Starting phenix.real_space_refine on Sat Aug 23 03:02:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8itf_35705/08_2025/8itf_35705_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8itf_35705/08_2025/8itf_35705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8itf_35705/08_2025/8itf_35705_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8itf_35705/08_2025/8itf_35705_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8itf_35705/08_2025/8itf_35705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8itf_35705/08_2025/8itf_35705.map" } resolution = 3.46 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= 0.005 sd= 0.051 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 57 5.16 5 C 6131 2.51 5 N 1638 2.21 5 O 1725 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 9551 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1806 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 2 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 11, 'GLU:plan': 11, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 92 Chain: "B" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2431 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain breaks: 1 Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 17, 'ARG:plan': 7, 'GLN:plan1': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 132 Chain: "C" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 372 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'GLU:plan': 5, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 42 Chain: "R" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2283 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 12, 'TRANS': 286} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 3, 'TRP:plan': 1, 'GLU:plan': 3, 'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 70 Chain: "S" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1712 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 10, 'TRANS': 217} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "N" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 938 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'8IA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.14, per 1000 atoms: 0.22 Number of scatterers: 9551 At special positions: 0 Unit cell: (121.55, 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 57 16.00 O 1725 8.00 N 1638 7.00 C 6131 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 186 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " 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: 0.75 Conformation dependent library (CDL) restraints added in 379.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2388 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 14 sheets defined 33.5% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.839A pdb=" N LYS A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 39 removed outlier: 3.509A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.661A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE A 238 " --> pdb=" O ILE A 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 234 through 238' Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.882A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.609A pdb=" N PHE A 315 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 312 through 316' Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.908A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 9 through 22 Processing helix chain 'C' and resid 29 through 43 Processing helix chain 'C' and resid 44 through 48 removed outlier: 3.834A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 59 removed outlier: 3.566A pdb=" N ASN C 59 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 34 through 60 removed outlier: 4.158A pdb=" N VAL R 38 " --> pdb=" O ILE R 34 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU R 39 " --> pdb=" O LEU R 35 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY R 42 " --> pdb=" O VAL R 38 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA R 43 " --> pdb=" O LEU R 39 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL R 47 " --> pdb=" O ALA R 43 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASN R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU R 52 " --> pdb=" O PHE R 48 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL R 53 " --> pdb=" O GLY R 49 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE R 54 " --> pdb=" O ASN R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 84 removed outlier: 4.081A pdb=" N VAL R 81 " --> pdb=" O ALA R 77 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY R 82 " --> pdb=" O ASP R 78 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL R 83 " --> pdb=" O PHE R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 93 removed outlier: 4.269A pdb=" N VAL R 91 " --> pdb=" O PRO R 87 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG R 92 " --> pdb=" O PHE R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 113 removed outlier: 3.800A pdb=" N CYS R 105 " --> pdb=" O GLY R 101 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS R 106 " --> pdb=" O GLU R 102 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE R 107 " --> pdb=" O SER R 103 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR R 109 " --> pdb=" O CYS R 105 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N CYS R 110 " --> pdb=" O LYS R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 120 through 136 removed outlier: 3.612A pdb=" N CYS R 124 " --> pdb=" O LEU R 120 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP R 136 " --> pdb=" O ILE R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 144 Processing helix chain 'R' and resid 145 through 168 removed outlier: 3.813A pdb=" N SER R 149 " --> pdb=" O THR R 145 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY R 150 " --> pdb=" O VAL R 146 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER R 156 " --> pdb=" O CYS R 152 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TRP R 157 " --> pdb=" O ILE R 153 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE R 167 " --> pdb=" O TYR R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 200 through 232 removed outlier: 4.109A pdb=" N LEU R 205 " --> pdb=" O LEU R 201 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE R 206 " --> pdb=" O CYS R 202 " (cutoff:3.500A) Proline residue: R 209 - end of helix removed outlier: 3.637A pdb=" N ARG R 229 " --> pdb=" O LYS R 225 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS R 230 " --> pdb=" O TYR R 226 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE R 231 " --> pdb=" O GLN R 227 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU R 232 " --> pdb=" O ALA R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 270 removed outlier: 3.867A pdb=" N ILE R 262 " --> pdb=" O LYS R 258 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA R 263 " --> pdb=" O THR R 259 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER R 270 " --> pdb=" O ALA R 266 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 282 Processing helix chain 'R' and resid 289 through 312 removed outlier: 3.885A pdb=" N TYR R 293 " --> pdb=" O PRO R 289 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU R 294 " --> pdb=" O ALA R 290 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE R 295 " --> pdb=" O TYR R 291 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR R 301 " --> pdb=" O VAL R 297 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR R 302 " --> pdb=" O TRP R 298 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN R 303 " --> pdb=" O CYS R 299 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER R 304 " --> pdb=" O VAL R 300 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA R 305 " --> pdb=" O TYR R 301 " (cutoff:3.500A) Proline residue: R 308 - end of helix removed outlier: 3.558A pdb=" N ALA R 312 " --> pdb=" O PRO R 308 " (cutoff:3.500A) Processing helix chain 'R' and resid 315 through 327 removed outlier: 3.671A pdb=" N ILE R 325 " --> pdb=" O ALA R 321 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL R 326 " --> pdb=" O ILE R 322 " (cutoff:3.500A) Processing helix chain 'R' and resid 328 through 332 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.248A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 220 through 224 removed outlier: 4.282A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.653A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 62 through 65 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.553A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.800A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.871A 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: 7.031A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.254A 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: 7.114A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN B 125 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.858A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.110A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 210 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.488A 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: 3.589A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.877A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.957A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 140 through 141 removed outlier: 3.514A pdb=" N ARG S 160 " --> pdb=" O THR S 141 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 194 through 195 removed outlier: 3.602A pdb=" N TYR S 190 " --> pdb=" O ASN S 194 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.612A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.129A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP N 50 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 381 hydrogen bonds defined for protein. 1065 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: 1.29 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1478 1.28 - 1.42: 2710 1.42 - 1.55: 5500 1.55 - 1.68: 1 1.68 - 1.82: 80 Bond restraints: 9769 Sorted by residual: bond pdb=" C VAL R 300 " pdb=" O VAL R 300 " ideal model delta sigma weight residual 1.237 1.151 0.086 1.17e-02 7.31e+03 5.41e+01 bond pdb=" CA CYS R 116 " pdb=" C CYS R 116 " ideal model delta sigma weight residual 1.525 1.439 0.086 1.25e-02 6.40e+03 4.78e+01 bond pdb=" CA ALA R 305 " pdb=" C ALA R 305 " ideal model delta sigma weight residual 1.519 1.446 0.074 1.32e-02 5.74e+03 3.12e+01 bond pdb=" CA VAL R 300 " pdb=" CB VAL R 300 " ideal model delta sigma weight residual 1.540 1.475 0.065 1.25e-02 6.40e+03 2.71e+01 bond pdb=" CA SER R 114 " pdb=" C SER R 114 " ideal model delta sigma weight residual 1.525 1.460 0.065 1.29e-02 6.01e+03 2.55e+01 ... (remaining 9764 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 13027 1.87 - 3.74: 210 3.74 - 5.61: 48 5.61 - 7.48: 8 7.48 - 9.35: 6 Bond angle restraints: 13299 Sorted by residual: angle pdb=" N SER R 304 " pdb=" CA SER R 304 " pdb=" C SER R 304 " ideal model delta sigma weight residual 113.02 104.63 8.39 1.20e+00 6.94e-01 4.89e+01 angle pdb=" N ALA R 305 " pdb=" CA ALA R 305 " pdb=" C ALA R 305 " ideal model delta sigma weight residual 113.88 106.04 7.84 1.23e+00 6.61e-01 4.06e+01 angle pdb=" N PHE R 115 " pdb=" CA PHE R 115 " pdb=" C PHE R 115 " ideal model delta sigma weight residual 111.71 117.49 -5.78 1.15e+00 7.56e-01 2.52e+01 angle pdb=" N VAL R 300 " pdb=" CA VAL R 300 " pdb=" C VAL R 300 " ideal model delta sigma weight residual 110.62 115.51 -4.89 1.02e+00 9.61e-01 2.30e+01 angle pdb=" N ALA R 290 " pdb=" CA ALA R 290 " pdb=" C ALA R 290 " ideal model delta sigma weight residual 113.17 107.38 5.79 1.26e+00 6.30e-01 2.11e+01 ... (remaining 13294 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 5151 17.87 - 35.73: 435 35.73 - 53.60: 94 53.60 - 71.46: 7 71.46 - 89.33: 10 Dihedral angle restraints: 5697 sinusoidal: 1988 harmonic: 3709 Sorted by residual: dihedral pdb=" CA GLY R 328 " pdb=" C GLY R 328 " pdb=" N LYS R 329 " pdb=" CA LYS R 329 " ideal model delta harmonic sigma weight residual -180.00 -152.36 -27.64 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CB CYS S 22 " pdb=" SG CYS S 22 " pdb=" SG CYS S 96 " pdb=" CB CYS S 96 " ideal model delta sinusoidal sigma weight residual 93.00 60.34 32.66 1 1.00e+01 1.00e-02 1.52e+01 dihedral pdb=" CA PRO R 31 " pdb=" C PRO R 31 " pdb=" N ARG R 32 " pdb=" CA ARG R 32 " ideal model delta harmonic sigma weight residual 180.00 160.84 19.16 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 5694 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1479 0.105 - 0.209: 55 0.209 - 0.314: 3 0.314 - 0.419: 1 0.419 - 0.523: 1 Chirality restraints: 1539 Sorted by residual: chirality pdb=" CA PHE R 115 " pdb=" N PHE R 115 " pdb=" C PHE R 115 " pdb=" CB PHE R 115 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.84e+00 chirality pdb=" CA CYS R 116 " pdb=" N CYS R 116 " pdb=" C CYS R 116 " pdb=" CB CYS R 116 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA VAL R 300 " pdb=" N VAL R 300 " pdb=" C VAL R 300 " pdb=" CB VAL R 300 " both_signs ideal model delta sigma weight residual False 2.44 2.17 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1536 not shown) Planarity restraints: 1672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER R 327 " 0.016 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C SER R 327 " -0.059 2.00e-02 2.50e+03 pdb=" O SER R 327 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY R 328 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP R 30 " 0.050 5.00e-02 4.00e+02 7.45e-02 8.88e+00 pdb=" N PRO R 31 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO R 31 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO R 31 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA R 28 " 0.037 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO R 29 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO R 29 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 29 " 0.031 5.00e-02 4.00e+02 ... (remaining 1669 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2107 2.78 - 3.31: 8415 3.31 - 3.84: 14228 3.84 - 4.37: 16009 4.37 - 4.90: 29094 Nonbonded interactions: 69853 Sorted by model distance: nonbonded pdb=" NH2 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.250 3.120 nonbonded pdb=" OG SER S 204 " pdb=" OG1 THR S 215 " model vdw 2.260 3.040 nonbonded pdb=" NH1 ARG A 15 " pdb=" O VAL B 90 " model vdw 2.293 3.120 nonbonded pdb=" OD2 ASP R 112 " pdb=" OH TYR R 301 " model vdw 2.306 3.040 nonbonded pdb=" O PRO A 332 " pdb=" OG1 THR A 335 " model vdw 2.333 3.040 ... (remaining 69848 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: 0.510 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.570 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 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 : 0.005 0.086 9772 Z= 0.306 Angle : 0.644 9.345 13305 Z= 0.383 Chirality : 0.048 0.523 1539 Planarity : 0.005 0.074 1672 Dihedral : 14.169 89.327 3300 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.95 % Allowed : 6.62 % Favored : 92.43 % 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: -0.32 (0.24), residues: 1255 helix: 0.86 (0.30), residues: 366 sheet: 0.57 (0.29), residues: 306 loop : -1.36 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 130 TYR 0.013 0.001 TYR R 226 PHE 0.014 0.001 PHE R 314 TRP 0.008 0.001 TRP R 317 HIS 0.009 0.001 HIS S 167 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 9769) covalent geometry : angle 0.64348 (13299) SS BOND : bond 0.00288 ( 3) SS BOND : angle 0.88294 ( 6) hydrogen bonds : bond 0.18136 ( 381) hydrogen bonds : angle 5.95514 ( 1065) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 288 time to evaluate : 0.266 Fit side-chains REVERT: A 60 MET cc_start: 0.7841 (mmm) cc_final: 0.7261 (tpp) REVERT: B 120 ILE cc_start: 0.8175 (mt) cc_final: 0.7932 (mt) REVERT: B 212 ASP cc_start: 0.7398 (t0) cc_final: 0.7028 (t0) REVERT: R 302 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.7654 (t80) REVERT: S 32 PHE cc_start: 0.8204 (m-80) cc_final: 0.7835 (m-80) REVERT: S 71 SER cc_start: 0.7561 (m) cc_final: 0.7204 (p) REVERT: S 76 LYS cc_start: 0.8311 (mttp) cc_final: 0.8082 (mttp) REVERT: S 115 THR cc_start: 0.8052 (m) cc_final: 0.7580 (p) REVERT: N 50 ASP cc_start: 0.7805 (p0) cc_final: 0.7561 (p0) outliers start: 9 outliers final: 7 residues processed: 292 average time/residue: 0.0971 time to fit residues: 38.0191 Evaluate side-chains 275 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 267 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 76 CYS Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 298 TRP Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain R residue 306 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN B 239 ASN R 64 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.110363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.092894 restraints weight = 15633.562| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.09 r_work: 0.2911 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9772 Z= 0.214 Angle : 0.625 9.928 13305 Z= 0.329 Chirality : 0.045 0.162 1539 Planarity : 0.005 0.060 1672 Dihedral : 5.290 58.112 1406 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.94 % Allowed : 14.41 % Favored : 82.65 % 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: 1255 helix: 0.96 (0.28), residues: 375 sheet: 0.44 (0.28), residues: 315 loop : -1.44 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 68 TYR 0.023 0.002 TYR S 235 PHE 0.022 0.002 PHE B 199 TRP 0.015 0.002 TRP N 47 HIS 0.007 0.002 HIS R 122 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 9769) covalent geometry : angle 0.62450 (13299) SS BOND : bond 0.00791 ( 3) SS BOND : angle 1.72829 ( 6) hydrogen bonds : bond 0.06037 ( 381) hydrogen bonds : angle 4.47077 ( 1065) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 262 time to evaluate : 0.241 Fit side-chains REVERT: A 60 MET cc_start: 0.8253 (mmm) cc_final: 0.7672 (tpp) REVERT: A 221 MET cc_start: 0.8422 (ttm) cc_final: 0.8220 (ttp) REVERT: B 72 SER cc_start: 0.8300 (t) cc_final: 0.7871 (p) REVERT: B 86 THR cc_start: 0.8751 (p) cc_final: 0.8374 (t) REVERT: B 212 ASP cc_start: 0.7757 (t0) cc_final: 0.7421 (t0) REVERT: R 73 SER cc_start: 0.8636 (t) cc_final: 0.8423 (t) REVERT: S 71 SER cc_start: 0.8020 (m) cc_final: 0.7631 (p) REVERT: S 76 LYS cc_start: 0.8577 (mttp) cc_final: 0.8320 (mttp) REVERT: S 230 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7466 (ttm) outliers start: 28 outliers final: 21 residues processed: 275 average time/residue: 0.1067 time to fit residues: 39.1786 Evaluate side-chains 286 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 264 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 275 ILE Chi-restraints excluded: chain R residue 298 TRP Chi-restraints excluded: chain R residue 299 CYS Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain N residue 85 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 109 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 117 optimal weight: 0.4980 chunk 73 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 GLN B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.110954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.093235 restraints weight = 15253.549| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.14 r_work: 0.2935 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9772 Z= 0.174 Angle : 0.572 9.018 13305 Z= 0.299 Chirality : 0.043 0.154 1539 Planarity : 0.004 0.064 1672 Dihedral : 4.990 56.241 1398 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.36 % Allowed : 17.25 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.23 (0.24), residues: 1255 helix: 1.18 (0.28), residues: 374 sheet: 0.49 (0.28), residues: 318 loop : -1.49 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 68 TYR 0.020 0.002 TYR R 226 PHE 0.016 0.002 PHE B 151 TRP 0.014 0.002 TRP S 36 HIS 0.005 0.001 HIS R 122 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 9769) covalent geometry : angle 0.57178 (13299) SS BOND : bond 0.00653 ( 3) SS BOND : angle 1.31891 ( 6) hydrogen bonds : bond 0.05309 ( 381) hydrogen bonds : angle 4.18082 ( 1065) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 270 time to evaluate : 0.268 Fit side-chains REVERT: A 60 MET cc_start: 0.8130 (mmm) cc_final: 0.7622 (tpp) REVERT: A 221 MET cc_start: 0.8369 (ttm) cc_final: 0.8160 (ttp) REVERT: A 384 GLN cc_start: 0.8332 (tt0) cc_final: 0.8084 (tt0) REVERT: B 72 SER cc_start: 0.8351 (t) cc_final: 0.7940 (p) REVERT: B 86 THR cc_start: 0.8764 (p) cc_final: 0.7963 (m) REVERT: R 73 SER cc_start: 0.8688 (t) cc_final: 0.8478 (t) REVERT: S 71 SER cc_start: 0.7972 (m) cc_final: 0.7518 (p) REVERT: S 76 LYS cc_start: 0.8567 (mttp) cc_final: 0.8291 (mttp) REVERT: S 228 TYR cc_start: 0.8484 (m-80) cc_final: 0.8221 (m-80) REVERT: S 230 MET cc_start: 0.7891 (mmm) cc_final: 0.7526 (ttm) outliers start: 32 outliers final: 29 residues processed: 285 average time/residue: 0.0984 time to fit residues: 37.7719 Evaluate side-chains 296 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 267 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 76 CYS Chi-restraints excluded: chain R residue 124 CYS Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 298 TRP Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain R residue 326 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 85 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 22 optimal weight: 0.9990 chunk 113 optimal weight: 0.1980 chunk 12 optimal weight: 1.9990 chunk 122 optimal weight: 0.0570 chunk 33 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 overall best weight: 1.0504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN R 196 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.112606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.094870 restraints weight = 15410.779| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.17 r_work: 0.2957 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9772 Z= 0.114 Angle : 0.520 8.828 13305 Z= 0.269 Chirality : 0.041 0.147 1539 Planarity : 0.004 0.062 1672 Dihedral : 4.726 56.769 1398 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.36 % Allowed : 19.87 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.02 (0.24), residues: 1255 helix: 1.48 (0.29), residues: 374 sheet: 0.63 (0.28), residues: 318 loop : -1.41 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 68 TYR 0.011 0.001 TYR S 235 PHE 0.014 0.001 PHE S 29 TRP 0.012 0.001 TRP N 47 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9769) covalent geometry : angle 0.51936 (13299) SS BOND : bond 0.00473 ( 3) SS BOND : angle 0.89478 ( 6) hydrogen bonds : bond 0.04184 ( 381) hydrogen bonds : angle 3.90087 ( 1065) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 276 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.8037 (mmm) cc_final: 0.7650 (tpp) REVERT: A 221 MET cc_start: 0.8424 (ttm) cc_final: 0.8166 (ttp) REVERT: A 384 GLN cc_start: 0.8283 (tt0) cc_final: 0.8031 (tt0) REVERT: B 72 SER cc_start: 0.8337 (t) cc_final: 0.7932 (p) REVERT: B 241 PHE cc_start: 0.8499 (p90) cc_final: 0.8233 (p90) REVERT: R 73 SER cc_start: 0.8689 (t) cc_final: 0.8471 (t) REVERT: R 158 PHE cc_start: 0.8447 (t80) cc_final: 0.8160 (t80) REVERT: S 71 SER cc_start: 0.7959 (m) cc_final: 0.7407 (p) REVERT: S 76 LYS cc_start: 0.8582 (mttp) cc_final: 0.8314 (mttp) REVERT: S 228 TYR cc_start: 0.8471 (m-80) cc_final: 0.8219 (m-80) REVERT: S 230 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7487 (ttm) outliers start: 32 outliers final: 25 residues processed: 294 average time/residue: 0.0921 time to fit residues: 36.4235 Evaluate side-chains 295 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 269 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 76 CYS Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 253 GLU Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain R residue 299 CYS Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain N residue 49 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 64 optimal weight: 0.7980 chunk 14 optimal weight: 10.0000 chunk 85 optimal weight: 0.9980 chunk 109 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 110 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 81 optimal weight: 0.0770 chunk 26 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.112817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.095180 restraints weight = 15346.847| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.15 r_work: 0.2972 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9772 Z= 0.108 Angle : 0.518 8.501 13305 Z= 0.267 Chirality : 0.041 0.157 1539 Planarity : 0.004 0.064 1672 Dihedral : 4.334 56.710 1396 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.79 % Allowed : 20.40 % Favored : 75.81 % 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: 0.12 (0.24), residues: 1255 helix: 1.56 (0.29), residues: 375 sheet: 0.69 (0.28), residues: 320 loop : -1.36 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 130 TYR 0.010 0.001 TYR S 60 PHE 0.011 0.001 PHE S 29 TRP 0.010 0.001 TRP N 47 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 9769) covalent geometry : angle 0.51766 (13299) SS BOND : bond 0.00485 ( 3) SS BOND : angle 0.90831 ( 6) hydrogen bonds : bond 0.03989 ( 381) hydrogen bonds : angle 3.79137 ( 1065) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 264 time to evaluate : 0.376 Fit side-chains REVERT: A 60 MET cc_start: 0.8079 (mmm) cc_final: 0.7757 (tpp) REVERT: A 221 MET cc_start: 0.8398 (ttm) cc_final: 0.8158 (ttp) REVERT: A 384 GLN cc_start: 0.8273 (tt0) cc_final: 0.8057 (tt0) REVERT: B 50 THR cc_start: 0.8545 (m) cc_final: 0.8291 (t) REVERT: B 72 SER cc_start: 0.8344 (t) cc_final: 0.7926 (p) REVERT: R 73 SER cc_start: 0.8690 (t) cc_final: 0.8482 (t) REVERT: S 71 SER cc_start: 0.7976 (m) cc_final: 0.7422 (p) REVERT: S 76 LYS cc_start: 0.8598 (mttp) cc_final: 0.8338 (mttp) REVERT: S 140 MET cc_start: 0.8250 (mtm) cc_final: 0.7573 (mtm) REVERT: S 228 TYR cc_start: 0.8463 (m-80) cc_final: 0.8222 (m-80) REVERT: S 230 MET cc_start: 0.7866 (mmm) cc_final: 0.7488 (ttm) REVERT: N 98 ARG cc_start: 0.8414 (ttp80) cc_final: 0.8155 (ttt-90) outliers start: 36 outliers final: 30 residues processed: 287 average time/residue: 0.1041 time to fit residues: 40.3646 Evaluate side-chains 287 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 257 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 76 CYS Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 124 CYS Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 299 CYS Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 25 optimal weight: 7.9990 chunk 4 optimal weight: 0.7980 chunk 102 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 57 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 112 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.113279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.095646 restraints weight = 15407.075| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.16 r_work: 0.2981 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9772 Z= 0.104 Angle : 0.510 8.523 13305 Z= 0.263 Chirality : 0.040 0.158 1539 Planarity : 0.004 0.063 1672 Dihedral : 4.269 56.665 1396 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.10 % Allowed : 21.14 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.16 (0.24), residues: 1255 helix: 1.66 (0.29), residues: 375 sheet: 0.65 (0.28), residues: 318 loop : -1.33 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 130 TYR 0.011 0.001 TYR A 391 PHE 0.016 0.001 PHE R 267 TRP 0.011 0.001 TRP N 47 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 9769) covalent geometry : angle 0.50948 (13299) SS BOND : bond 0.00456 ( 3) SS BOND : angle 0.84712 ( 6) hydrogen bonds : bond 0.03816 ( 381) hydrogen bonds : angle 3.72614 ( 1065) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 268 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 59 GLN cc_start: 0.7870 (mm110) cc_final: 0.7487 (mm110) REVERT: A 60 MET cc_start: 0.8079 (mmm) cc_final: 0.7734 (tpp) REVERT: A 221 MET cc_start: 0.8406 (ttm) cc_final: 0.8169 (ttp) REVERT: A 384 GLN cc_start: 0.8269 (tt0) cc_final: 0.8043 (tt0) REVERT: B 50 THR cc_start: 0.8526 (m) cc_final: 0.8279 (t) REVERT: B 241 PHE cc_start: 0.8511 (p90) cc_final: 0.8189 (p90) REVERT: R 73 SER cc_start: 0.8693 (t) cc_final: 0.8483 (t) REVERT: S 71 SER cc_start: 0.8004 (m) cc_final: 0.7414 (p) REVERT: S 76 LYS cc_start: 0.8608 (mttp) cc_final: 0.8353 (mttp) REVERT: S 140 MET cc_start: 0.8267 (mtm) cc_final: 0.7609 (mtm) REVERT: S 228 TYR cc_start: 0.8481 (m-80) cc_final: 0.8229 (m-80) REVERT: S 230 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7451 (ttm) REVERT: N 98 ARG cc_start: 0.8420 (ttp80) cc_final: 0.8201 (ttt-90) outliers start: 39 outliers final: 32 residues processed: 291 average time/residue: 0.0918 time to fit residues: 35.9652 Evaluate side-chains 302 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 269 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 76 CYS Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 124 CYS Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 253 GLU Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain R residue 326 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 5 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 123 optimal weight: 0.0050 chunk 85 optimal weight: 0.4980 chunk 118 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 112 optimal weight: 9.9990 chunk 70 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 53 optimal weight: 10.0000 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS B 88 ASN B 156 GLN S 35 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.115164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.097962 restraints weight = 15149.790| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.07 r_work: 0.3007 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9772 Z= 0.092 Angle : 0.496 8.380 13305 Z= 0.255 Chirality : 0.040 0.156 1539 Planarity : 0.004 0.063 1672 Dihedral : 4.150 56.910 1396 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.89 % Allowed : 21.77 % Favored : 74.34 % 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: 0.25 (0.24), residues: 1255 helix: 1.80 (0.29), residues: 373 sheet: 0.86 (0.29), residues: 314 loop : -1.42 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 197 TYR 0.013 0.001 TYR A 391 PHE 0.012 0.001 PHE R 267 TRP 0.008 0.001 TRP N 47 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00202 ( 9769) covalent geometry : angle 0.49558 (13299) SS BOND : bond 0.00388 ( 3) SS BOND : angle 0.71781 ( 6) hydrogen bonds : bond 0.03407 ( 381) hydrogen bonds : angle 3.59273 ( 1065) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 264 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 59 GLN cc_start: 0.7913 (mm110) cc_final: 0.7520 (mm110) REVERT: A 60 MET cc_start: 0.8044 (mmm) cc_final: 0.7684 (tpp) REVERT: A 221 MET cc_start: 0.8402 (ttm) cc_final: 0.8151 (ttp) REVERT: A 384 GLN cc_start: 0.8276 (tt0) cc_final: 0.8034 (tt0) REVERT: B 50 THR cc_start: 0.8463 (m) cc_final: 0.8234 (t) REVERT: B 61 MET cc_start: 0.7774 (ppp) cc_final: 0.7307 (ppp) REVERT: B 241 PHE cc_start: 0.8481 (p90) cc_final: 0.8197 (p90) REVERT: C 46 LYS cc_start: 0.8714 (mmpt) cc_final: 0.8472 (mmpt) REVERT: R 73 SER cc_start: 0.8685 (t) cc_final: 0.8479 (t) REVERT: R 120 LEU cc_start: 0.8188 (tp) cc_final: 0.7924 (tt) REVERT: R 314 PHE cc_start: 0.8619 (t80) cc_final: 0.8404 (t80) REVERT: S 71 SER cc_start: 0.7974 (m) cc_final: 0.7386 (p) REVERT: S 76 LYS cc_start: 0.8618 (mttp) cc_final: 0.8364 (mttp) REVERT: S 140 MET cc_start: 0.8251 (mtm) cc_final: 0.7581 (mtm) REVERT: S 228 TYR cc_start: 0.8454 (m-80) cc_final: 0.8192 (m-80) REVERT: S 230 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7408 (ttm) outliers start: 37 outliers final: 29 residues processed: 282 average time/residue: 0.1069 time to fit residues: 40.5443 Evaluate side-chains 295 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 265 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 76 CYS Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 124 CYS Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 253 GLU Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 299 CYS Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain N residue 52 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 46 optimal weight: 0.0170 chunk 57 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 58 optimal weight: 0.4980 chunk 114 optimal weight: 8.9990 chunk 69 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 overall best weight: 1.6822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.112144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.095100 restraints weight = 15149.400| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.06 r_work: 0.2957 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9772 Z= 0.158 Angle : 0.558 8.247 13305 Z= 0.290 Chirality : 0.042 0.171 1539 Planarity : 0.004 0.064 1672 Dihedral : 4.471 55.145 1396 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.79 % Allowed : 23.03 % Favored : 73.19 % 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: 0.15 (0.24), residues: 1255 helix: 1.69 (0.29), residues: 375 sheet: 0.79 (0.29), residues: 314 loop : -1.47 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 197 TYR 0.032 0.002 TYR A 391 PHE 0.019 0.002 PHE N 108 TRP 0.015 0.001 TRP N 47 HIS 0.005 0.001 HIS R 108 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 9769) covalent geometry : angle 0.55704 (13299) SS BOND : bond 0.00675 ( 3) SS BOND : angle 1.31049 ( 6) hydrogen bonds : bond 0.04811 ( 381) hydrogen bonds : angle 3.87719 ( 1065) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 269 time to evaluate : 0.416 Fit side-chains REVERT: A 59 GLN cc_start: 0.7918 (mm110) cc_final: 0.7497 (mm110) REVERT: A 60 MET cc_start: 0.8163 (mmm) cc_final: 0.7720 (tpp) REVERT: A 221 MET cc_start: 0.8409 (ttm) cc_final: 0.8174 (ttp) REVERT: A 384 GLN cc_start: 0.8326 (tt0) cc_final: 0.8088 (tt0) REVERT: B 72 SER cc_start: 0.8321 (t) cc_final: 0.7883 (p) REVERT: B 247 ASP cc_start: 0.8240 (p0) cc_final: 0.7999 (p0) REVERT: S 71 SER cc_start: 0.8035 (m) cc_final: 0.7515 (p) REVERT: S 76 LYS cc_start: 0.8640 (mttp) cc_final: 0.8392 (mttp) REVERT: S 140 MET cc_start: 0.8306 (mtm) cc_final: 0.7637 (mtm) REVERT: S 168 SER cc_start: 0.8285 (p) cc_final: 0.7992 (p) REVERT: S 228 TYR cc_start: 0.8503 (m-80) cc_final: 0.8226 (m-80) REVERT: S 230 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7578 (ttt) outliers start: 36 outliers final: 30 residues processed: 287 average time/residue: 0.0981 time to fit residues: 38.0591 Evaluate side-chains 296 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 265 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 76 CYS Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 124 CYS Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 253 GLU Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 299 CYS Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.3980 chunk 72 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.113418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.096276 restraints weight = 15224.566| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.06 r_work: 0.2984 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9772 Z= 0.112 Angle : 0.524 8.689 13305 Z= 0.271 Chirality : 0.041 0.203 1539 Planarity : 0.004 0.063 1672 Dihedral : 4.335 55.861 1396 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.58 % Allowed : 22.71 % Favored : 73.71 % 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: 1255 helix: 1.80 (0.29), residues: 375 sheet: 0.67 (0.29), residues: 318 loop : -1.37 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 130 TYR 0.021 0.001 TYR A 391 PHE 0.017 0.001 PHE A 376 TRP 0.013 0.001 TRP N 47 HIS 0.009 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9769) covalent geometry : angle 0.52350 (13299) SS BOND : bond 0.00492 ( 3) SS BOND : angle 0.91321 ( 6) hydrogen bonds : bond 0.03974 ( 381) hydrogen bonds : angle 3.73668 ( 1065) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 262 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 59 GLN cc_start: 0.7939 (mm110) cc_final: 0.7533 (mm110) REVERT: A 60 MET cc_start: 0.8095 (mmm) cc_final: 0.7706 (tpp) REVERT: A 221 MET cc_start: 0.8350 (ttm) cc_final: 0.8097 (ttp) REVERT: A 384 GLN cc_start: 0.8298 (tt0) cc_final: 0.8063 (tt0) REVERT: B 50 THR cc_start: 0.8494 (m) cc_final: 0.8233 (t) REVERT: B 241 PHE cc_start: 0.8535 (p90) cc_final: 0.8215 (p90) REVERT: S 71 SER cc_start: 0.8012 (m) cc_final: 0.7428 (p) REVERT: S 76 LYS cc_start: 0.8611 (mttp) cc_final: 0.8309 (mttp) REVERT: S 140 MET cc_start: 0.8255 (mtm) cc_final: 0.7610 (mtm) REVERT: S 168 SER cc_start: 0.8287 (p) cc_final: 0.8004 (p) REVERT: S 228 TYR cc_start: 0.8443 (m-80) cc_final: 0.8173 (m-80) REVERT: S 230 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7262 (ttt) outliers start: 34 outliers final: 32 residues processed: 277 average time/residue: 0.1129 time to fit residues: 41.7306 Evaluate side-chains 294 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 261 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 76 CYS Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 124 CYS Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 253 GLU Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 84 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 16 optimal weight: 0.0370 chunk 123 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.112752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.095664 restraints weight = 15114.637| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.06 r_work: 0.2970 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9772 Z= 0.136 Angle : 0.551 8.259 13305 Z= 0.284 Chirality : 0.042 0.197 1539 Planarity : 0.004 0.064 1672 Dihedral : 4.417 55.314 1396 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.26 % Allowed : 22.92 % Favored : 73.82 % 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: 0.19 (0.24), residues: 1255 helix: 1.80 (0.29), residues: 374 sheet: 0.61 (0.29), residues: 320 loop : -1.38 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 68 TYR 0.027 0.001 TYR A 391 PHE 0.020 0.002 PHE A 376 TRP 0.015 0.001 TRP N 47 HIS 0.008 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9769) covalent geometry : angle 0.55020 (13299) SS BOND : bond 0.00611 ( 3) SS BOND : angle 1.15807 ( 6) hydrogen bonds : bond 0.04469 ( 381) hydrogen bonds : angle 3.82659 ( 1065) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 266 time to evaluate : 0.388 Fit side-chains REVERT: A 59 GLN cc_start: 0.7902 (mm110) cc_final: 0.7444 (mm110) REVERT: A 60 MET cc_start: 0.8131 (mmm) cc_final: 0.7710 (tpp) REVERT: A 221 MET cc_start: 0.8375 (ttm) cc_final: 0.8125 (ttp) REVERT: A 384 GLN cc_start: 0.8318 (tt0) cc_final: 0.8086 (tt0) REVERT: B 72 SER cc_start: 0.8328 (t) cc_final: 0.7891 (p) REVERT: S 71 SER cc_start: 0.8021 (m) cc_final: 0.7469 (p) REVERT: S 76 LYS cc_start: 0.8629 (mttp) cc_final: 0.8333 (mttp) REVERT: S 140 MET cc_start: 0.8286 (mtm) cc_final: 0.7629 (mtm) REVERT: S 168 SER cc_start: 0.8294 (p) cc_final: 0.8010 (p) REVERT: S 228 TYR cc_start: 0.8453 (m-80) cc_final: 0.8166 (m-80) REVERT: S 230 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7522 (ttt) outliers start: 31 outliers final: 26 residues processed: 279 average time/residue: 0.1145 time to fit residues: 42.6569 Evaluate side-chains 282 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 255 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 76 CYS Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 124 CYS Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 253 GLU Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 25 optimal weight: 9.9990 chunk 100 optimal weight: 0.8980 chunk 115 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 76 optimal weight: 20.0000 chunk 8 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN R 108 HIS S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.109254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.091752 restraints weight = 15481.026| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.14 r_work: 0.2895 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9772 Z= 0.277 Angle : 0.663 8.935 13305 Z= 0.349 Chirality : 0.046 0.226 1539 Planarity : 0.005 0.066 1672 Dihedral : 4.984 53.241 1396 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.47 % Allowed : 23.03 % Favored : 73.50 % 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: -0.07 (0.24), residues: 1255 helix: 1.44 (0.29), residues: 374 sheet: 0.57 (0.29), residues: 320 loop : -1.49 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 68 TYR 0.041 0.002 TYR A 391 PHE 0.031 0.003 PHE N 108 TRP 0.025 0.002 TRP N 47 HIS 0.014 0.002 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00640 ( 9769) covalent geometry : angle 0.66166 (13299) SS BOND : bond 0.00953 ( 3) SS BOND : angle 1.94661 ( 6) hydrogen bonds : bond 0.06441 ( 381) hydrogen bonds : angle 4.33431 ( 1065) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2257.52 seconds wall clock time: 39 minutes 15.60 seconds (2355.60 seconds total)