \ e CA or name C or name O or name CB )) or resid 401)) } ncs_group { reference = (chain 'B' and (resid 23 through 77 or resid 79 through 140 or resid 142 through \ 250 or (resid 251 and (name N or name CA or name C or name O or name CB )) or r \ esid 252 through 308 or (resid 309 and (name N or name CA or name C or name O or \ name CB )))) selection = (chain 'E' and (resid 23 through 24 or (resid 25 and (name N or name CA or name \ C or name O or name CB )) or resid 26 through 33 or (resid 34 and (name N or nam \ e CA or name C or name O or name CB )) or resid 35 through 59 or (resid 60 and ( \ name N or name CA or name C or name O or name CB )) or resid 61 through 65 or (r \ esid 66 and (name N or name CA or name C or name O or name CB )) or resid 67 thr \ ough 77 or resid 79 through 106 or (resid 107 and (name N or name CA or name C o \ r name O or name CB )) or resid 108 through 140 or resid 142 through 245 or (res \ id 246 and (name N or name CA or name C or name O or name CB )) or resid 247 thr \ ough 309)) } ncs_group { reference = (chain 'C' and (resid 29 through 58 or resid 60 through 86 or (resid 87 through \ 89 and (name N or name CA or name C or name O or name CB )) or resid 90 through \ 148 or resid 150 through 223 or (resid 224 through 225 and (name N or name CA or \ name C or name O or name CB )) or resid 226 or (resid 240 through 243 and (name \ N or name CA or name C or name O or name CB )) or resid 244 through 255 or (res \ id 262 through 263 and (name N or name CA or name C or name O or name CB )) or r \ esid 264 through 301 or resid 303 through 501)) selection = (chain 'D' and (resid 29 through 58 or resid 60 through 73 or (resid 74 and (nam \ e N or name CA or name C or name O or name CB )) or resid 75 through 78 or (resi \ d 79 and (name N or name CA or name C or name O or name CB )) or resid 80 throug \ h 88 or (resid 89 and (name N or name CA or name C or name O or name CB )) or re \ sid 90 through 148 or resid 150 through 226 or (resid 240 through 243 and (name \ N or name CA or name C or name O or name CB )) or resid 244 through 255 or (resi \ d 262 through 263 and (name N or name CA or name C or name O or name CB )) or re \ sid 264 through 290 or (resid 291 and (name N or name CA or name C or name O or \ name CB )) or resid 292 through 301 or resid 303 through 316 or resid 501)) } 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=0.34 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 10.610 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.970 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 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 : 0.004 0.113 13166 Z= 0.183 Angle : 0.757 27.264 17874 Z= 0.405 Chirality : 0.050 0.662 2039 Planarity : 0.004 0.054 2266 Dihedral : 16.052 176.743 4872 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 0.79 % Allowed : 0.79 % Favored : 98.41 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.21), residues: 1601 helix: -0.35 (0.21), residues: 607 sheet: -1.27 (0.36), residues: 208 loop : -2.18 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 254 TYR 0.021 0.002 TYR E 213 PHE 0.019 0.001 PHE E 25 TRP 0.012 0.002 TRP A 260 HIS 0.005 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00388 (13164) covalent geometry : angle 0.75637 (17870) SS BOND : bond 0.00140 ( 2) SS BOND : angle 2.43688 ( 4) hydrogen bonds : bond 0.15406 ( 470) hydrogen bonds : angle 6.61229 ( 1342) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 180 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 PHE cc_start: 0.4985 (m-10) cc_final: 0.4734 (m-10) REVERT: B 133 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7636 (tp30) REVERT: D 52 THR cc_start: 0.8163 (m) cc_final: 0.7763 (p) REVERT: D 95 GLN cc_start: 0.7766 (pp30) cc_final: 0.7441 (pp30) REVERT: D 211 ILE cc_start: 0.8299 (mm) cc_final: 0.8092 (mm) REVERT: F 151 TYR cc_start: 0.8608 (t80) cc_final: 0.7686 (t80) REVERT: F 245 LEU cc_start: 0.7736 (tt) cc_final: 0.7454 (pp) outliers start: 5 outliers final: 1 residues processed: 184 average time/residue: 0.0975 time to fit residues: 27.6082 Evaluate side-chains 142 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 0.0970 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN A 176 ASN A 295 HIS D 276 ASN E 262 GLN E 268 HIS F 131 HIS F 147 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.143187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.121497 restraints weight = 94271.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.126722 restraints weight = 42331.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.127735 restraints weight = 19441.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.128727 restraints weight = 13360.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.131065 restraints weight = 11171.949| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3892 r_free = 0.3892 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3889 r_free = 0.3889 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13166 Z= 0.150 Angle : 0.683 11.537 17874 Z= 0.336 Chirality : 0.047 0.204 2039 Planarity : 0.004 0.048 2266 Dihedral : 11.127 177.884 1815 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 1.08 % Allowed : 9.47 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.21), residues: 1601 helix: 0.07 (0.21), residues: 629 sheet: -1.18 (0.36), residues: 210 loop : -2.19 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 293 TYR 0.019 0.002 TYR D 223 PHE 0.013 0.001 PHE A 167 TRP 0.009 0.001 TRP A 260 HIS 0.014 0.001 HIS F 131 Details of bonding type rmsd covalent geometry : bond 0.00338 (13164) covalent geometry : angle 0.68194 (17870) SS BOND : bond 0.00358 ( 2) SS BOND : angle 2.07054 ( 4) hydrogen bonds : bond 0.04365 ( 470) hydrogen bonds : angle 5.17562 ( 1342) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 157 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 251 MET cc_start: 0.5886 (ppp) cc_final: 0.5640 (ppp) REVERT: D 52 THR cc_start: 0.8275 (m) cc_final: 0.7981 (p) REVERT: D 211 ILE cc_start: 0.8720 (mm) cc_final: 0.8503 (mm) outliers start: 9 outliers final: 6 residues processed: 163 average time/residue: 0.0923 time to fit residues: 23.6305 Evaluate side-chains 147 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 141 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain C residue 161 CYS Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain E residue 283 MET Chi-restraints excluded: chain F residue 189 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 104 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 117 optimal weight: 0.1980 chunk 72 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 85 optimal weight: 0.2980 chunk 118 optimal weight: 0.6980 chunk 101 optimal weight: 0.6980 chunk 126 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN A 176 ASN C 188 ASN D 276 ASN E 149 HIS ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.144621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.122569 restraints weight = 87906.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.127266 restraints weight = 39777.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.128199 restraints weight = 21141.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.130462 restraints weight = 14126.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.130608 restraints weight = 11054.885| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3887 r_free = 0.3887 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3887 r_free = 0.3887 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13166 Z= 0.124 Angle : 0.649 14.515 17874 Z= 0.315 Chirality : 0.046 0.206 2039 Planarity : 0.004 0.046 2266 Dihedral : 10.852 176.227 1813 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 1.59 % Allowed : 12.14 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.21), residues: 1601 helix: 0.30 (0.21), residues: 632 sheet: -1.04 (0.37), residues: 203 loop : -2.15 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 293 TYR 0.016 0.001 TYR F 121 PHE 0.010 0.001 PHE D 33 TRP 0.007 0.001 TRP A 260 HIS 0.006 0.001 HIS F 295 Details of bonding type rmsd covalent geometry : bond 0.00277 (13164) covalent geometry : angle 0.64889 (17870) SS BOND : bond 0.00346 ( 2) SS BOND : angle 1.52886 ( 4) hydrogen bonds : bond 0.03723 ( 470) hydrogen bonds : angle 4.91573 ( 1342) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 251 MET cc_start: 0.5945 (ppp) cc_final: 0.5637 (ppp) REVERT: D 52 THR cc_start: 0.8278 (m) cc_final: 0.7948 (p) REVERT: D 211 ILE cc_start: 0.8714 (mm) cc_final: 0.8506 (mm) REVERT: E 133 GLU cc_start: 0.6781 (mm-30) cc_final: 0.5992 (tp30) outliers start: 15 outliers final: 8 residues processed: 164 average time/residue: 0.0958 time to fit residues: 24.3597 Evaluate side-chains 152 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 160 CYS Chi-restraints excluded: chain C residue 161 CYS Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 189 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 19 optimal weight: 0.4980 chunk 109 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 63 optimal weight: 0.0370 chunk 38 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 7 optimal weight: 8.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN B 125 GLN B 208 ASN D 276 ASN D 287 ASN ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.144513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.122774 restraints weight = 94604.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.127579 restraints weight = 41913.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.128175 restraints weight = 22973.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.131033 restraints weight = 14677.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.131077 restraints weight = 10414.807| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3892 r_free = 0.3892 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3892 r_free = 0.3892 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13166 Z= 0.124 Angle : 0.646 16.234 17874 Z= 0.311 Chirality : 0.046 0.162 2039 Planarity : 0.004 0.046 2266 Dihedral : 10.710 175.359 1813 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 1.88 % Allowed : 13.66 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.21), residues: 1601 helix: 0.41 (0.22), residues: 639 sheet: -0.94 (0.37), residues: 203 loop : -2.14 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 293 TYR 0.015 0.001 TYR C 309 PHE 0.011 0.001 PHE E 25 TRP 0.006 0.001 TRP A 260 HIS 0.004 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00280 (13164) covalent geometry : angle 0.64538 (17870) SS BOND : bond 0.00338 ( 2) SS BOND : angle 1.42483 ( 4) hydrogen bonds : bond 0.03579 ( 470) hydrogen bonds : angle 4.79496 ( 1342) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.7948 (m-10) cc_final: 0.7600 (m-10) REVERT: B 251 MET cc_start: 0.6078 (ppp) cc_final: 0.5788 (ppp) REVERT: D 176 ASP cc_start: 0.7183 (OUTLIER) cc_final: 0.6806 (p0) REVERT: D 211 ILE cc_start: 0.8697 (mm) cc_final: 0.8456 (mm) REVERT: E 133 GLU cc_start: 0.6791 (mm-30) cc_final: 0.6003 (tp30) REVERT: F 168 MET cc_start: 0.7467 (mtm) cc_final: 0.7184 (mtt) outliers start: 19 outliers final: 13 residues processed: 167 average time/residue: 0.0932 time to fit residues: 24.5225 Evaluate side-chains 161 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 160 CYS Chi-restraints excluded: chain C residue 161 CYS Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 189 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 70 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 153 optimal weight: 0.0980 chunk 40 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 148 optimal weight: 0.0270 overall best weight: 0.5842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN D 276 ASN ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.144239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.122157 restraints weight = 90004.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.126865 restraints weight = 39652.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.127915 restraints weight = 20516.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.129980 restraints weight = 13835.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.130212 restraints weight = 10959.674| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3883 r_free = 0.3883 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3883 r_free = 0.3883 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13166 Z= 0.125 Angle : 0.646 16.697 17874 Z= 0.311 Chirality : 0.046 0.161 2039 Planarity : 0.004 0.045 2266 Dihedral : 10.586 174.932 1813 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 2.24 % Allowed : 14.09 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.21), residues: 1601 helix: 0.50 (0.22), residues: 640 sheet: -0.88 (0.37), residues: 203 loop : -2.11 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 293 TYR 0.016 0.001 TYR F 121 PHE 0.011 0.001 PHE E 25 TRP 0.006 0.001 TRP A 260 HIS 0.004 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00283 (13164) covalent geometry : angle 0.64525 (17870) SS BOND : bond 0.00336 ( 2) SS BOND : angle 1.37242 ( 4) hydrogen bonds : bond 0.03484 ( 470) hydrogen bonds : angle 4.70471 ( 1342) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.7935 (m-10) cc_final: 0.7611 (m-10) REVERT: B 251 MET cc_start: 0.5968 (ppp) cc_final: 0.5416 (ppp) REVERT: C 182 ARG cc_start: 0.6985 (ttm-80) cc_final: 0.6746 (ttm-80) REVERT: C 307 GLU cc_start: 0.7473 (tm-30) cc_final: 0.7238 (tm-30) REVERT: D 52 THR cc_start: 0.8274 (m) cc_final: 0.7878 (p) REVERT: D 176 ASP cc_start: 0.7081 (OUTLIER) cc_final: 0.6861 (p0) REVERT: D 211 ILE cc_start: 0.8721 (mm) cc_final: 0.8490 (mm) REVERT: E 133 GLU cc_start: 0.6837 (mm-30) cc_final: 0.6024 (tp30) REVERT: F 168 MET cc_start: 0.7445 (mtm) cc_final: 0.7159 (mtt) outliers start: 24 outliers final: 16 residues processed: 171 average time/residue: 0.0956 time to fit residues: 25.4055 Evaluate side-chains 161 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 160 CYS Chi-restraints excluded: chain C residue 161 CYS Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain F residue 40 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 113 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 156 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 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 173 ASN D 276 ASN ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.143233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.121882 restraints weight = 93465.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.125964 restraints weight = 48814.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.127915 restraints weight = 22267.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.129180 restraints weight = 14678.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.129732 restraints weight = 11982.244| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3875 r_free = 0.3875 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3875 r_free = 0.3875 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13166 Z= 0.146 Angle : 0.664 17.059 17874 Z= 0.320 Chirality : 0.047 0.152 2039 Planarity : 0.004 0.047 2266 Dihedral : 10.559 174.969 1813 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 2.31 % Allowed : 15.61 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.21), residues: 1601 helix: 0.51 (0.22), residues: 634 sheet: -0.94 (0.37), residues: 213 loop : -2.15 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 293 TYR 0.018 0.001 TYR C 309 PHE 0.015 0.001 PHE E 25 TRP 0.007 0.001 TRP A 260 HIS 0.004 0.001 HIS D 85 Details of bonding type rmsd covalent geometry : bond 0.00334 (13164) covalent geometry : angle 0.66402 (17870) SS BOND : bond 0.00334 ( 2) SS BOND : angle 1.34967 ( 4) hydrogen bonds : bond 0.03647 ( 470) hydrogen bonds : angle 4.75752 ( 1342) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.7896 (m-10) cc_final: 0.7591 (m-10) REVERT: B 251 MET cc_start: 0.6108 (ppp) cc_final: 0.5652 (ppp) REVERT: C 182 ARG cc_start: 0.6924 (ttm-80) cc_final: 0.6663 (ttm-80) REVERT: C 307 GLU cc_start: 0.7466 (tm-30) cc_final: 0.7220 (tm-30) REVERT: D 176 ASP cc_start: 0.7072 (OUTLIER) cc_final: 0.6856 (p0) REVERT: D 211 ILE cc_start: 0.8768 (mm) cc_final: 0.8505 (mm) REVERT: E 95 LEU cc_start: 0.8380 (mp) cc_final: 0.8060 (mt) REVERT: E 133 GLU cc_start: 0.6826 (mm-30) cc_final: 0.6444 (mm-30) REVERT: F 65 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: F 168 MET cc_start: 0.7508 (mtm) cc_final: 0.7250 (mtt) outliers start: 25 outliers final: 17 residues processed: 172 average time/residue: 0.0919 time to fit residues: 24.9891 Evaluate side-chains 168 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 160 CYS Chi-restraints excluded: chain C residue 161 CYS Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 189 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 76 optimal weight: 0.5980 chunk 146 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 276 ASN D 287 ASN ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.143153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.121298 restraints weight = 98311.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.126426 restraints weight = 44258.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.127613 restraints weight = 19906.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.128480 restraints weight = 13526.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.130821 restraints weight = 11444.784| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3884 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3884 r_free = 0.3884 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3884 r_free = 0.3884 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3884 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13166 Z= 0.144 Angle : 0.669 18.078 17874 Z= 0.321 Chirality : 0.046 0.149 2039 Planarity : 0.004 0.047 2266 Dihedral : 10.523 175.011 1813 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 2.24 % Allowed : 16.26 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.21), residues: 1601 helix: 0.52 (0.22), residues: 635 sheet: -0.89 (0.37), residues: 213 loop : -2.13 (0.21), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 293 TYR 0.018 0.002 TYR F 121 PHE 0.012 0.001 PHE E 25 TRP 0.007 0.001 TRP A 260 HIS 0.004 0.001 HIS D 85 Details of bonding type rmsd covalent geometry : bond 0.00329 (13164) covalent geometry : angle 0.66837 (17870) SS BOND : bond 0.00338 ( 2) SS BOND : angle 1.34765 ( 4) hydrogen bonds : bond 0.03605 ( 470) hydrogen bonds : angle 4.73979 ( 1342) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.7908 (m-10) cc_final: 0.7580 (m-10) REVERT: B 251 MET cc_start: 0.6098 (ppp) cc_final: 0.5516 (ppp) REVERT: C 182 ARG cc_start: 0.6892 (ttm-80) cc_final: 0.6646 (ttm-80) REVERT: C 307 GLU cc_start: 0.7473 (tm-30) cc_final: 0.7179 (tm-30) REVERT: D 176 ASP cc_start: 0.7074 (OUTLIER) cc_final: 0.6838 (p0) REVERT: D 211 ILE cc_start: 0.8751 (mm) cc_final: 0.8502 (mm) REVERT: E 95 LEU cc_start: 0.8358 (mp) cc_final: 0.8047 (mt) REVERT: E 217 THR cc_start: 0.8095 (OUTLIER) cc_final: 0.7885 (m) REVERT: F 65 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.7010 (mp0) REVERT: F 168 MET cc_start: 0.7561 (mtm) cc_final: 0.7292 (mtt) outliers start: 24 outliers final: 20 residues processed: 164 average time/residue: 0.0919 time to fit residues: 23.6667 Evaluate side-chains 166 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 160 CYS Chi-restraints excluded: chain C residue 161 CYS Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 189 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.0370 chunk 150 optimal weight: 0.6980 chunk 11 optimal weight: 9.9990 chunk 138 optimal weight: 3.9990 chunk 140 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 276 ASN ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.144333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.122476 restraints weight = 100205.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.127881 restraints weight = 43108.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.128780 restraints weight = 19359.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.130486 restraints weight = 13224.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.130790 restraints weight = 10809.118| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3886 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3886 r_free = 0.3886 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3886 r_free = 0.3886 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3886 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13166 Z= 0.124 Angle : 0.654 17.013 17874 Z= 0.314 Chirality : 0.046 0.146 2039 Planarity : 0.004 0.046 2266 Dihedral : 10.416 174.486 1813 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 2.31 % Allowed : 17.27 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.21), residues: 1601 helix: 0.64 (0.22), residues: 635 sheet: -0.84 (0.36), residues: 213 loop : -2.06 (0.21), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 293 TYR 0.020 0.001 TYR F 121 PHE 0.012 0.001 PHE E 25 TRP 0.006 0.001 TRP A 260 HIS 0.004 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00283 (13164) covalent geometry : angle 0.65389 (17870) SS BOND : bond 0.00344 ( 2) SS BOND : angle 1.30994 ( 4) hydrogen bonds : bond 0.03414 ( 470) hydrogen bonds : angle 4.64966 ( 1342) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.7898 (m-10) cc_final: 0.7566 (m-10) REVERT: A 204 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8296 (tm-30) REVERT: B 166 ASP cc_start: 0.7166 (m-30) cc_final: 0.6796 (m-30) REVERT: B 191 LYS cc_start: 0.7133 (mmtt) cc_final: 0.6816 (tptt) REVERT: B 251 MET cc_start: 0.6026 (ppp) cc_final: 0.5530 (ppp) REVERT: C 182 ARG cc_start: 0.6921 (ttm-80) cc_final: 0.6674 (ttm-80) REVERT: C 183 LEU cc_start: 0.7511 (tp) cc_final: 0.7287 (tt) REVERT: C 307 GLU cc_start: 0.7472 (tm-30) cc_final: 0.7195 (tm-30) REVERT: D 176 ASP cc_start: 0.7026 (OUTLIER) cc_final: 0.6816 (p0) REVERT: D 211 ILE cc_start: 0.8710 (mm) cc_final: 0.8417 (mm) REVERT: E 95 LEU cc_start: 0.8345 (mp) cc_final: 0.8041 (mt) REVERT: E 217 THR cc_start: 0.8060 (OUTLIER) cc_final: 0.7848 (m) REVERT: F 65 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6990 (mp0) REVERT: F 168 MET cc_start: 0.7504 (mtm) cc_final: 0.7226 (mtt) outliers start: 24 outliers final: 18 residues processed: 173 average time/residue: 0.0945 time to fit residues: 25.5149 Evaluate side-chains 170 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 160 CYS Chi-restraints excluded: chain C residue 161 CYS Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 189 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 68 optimal weight: 0.1980 chunk 141 optimal weight: 0.1980 chunk 57 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 144 optimal weight: 0.0770 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.143847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.119312 restraints weight = 105649.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.125107 restraints weight = 36943.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.127152 restraints weight = 16734.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.127454 restraints weight = 12201.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.128102 restraints weight = 10459.217| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3847 r_free = 0.3847 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3847 r_free = 0.3847 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13166 Z= 0.114 Angle : 0.660 19.060 17874 Z= 0.313 Chirality : 0.045 0.169 2039 Planarity : 0.004 0.046 2266 Dihedral : 10.256 173.345 1813 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.17 % Allowed : 17.49 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.21), residues: 1601 helix: 0.76 (0.22), residues: 636 sheet: -0.71 (0.37), residues: 213 loop : -1.98 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 293 TYR 0.023 0.001 TYR F 121 PHE 0.013 0.001 PHE E 25 TRP 0.005 0.001 TRP A 260 HIS 0.003 0.001 HIS C 218 Details of bonding type rmsd covalent geometry : bond 0.00258 (13164) covalent geometry : angle 0.65945 (17870) SS BOND : bond 0.00358 ( 2) SS BOND : angle 1.27047 ( 4) hydrogen bonds : bond 0.03200 ( 470) hydrogen bonds : angle 4.50889 ( 1342) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.7912 (m-10) cc_final: 0.7591 (m-10) REVERT: A 204 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8328 (tm-30) REVERT: A 242 SER cc_start: 0.7675 (OUTLIER) cc_final: 0.7359 (m) REVERT: B 191 LYS cc_start: 0.7113 (mmtt) cc_final: 0.6743 (tptt) REVERT: B 251 MET cc_start: 0.5592 (ppp) cc_final: 0.5188 (ppp) REVERT: C 182 ARG cc_start: 0.6951 (ttm-80) cc_final: 0.6345 (ttm-80) REVERT: C 183 LEU cc_start: 0.7679 (tp) cc_final: 0.7461 (tt) REVERT: C 307 GLU cc_start: 0.7559 (tm-30) cc_final: 0.7229 (tm-30) REVERT: D 176 ASP cc_start: 0.7055 (OUTLIER) cc_final: 0.6653 (p0) REVERT: D 211 ILE cc_start: 0.8497 (mm) cc_final: 0.8280 (mm) REVERT: E 95 LEU cc_start: 0.8372 (mp) cc_final: 0.8166 (mt) REVERT: E 217 THR cc_start: 0.8052 (OUTLIER) cc_final: 0.7824 (m) REVERT: F 65 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6910 (mp0) REVERT: F 168 MET cc_start: 0.7499 (mtm) cc_final: 0.7186 (mtt) outliers start: 22 outliers final: 16 residues processed: 185 average time/residue: 0.0959 time to fit residues: 27.8013 Evaluate side-chains 176 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 160 CYS Chi-restraints excluded: chain C residue 161 CYS Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 189 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 79 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 123 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 144 optimal weight: 0.5980 chunk 146 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 134 optimal weight: 0.0980 chunk 95 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.143753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.119210 restraints weight = 107185.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.125467 restraints weight = 36802.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.126744 restraints weight = 16470.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.127340 restraints weight = 12447.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.128885 restraints weight = 10064.127| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3860 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3860 r_free = 0.3860 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3860 r_free = 0.3860 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13166 Z= 0.121 Angle : 0.664 18.355 17874 Z= 0.317 Chirality : 0.046 0.160 2039 Planarity : 0.004 0.045 2266 Dihedral : 10.242 173.085 1813 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 2.02 % Allowed : 18.21 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.21), residues: 1601 helix: 0.73 (0.22), residues: 637 sheet: -0.61 (0.38), residues: 203 loop : -1.95 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 293 TYR 0.014 0.001 TYR C 309 PHE 0.016 0.001 PHE E 25 TRP 0.006 0.001 TRP A 260 HIS 0.003 0.001 HIS C 218 Details of bonding type rmsd covalent geometry : bond 0.00277 (13164) covalent geometry : angle 0.66374 (17870) SS BOND : bond 0.00359 ( 2) SS BOND : angle 1.28393 ( 4) hydrogen bonds : bond 0.03339 ( 470) hydrogen bonds : angle 4.53724 ( 1342) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3202 Ramachandran restraints generated. 1601 Oldfield, 0 Emsley, 1601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.7874 (m-10) cc_final: 0.7576 (m-10) REVERT: A 204 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8290 (tm-30) REVERT: A 242 SER cc_start: 0.7791 (OUTLIER) cc_final: 0.7492 (m) REVERT: B 191 LYS cc_start: 0.7090 (mmtt) cc_final: 0.6755 (tptt) REVERT: B 251 MET cc_start: 0.5670 (ppp) cc_final: 0.5241 (ppp) REVERT: C 182 ARG cc_start: 0.6945 (ttm-80) cc_final: 0.6293 (ttm-80) REVERT: C 183 LEU cc_start: 0.7650 (tp) cc_final: 0.7428 (tt) REVERT: C 307 GLU cc_start: 0.7542 (tm-30) cc_final: 0.7199 (tm-30) REVERT: D 176 ASP cc_start: 0.6972 (OUTLIER) cc_final: 0.6734 (p0) REVERT: D 211 ILE cc_start: 0.8505 (mm) cc_final: 0.8290 (mm) REVERT: E 217 THR cc_start: 0.8048 (OUTLIER) cc_final: 0.7819 (m) REVERT: F 65 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6941 (mp0) REVERT: F 168 MET cc_start: 0.7470 (mtm) cc_final: 0.7172 (mtt) outliers start: 20 outliers final: 15 residues processed: 173 average time/residue: 0.0960 time to fit residues: 25.7992 Evaluate side-chains 172 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 161 CYS Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 189 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 101 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 136 optimal weight: 0.0050 chunk 50 optimal weight: 0.9980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 ASN ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.142899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.118203 restraints weight = 100773.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.123933 restraints weight = 36166.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.126779 restraints weight = 15634.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.126595 restraints weight = 11398.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.127158 restraints weight = 9978.428| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3838 r_free = 0.3838 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3838 r_free = 0.3838 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13166 Z= 0.132 Angle : 0.673 18.287 17874 Z= 0.321 Chirality : 0.046 0.162 2039 Planarity : 0.004 0.046 2266 Dihedral : 10.274 173.329 1813 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 2.17 % Allowed : 18.21 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.21), residues: 1601 helix: 0.69 (0.22), residues: 637 sheet: -0.64 (0.38), residues: 201 loop : -1.94 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 293 TYR 0.015 0.001 TYR C 309 PHE 0.017 0.001 PHE E 25 TRP 0.007 0.001 TRP A 260 HIS 0.004 0.001 HIS F 147 Details of bonding type rmsd covalent geometry : bond 0.00303 (13164) covalent geometry : angle 0.67314 (17870) SS BOND : bond 0.00342 ( 2) SS BOND : angle 1.30606 ( 4) hydrogen bonds : bond 0.03432 ( 470) hydrogen bonds : angle 4.57825 ( 1342) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2180.68 seconds wall clock time: 38 minutes 36.57 seconds (2316.57 seconds total)