Starting phenix.real_space_refine on Sat Aug 23 01:49:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wc6_37432/08_2025/8wc6_37432_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wc6_37432/08_2025/8wc6_37432.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wc6_37432/08_2025/8wc6_37432_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wc6_37432/08_2025/8wc6_37432_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wc6_37432/08_2025/8wc6_37432.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wc6_37432/08_2025/8wc6_37432.map" } resolution = 3.2 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 5875 2.51 5 N 1546 2.21 5 O 1709 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9183 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1789 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 5, 'TRANS': 221} Chain breaks: 4 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 8, 'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 65 Chain: "B" Number of atoms: 2476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2476 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 5, 'ARG:plan': 7, 'GLU:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 78 Chain: "N" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 795 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 2, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 79 Chain: "R" Number of atoms: 2007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2007 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 12, 'TRANS': 254} Chain breaks: 2 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 5, 'PHE:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 68 Chain: "S" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1733 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "Y" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 374 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'PEA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.33, per 1000 atoms: 0.25 Number of scatterers: 9183 At special positions: 0 Unit cell: (115.6, 91.8, 133.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 1709 8.00 N 1546 7.00 C 5875 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " 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: 0.85 Conformation dependent library (CDL) restraints added in 353.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2322 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 15 sheets defined 34.8% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 4.004A pdb=" N ALA A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.544A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.867A pdb=" N GLN A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 210 through 216' Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 260 through 270 removed outlier: 3.599A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA A 270 " --> pdb=" O GLU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 285 removed outlier: 3.955A pdb=" N ALA A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 318 Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 5 through 27 removed outlier: 4.266A pdb=" N ALA B 21 " --> pdb=" O GLN B 17 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASP B 27 " --> pdb=" O LYS B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.857A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.546A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 74 through 77 Processing helix chain 'R' and resid 27 through 50 removed outlier: 3.953A pdb=" N ILE R 32 " --> pdb=" O LEU R 28 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE R 33 " --> pdb=" O MET R 29 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU R 34 " --> pdb=" O SER R 30 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL R 43 " --> pdb=" O GLY R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 54 removed outlier: 3.980A pdb=" N HIS R 54 " --> pdb=" O LYS R 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 51 through 54' Processing helix chain 'R' and resid 55 through 56 No H-bonds generated for 'chain 'R' and resid 55 through 56' Processing helix chain 'R' and resid 57 through 86 removed outlier: 3.856A pdb=" N LEU R 61 " --> pdb=" O THR R 57 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N MET R 76 " --> pdb=" O GLY R 72 " (cutoff:3.500A) Proline residue: R 77 - end of helix Processing helix chain 'R' and resid 94 through 126 removed outlier: 4.006A pdb=" N SER R 100 " --> pdb=" O LYS R 96 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP R 126 " --> pdb=" O CYS R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 134 removed outlier: 3.511A pdb=" N LYS R 133 " --> pdb=" O ARG R 129 " (cutoff:3.500A) Processing helix chain 'R' and resid 135 through 159 removed outlier: 3.551A pdb=" N ILE R 139 " --> pdb=" O ASN R 135 " (cutoff:3.500A) Proline residue: R 150 - end of helix Processing helix chain 'R' and resid 167 through 176 Processing helix chain 'R' and resid 188 through 225 Proline residue: R 201 - end of helix removed outlier: 3.538A pdb=" N PHE R 207 " --> pdb=" O SER R 203 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL R 208 " --> pdb=" O VAL R 204 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 275 Proline residue: R 263 - end of helix Proline residue: R 272 - end of helix Processing helix chain 'R' and resid 281 through 303 removed outlier: 4.473A pdb=" N ALA R 285 " --> pdb=" O SER R 281 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU R 286 " --> pdb=" O LEU R 282 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER R 294 " --> pdb=" O GLY R 290 " (cutoff:3.500A) Proline residue: R 298 - end of helix Processing helix chain 'R' and resid 305 through 312 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'Y' and resid 9 through 24 removed outlier: 3.691A pdb=" N ASN Y 24 " --> pdb=" O LYS Y 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 44 Processing helix chain 'Y' and resid 45 through 48 removed outlier: 3.866A pdb=" N ASP Y 48 " --> pdb=" O ALA Y 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 45 through 48' Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 3.503A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL A 254 " --> pdb=" O TYR A 327 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 4.067A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.050A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.931A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.588A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.917A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.818A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR B 243 " --> pdb=" O ARG B 251 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.630A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.717A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR N 69 " --> pdb=" O GLN N 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 46 through 47 removed outlier: 3.597A pdb=" N VAL N 37 " --> pdb=" O TYR N 95 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA N 92 " --> pdb=" O VAL N 124 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR N 122 " --> pdb=" O TYR N 94 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.518A pdb=" N GLN S 3 " --> pdb=" O SER S 25 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.867A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 142 Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.736A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 194 through 195 removed outlier: 3.615A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) 421 hydrogen bonds defined for protein. 1197 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: 1.40 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1480 1.30 - 1.43: 2592 1.43 - 1.56: 5237 1.56 - 1.69: 1 1.69 - 1.82: 76 Bond restraints: 9386 Sorted by residual: bond pdb=" CA PHE R 90 " pdb=" C PHE R 90 " ideal model delta sigma weight residual 1.527 1.446 0.081 9.80e-03 1.04e+04 6.87e+01 bond pdb=" C TYR R 171 " pdb=" O TYR R 171 " ideal model delta sigma weight residual 1.236 1.166 0.071 1.15e-02 7.56e+03 3.77e+01 bond pdb=" C VAL R 124 " pdb=" O VAL R 124 " ideal model delta sigma weight residual 1.237 1.171 0.066 1.19e-02 7.06e+03 3.05e+01 bond pdb=" CA VAL R 124 " pdb=" C VAL R 124 " ideal model delta sigma weight residual 1.524 1.452 0.072 1.30e-02 5.92e+03 3.05e+01 bond pdb=" C THR R 268 " pdb=" O THR R 268 " ideal model delta sigma weight residual 1.237 1.172 0.065 1.19e-02 7.06e+03 2.94e+01 ... (remaining 9381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 12491 2.95 - 5.90: 247 5.90 - 8.85: 32 8.85 - 11.80: 15 11.80 - 14.75: 2 Bond angle restraints: 12787 Sorted by residual: angle pdb=" N VAL R 124 " pdb=" CA VAL R 124 " pdb=" C VAL R 124 " ideal model delta sigma weight residual 110.72 121.03 -10.31 1.01e+00 9.80e-01 1.04e+02 angle pdb=" N MET R 157 " pdb=" CA MET R 157 " pdb=" C MET R 157 " ideal model delta sigma weight residual 111.33 121.98 -10.65 1.21e+00 6.83e-01 7.74e+01 angle pdb=" N VAL R 175 " pdb=" CA VAL R 175 " pdb=" C VAL R 175 " ideal model delta sigma weight residual 111.00 120.53 -9.53 1.09e+00 8.42e-01 7.65e+01 angle pdb=" N SER N 49 " pdb=" CA SER N 49 " pdb=" C SER N 49 " ideal model delta sigma weight residual 108.18 122.93 -14.75 2.01e+00 2.48e-01 5.39e+01 angle pdb=" C VAL R 175 " pdb=" CA VAL R 175 " pdb=" CB VAL R 175 " ideal model delta sigma weight residual 112.24 102.72 9.52 1.34e+00 5.57e-01 5.05e+01 ... (remaining 12782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4984 17.98 - 35.96: 382 35.96 - 53.94: 63 53.94 - 71.92: 11 71.92 - 89.90: 5 Dihedral angle restraints: 5445 sinusoidal: 1849 harmonic: 3596 Sorted by residual: dihedral pdb=" C PRO R 127 " pdb=" N PRO R 127 " pdb=" CA PRO R 127 " pdb=" CB PRO R 127 " ideal model delta harmonic sigma weight residual -120.70 -139.85 19.15 0 2.50e+00 1.60e-01 5.87e+01 dihedral pdb=" N PRO R 127 " pdb=" C PRO R 127 " pdb=" CA PRO R 127 " pdb=" CB PRO R 127 " ideal model delta harmonic sigma weight residual 115.10 131.69 -16.59 0 2.50e+00 1.60e-01 4.40e+01 dihedral pdb=" C GLN A 24 " pdb=" N GLN A 24 " pdb=" CA GLN A 24 " pdb=" CB GLN A 24 " ideal model delta harmonic sigma weight residual -122.60 -109.53 -13.07 0 2.50e+00 1.60e-01 2.73e+01 ... (remaining 5442 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.176: 1449 0.176 - 0.352: 29 0.352 - 0.528: 3 0.528 - 0.703: 0 0.703 - 0.879: 1 Chirality restraints: 1482 Sorted by residual: chirality pdb=" CA PRO R 127 " pdb=" N PRO R 127 " pdb=" C PRO R 127 " pdb=" CB PRO R 127 " both_signs ideal model delta sigma weight residual False 2.72 1.84 0.88 2.00e-01 2.50e+01 1.93e+01 chirality pdb=" CA MET R 157 " pdb=" N MET R 157 " pdb=" C MET R 157 " pdb=" CB MET R 157 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.60e+00 chirality pdb=" CA VAL R 124 " pdb=" N VAL R 124 " pdb=" C VAL R 124 " pdb=" CB VAL R 124 " both_signs ideal model delta sigma weight residual False 2.44 2.02 0.42 2.00e-01 2.50e+01 4.34e+00 ... (remaining 1479 not shown) Planarity restraints: 1619 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY R 156 " 0.024 2.00e-02 2.50e+03 4.65e-02 2.16e+01 pdb=" C GLY R 156 " -0.080 2.00e-02 2.50e+03 pdb=" O GLY R 156 " 0.029 2.00e-02 2.50e+03 pdb=" N MET R 157 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 123 " -0.023 2.00e-02 2.50e+03 4.55e-02 2.07e+01 pdb=" C ALA R 123 " 0.079 2.00e-02 2.50e+03 pdb=" O ALA R 123 " -0.029 2.00e-02 2.50e+03 pdb=" N VAL R 124 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO R 127 " 0.022 2.00e-02 2.50e+03 4.51e-02 2.03e+01 pdb=" C PRO R 127 " -0.078 2.00e-02 2.50e+03 pdb=" O PRO R 127 " 0.029 2.00e-02 2.50e+03 pdb=" N LEU R 128 " 0.028 2.00e-02 2.50e+03 ... (remaining 1616 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 251 2.68 - 3.24: 8418 3.24 - 3.79: 13372 3.79 - 4.35: 17485 4.35 - 4.90: 30529 Nonbonded interactions: 70055 Sorted by model distance: nonbonded pdb=" O ASP R 126 " pdb=" OD1 ASP R 126 " model vdw 2.130 3.040 nonbonded pdb=" O SER N 85 " pdb=" OG SER N 85 " model vdw 2.150 3.040 nonbonded pdb=" ND2 ASN B 230 " pdb=" OD1 ASP B 246 " model vdw 2.243 3.120 nonbonded pdb=" OD1 ASP B 205 " pdb=" OG SER B 207 " model vdw 2.282 3.040 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.285 3.040 ... (remaining 70050 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.870 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 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 : 0.008 0.083 9388 Z= 0.502 Angle : 0.992 14.751 12791 Z= 0.633 Chirality : 0.067 0.879 1482 Planarity : 0.006 0.112 1619 Dihedral : 13.339 89.902 3117 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.10 % Allowed : 2.87 % Favored : 96.03 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.24), residues: 1205 helix: 1.63 (0.28), residues: 383 sheet: 0.11 (0.30), residues: 324 loop : -1.79 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 82 TYR 0.030 0.002 TYR B 59 PHE 0.023 0.002 PHE N 108 TRP 0.030 0.002 TRP N 47 HIS 0.004 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00754 ( 9386) covalent geometry : angle 0.99225 (12787) SS BOND : bond 0.00658 ( 2) SS BOND : angle 0.65872 ( 4) hydrogen bonds : bond 0.20706 ( 421) hydrogen bonds : angle 6.60957 ( 1197) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.7328 (tp-100) cc_final: 0.7114 (mt0) REVERT: S 87 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.6222 (mtm-85) outliers start: 10 outliers final: 3 residues processed: 143 average time/residue: 0.1020 time to fit residues: 20.3270 Evaluate side-chains 110 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 106 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 126 ASP Chi-restraints excluded: chain R residue 268 THR Chi-restraints excluded: chain S residue 87 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.0070 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.137651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.102089 restraints weight = 12090.673| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.27 r_work: 0.2988 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9388 Z= 0.161 Angle : 0.596 8.426 12791 Z= 0.319 Chirality : 0.044 0.160 1482 Planarity : 0.005 0.077 1619 Dihedral : 5.448 76.255 1329 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.66 % Allowed : 9.48 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.24), residues: 1205 helix: 2.12 (0.27), residues: 384 sheet: 0.35 (0.30), residues: 316 loop : -1.70 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 309 TYR 0.027 0.002 TYR B 59 PHE 0.013 0.002 PHE B 199 TRP 0.013 0.001 TRP S 47 HIS 0.008 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 9386) covalent geometry : angle 0.59587 (12787) SS BOND : bond 0.00809 ( 2) SS BOND : angle 0.82166 ( 4) hydrogen bonds : bond 0.05806 ( 421) hydrogen bonds : angle 4.60527 ( 1197) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 112 time to evaluate : 0.342 Fit side-chains REVERT: A 24 GLN cc_start: 0.7806 (tp40) cc_final: 0.7313 (mt0) REVERT: B 59 TYR cc_start: 0.8522 (m-10) cc_final: 0.7888 (m-10) REVERT: N 7 SER cc_start: 0.6705 (m) cc_final: 0.6450 (p) REVERT: N 30 SER cc_start: 0.8565 (t) cc_final: 0.8297 (p) REVERT: R 157 MET cc_start: 0.7922 (ttt) cc_final: 0.7529 (ttt) REVERT: S 93 MET cc_start: 0.8468 (ttm) cc_final: 0.8227 (ttp) outliers start: 6 outliers final: 4 residues processed: 116 average time/residue: 0.0839 time to fit residues: 14.4782 Evaluate side-chains 109 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 105 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain S residue 179 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 20 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 115 optimal weight: 0.0050 chunk 90 optimal weight: 0.0870 chunk 64 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 overall best weight: 2.2178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.137366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.102308 restraints weight = 12138.024| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.19 r_work: 0.2986 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9388 Z= 0.139 Angle : 0.541 6.444 12791 Z= 0.291 Chirality : 0.042 0.154 1482 Planarity : 0.004 0.066 1619 Dihedral : 4.230 47.146 1321 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.32 % Allowed : 10.69 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.24), residues: 1205 helix: 2.32 (0.27), residues: 384 sheet: 0.37 (0.30), residues: 309 loop : -1.60 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 19 TYR 0.021 0.001 TYR B 59 PHE 0.012 0.001 PHE B 199 TRP 0.012 0.001 TRP S 47 HIS 0.005 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9386) covalent geometry : angle 0.54077 (12787) SS BOND : bond 0.00772 ( 2) SS BOND : angle 0.67025 ( 4) hydrogen bonds : bond 0.05296 ( 421) hydrogen bonds : angle 4.34971 ( 1197) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.387 Fit side-chains REVERT: A 24 GLN cc_start: 0.7786 (tp40) cc_final: 0.7302 (mt0) REVERT: B 59 TYR cc_start: 0.8539 (m-10) cc_final: 0.7922 (m-10) REVERT: B 215 GLU cc_start: 0.7537 (pp20) cc_final: 0.7124 (pp20) REVERT: N 34 MET cc_start: 0.7731 (mmm) cc_final: 0.7419 (mmm) REVERT: R 102 ASP cc_start: 0.7764 (t70) cc_final: 0.7533 (t0) REVERT: R 157 MET cc_start: 0.7988 (ttt) cc_final: 0.7627 (ttt) outliers start: 12 outliers final: 6 residues processed: 121 average time/residue: 0.0864 time to fit residues: 15.5631 Evaluate side-chains 111 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 268 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 179 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 52 optimal weight: 8.9990 chunk 106 optimal weight: 50.0000 chunk 27 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 24 optimal weight: 20.0000 chunk 94 optimal weight: 20.0000 chunk 59 optimal weight: 0.0870 chunk 112 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.137404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.102133 restraints weight = 12116.168| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.20 r_work: 0.2973 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9388 Z= 0.127 Angle : 0.517 6.055 12791 Z= 0.277 Chirality : 0.042 0.150 1482 Planarity : 0.004 0.062 1619 Dihedral : 4.114 45.295 1321 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.21 % Allowed : 11.91 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.24), residues: 1205 helix: 2.34 (0.27), residues: 386 sheet: 0.40 (0.30), residues: 315 loop : -1.57 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 211 TYR 0.017 0.001 TYR B 59 PHE 0.012 0.001 PHE R 207 TRP 0.010 0.001 TRP S 47 HIS 0.005 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9386) covalent geometry : angle 0.51673 (12787) SS BOND : bond 0.00631 ( 2) SS BOND : angle 0.54714 ( 4) hydrogen bonds : bond 0.04944 ( 421) hydrogen bonds : angle 4.19021 ( 1197) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.359 Fit side-chains REVERT: A 24 GLN cc_start: 0.7744 (tp40) cc_final: 0.7279 (mt0) REVERT: B 59 TYR cc_start: 0.8594 (m-10) cc_final: 0.8224 (m-10) REVERT: B 215 GLU cc_start: 0.7561 (pp20) cc_final: 0.7020 (pp20) REVERT: R 102 ASP cc_start: 0.7735 (t70) cc_final: 0.7495 (t0) REVERT: R 157 MET cc_start: 0.8135 (ttt) cc_final: 0.7764 (ttt) REVERT: R 164 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7336 (mm) outliers start: 11 outliers final: 6 residues processed: 116 average time/residue: 0.0852 time to fit residues: 14.6695 Evaluate side-chains 110 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain S residue 155 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 96 optimal weight: 8.9990 chunk 116 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 63 optimal weight: 50.0000 chunk 97 optimal weight: 0.1980 chunk 88 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 197 HIS B 16 ASN B 17 GLN B 220 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.132636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.097027 restraints weight = 12233.591| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.35 r_work: 0.2903 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 9388 Z= 0.236 Angle : 0.624 9.409 12791 Z= 0.336 Chirality : 0.046 0.169 1482 Planarity : 0.005 0.061 1619 Dihedral : 4.631 51.765 1321 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.87 % Allowed : 12.46 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.24), residues: 1205 helix: 2.02 (0.27), residues: 382 sheet: 0.13 (0.30), residues: 319 loop : -1.59 (0.24), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 211 TYR 0.028 0.002 TYR B 59 PHE 0.015 0.002 PHE B 241 TRP 0.012 0.002 TRP B 63 HIS 0.007 0.002 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00577 ( 9386) covalent geometry : angle 0.62409 (12787) SS BOND : bond 0.00988 ( 2) SS BOND : angle 0.73472 ( 4) hydrogen bonds : bond 0.06881 ( 421) hydrogen bonds : angle 4.53174 ( 1197) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.352 Fit side-chains REVERT: A 24 GLN cc_start: 0.7856 (tp40) cc_final: 0.7298 (mt0) REVERT: B 59 TYR cc_start: 0.8763 (m-10) cc_final: 0.8313 (m-80) REVERT: B 215 GLU cc_start: 0.7632 (pp20) cc_final: 0.7072 (pp20) REVERT: B 273 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8410 (mp) REVERT: R 102 ASP cc_start: 0.8071 (t70) cc_final: 0.7844 (t0) REVERT: R 157 MET cc_start: 0.8218 (ttt) cc_final: 0.7857 (ttt) REVERT: R 164 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7264 (mm) outliers start: 17 outliers final: 10 residues processed: 122 average time/residue: 0.0809 time to fit residues: 14.6718 Evaluate side-chains 117 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 268 THR Chi-restraints excluded: chain S residue 155 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 97 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 57 optimal weight: 0.0170 chunk 93 optimal weight: 7.9990 chunk 117 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 55 optimal weight: 40.0000 chunk 12 optimal weight: 0.7980 overall best weight: 1.7624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN B 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.136382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.100989 restraints weight = 12135.962| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.23 r_work: 0.2962 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9388 Z= 0.121 Angle : 0.517 6.484 12791 Z= 0.277 Chirality : 0.041 0.149 1482 Planarity : 0.004 0.058 1619 Dihedral : 4.211 44.694 1321 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.76 % Allowed : 13.45 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.24), residues: 1205 helix: 2.21 (0.27), residues: 386 sheet: 0.32 (0.30), residues: 310 loop : -1.53 (0.25), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 211 TYR 0.014 0.001 TYR S 190 PHE 0.013 0.001 PHE R 207 TRP 0.011 0.001 TRP S 47 HIS 0.005 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9386) covalent geometry : angle 0.51687 (12787) SS BOND : bond 0.00696 ( 2) SS BOND : angle 0.65300 ( 4) hydrogen bonds : bond 0.05043 ( 421) hydrogen bonds : angle 4.23903 ( 1197) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.392 Fit side-chains REVERT: A 24 GLN cc_start: 0.7787 (tp40) cc_final: 0.7285 (mt0) REVERT: B 59 TYR cc_start: 0.8693 (OUTLIER) cc_final: 0.8131 (m-80) REVERT: B 215 GLU cc_start: 0.7563 (pp20) cc_final: 0.7110 (pp20) REVERT: B 273 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8428 (mp) REVERT: R 102 ASP cc_start: 0.7821 (t70) cc_final: 0.7562 (t0) REVERT: R 211 ARG cc_start: 0.8244 (mmm-85) cc_final: 0.7871 (mtt-85) REVERT: S 43 LYS cc_start: 0.8720 (mppt) cc_final: 0.8357 (mppt) outliers start: 16 outliers final: 10 residues processed: 122 average time/residue: 0.0752 time to fit residues: 13.6160 Evaluate side-chains 118 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 268 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 192 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 43 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 93 optimal weight: 0.6980 chunk 99 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 53 optimal weight: 0.3980 chunk 58 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.134327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.098716 restraints weight = 12281.457| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.25 r_work: 0.2933 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9388 Z= 0.167 Angle : 0.558 7.951 12791 Z= 0.299 Chirality : 0.043 0.157 1482 Planarity : 0.004 0.058 1619 Dihedral : 4.303 46.348 1321 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.76 % Allowed : 13.56 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.24), residues: 1205 helix: 2.13 (0.27), residues: 386 sheet: 0.29 (0.30), residues: 309 loop : -1.58 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 211 TYR 0.020 0.002 TYR B 59 PHE 0.013 0.002 PHE B 241 TRP 0.011 0.001 TRP B 63 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 9386) covalent geometry : angle 0.55756 (12787) SS BOND : bond 0.00783 ( 2) SS BOND : angle 0.74421 ( 4) hydrogen bonds : bond 0.05726 ( 421) hydrogen bonds : angle 4.29540 ( 1197) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.263 Fit side-chains REVERT: A 24 GLN cc_start: 0.7822 (tp40) cc_final: 0.7315 (mt0) REVERT: B 59 TYR cc_start: 0.8821 (OUTLIER) cc_final: 0.8160 (m-80) REVERT: B 215 GLU cc_start: 0.7597 (pp20) cc_final: 0.7146 (pp20) REVERT: B 273 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8438 (mp) REVERT: R 102 ASP cc_start: 0.7910 (t70) cc_final: 0.7655 (t0) REVERT: R 211 ARG cc_start: 0.8287 (mmm-85) cc_final: 0.7915 (mtt-85) REVERT: S 43 LYS cc_start: 0.8799 (mppt) cc_final: 0.8418 (mppt) outliers start: 16 outliers final: 13 residues processed: 115 average time/residue: 0.0794 time to fit residues: 13.5661 Evaluate side-chains 118 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 268 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 192 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 109 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 115 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.134203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.098885 restraints weight = 12157.767| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.40 r_work: 0.2930 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9388 Z= 0.165 Angle : 0.564 8.980 12791 Z= 0.299 Chirality : 0.043 0.156 1482 Planarity : 0.004 0.058 1619 Dihedral : 4.303 45.382 1321 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.98 % Allowed : 13.78 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.24), residues: 1205 helix: 2.11 (0.27), residues: 386 sheet: 0.23 (0.30), residues: 312 loop : -1.53 (0.24), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 211 TYR 0.020 0.002 TYR B 59 PHE 0.012 0.002 PHE B 199 TRP 0.010 0.001 TRP B 63 HIS 0.004 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 9386) covalent geometry : angle 0.56375 (12787) SS BOND : bond 0.00813 ( 2) SS BOND : angle 0.71611 ( 4) hydrogen bonds : bond 0.05681 ( 421) hydrogen bonds : angle 4.29078 ( 1197) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.413 Fit side-chains REVERT: A 24 GLN cc_start: 0.7845 (tp40) cc_final: 0.7326 (mt0) REVERT: A 337 GLU cc_start: 0.7686 (mp0) cc_final: 0.7472 (tt0) REVERT: B 59 TYR cc_start: 0.8818 (OUTLIER) cc_final: 0.8197 (m-80) REVERT: B 215 GLU cc_start: 0.7590 (pp20) cc_final: 0.7196 (pp20) REVERT: B 273 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8445 (mp) REVERT: R 102 ASP cc_start: 0.7913 (t70) cc_final: 0.7658 (t0) REVERT: R 211 ARG cc_start: 0.8283 (mmm-85) cc_final: 0.7914 (mtt-85) REVERT: S 43 LYS cc_start: 0.8757 (mppt) cc_final: 0.8364 (mppt) REVERT: S 46 GLU cc_start: 0.8360 (tt0) cc_final: 0.8099 (tt0) outliers start: 18 outliers final: 12 residues processed: 119 average time/residue: 0.0825 time to fit residues: 14.6070 Evaluate side-chains 119 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 268 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 192 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 70 optimal weight: 0.9980 chunk 87 optimal weight: 0.0470 chunk 16 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 62 optimal weight: 20.0000 chunk 65 optimal weight: 20.0000 chunk 58 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 overall best weight: 4.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.132823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.097878 restraints weight = 12294.340| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.29 r_work: 0.2919 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9388 Z= 0.210 Angle : 0.603 10.075 12791 Z= 0.323 Chirality : 0.044 0.163 1482 Planarity : 0.005 0.057 1619 Dihedral : 4.495 48.254 1321 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.76 % Allowed : 13.89 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.24), residues: 1205 helix: 2.02 (0.27), residues: 382 sheet: 0.11 (0.30), residues: 316 loop : -1.55 (0.24), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 211 TYR 0.024 0.002 TYR B 59 PHE 0.014 0.002 PHE B 151 TRP 0.012 0.002 TRP B 63 HIS 0.005 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00512 ( 9386) covalent geometry : angle 0.60293 (12787) SS BOND : bond 0.00928 ( 2) SS BOND : angle 0.81834 ( 4) hydrogen bonds : bond 0.06392 ( 421) hydrogen bonds : angle 4.43985 ( 1197) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.389 Fit side-chains REVERT: A 24 GLN cc_start: 0.7845 (tp40) cc_final: 0.7321 (mt0) REVERT: A 337 GLU cc_start: 0.7758 (mp0) cc_final: 0.7508 (tt0) REVERT: B 59 TYR cc_start: 0.8859 (OUTLIER) cc_final: 0.8160 (m-80) REVERT: B 215 GLU cc_start: 0.7597 (pp20) cc_final: 0.7197 (pp20) REVERT: B 273 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8438 (mp) REVERT: R 102 ASP cc_start: 0.8036 (t70) cc_final: 0.7763 (t0) REVERT: R 211 ARG cc_start: 0.8291 (mmm-85) cc_final: 0.7915 (mtt-85) REVERT: S 43 LYS cc_start: 0.8831 (mppt) cc_final: 0.8415 (mppt) REVERT: S 46 GLU cc_start: 0.8408 (tt0) cc_final: 0.8131 (tt0) REVERT: S 183 GLN cc_start: 0.8781 (mm110) cc_final: 0.8547 (mm110) outliers start: 16 outliers final: 12 residues processed: 117 average time/residue: 0.0811 time to fit residues: 14.4813 Evaluate side-chains 119 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 268 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 192 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 6 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 20 optimal weight: 0.0970 chunk 69 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 120 optimal weight: 0.1980 chunk 94 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 56 optimal weight: 30.0000 chunk 35 optimal weight: 0.3980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.139393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.104317 restraints weight = 12136.712| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.26 r_work: 0.3020 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9388 Z= 0.094 Angle : 0.486 6.296 12791 Z= 0.259 Chirality : 0.040 0.143 1482 Planarity : 0.004 0.057 1619 Dihedral : 3.909 38.011 1321 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.88 % Allowed : 14.77 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.24), residues: 1205 helix: 2.33 (0.27), residues: 386 sheet: 0.36 (0.30), residues: 305 loop : -1.42 (0.25), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 211 TYR 0.018 0.001 TYR S 190 PHE 0.012 0.001 PHE B 199 TRP 0.014 0.001 TRP S 47 HIS 0.003 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00187 ( 9386) covalent geometry : angle 0.48635 (12787) SS BOND : bond 0.00493 ( 2) SS BOND : angle 0.62167 ( 4) hydrogen bonds : bond 0.03878 ( 421) hydrogen bonds : angle 4.08066 ( 1197) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.358 Fit side-chains REVERT: A 24 GLN cc_start: 0.7729 (tp40) cc_final: 0.7154 (mt0) REVERT: A 337 GLU cc_start: 0.7616 (mp0) cc_final: 0.7221 (tt0) REVERT: B 59 TYR cc_start: 0.8705 (OUTLIER) cc_final: 0.8091 (m-80) REVERT: B 215 GLU cc_start: 0.7500 (pp20) cc_final: 0.7146 (pp20) REVERT: R 102 ASP cc_start: 0.7538 (t70) cc_final: 0.7309 (t0) REVERT: R 182 SER cc_start: 0.8577 (OUTLIER) cc_final: 0.8291 (m) REVERT: R 211 ARG cc_start: 0.8165 (mmm-85) cc_final: 0.7815 (mtt-85) REVERT: S 46 GLU cc_start: 0.8194 (tt0) cc_final: 0.7962 (tt0) REVERT: S 183 GLN cc_start: 0.8605 (mm110) cc_final: 0.8282 (mm-40) outliers start: 8 outliers final: 6 residues processed: 116 average time/residue: 0.0817 time to fit residues: 14.2406 Evaluate side-chains 116 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 192 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 49 optimal weight: 0.5980 chunk 15 optimal weight: 0.3980 chunk 99 optimal weight: 0.0980 chunk 19 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.141699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.106382 restraints weight = 11913.136| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.16 r_work: 0.3066 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9388 Z= 0.090 Angle : 0.471 6.356 12791 Z= 0.248 Chirality : 0.040 0.142 1482 Planarity : 0.004 0.055 1619 Dihedral : 3.601 36.733 1321 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.88 % Allowed : 15.10 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.25), residues: 1205 helix: 2.56 (0.27), residues: 380 sheet: 0.38 (0.30), residues: 315 loop : -1.24 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 211 TYR 0.015 0.001 TYR S 190 PHE 0.012 0.001 PHE R 207 TRP 0.009 0.001 TRP B 297 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00182 ( 9386) covalent geometry : angle 0.47125 (12787) SS BOND : bond 0.00527 ( 2) SS BOND : angle 0.49544 ( 4) hydrogen bonds : bond 0.03493 ( 421) hydrogen bonds : angle 3.84863 ( 1197) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2736.99 seconds wall clock time: 47 minutes 31.73 seconds (2851.73 seconds total)