Starting phenix.real_space_refine on Thu Mar 13 23:14:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8itf_35705/03_2025/8itf_35705_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8itf_35705/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8itf_35705/03_2025/8itf_35705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8itf_35705/03_2025/8itf_35705.map" model { file = "/net/cci-nas-00/data/ceres_data/8itf_35705/03_2025/8itf_35705_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8itf_35705/03_2025/8itf_35705_neut.cif" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLU:plan': 11, 'ARG:plan': 3, 'ASP:plan': 11} 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: {'GLN:plan1': 4, 'GLU:plan': 6, 'ARG:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 17} 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, 'GLU:plan': 5, 'ARG:plan': 1, '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: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} 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, 'ARG:plan': 2, 'ASP:plan': 1} 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: 5.56, per 1000 atoms: 0.58 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: 2.48 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.16 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: 2.72 Time building geometry restraints manager: 2.93 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.090 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.650 ------------------------------------------------------------------------------- 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 9769 Z= 0.282 Angle : 0.643 9.345 13299 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 : 5.05 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (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 TRP 0.008 0.001 TRP R 317 HIS 0.009 0.001 HIS S 167 PHE 0.014 0.001 PHE R 314 TYR 0.013 0.001 TYR R 226 ARG 0.006 0.000 ARG R 130 *********************** 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 : 0.980 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: 0.7027 (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: 0.7836 (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: 0.8081 (mttp) REVERT: S 115 THR cc_start: 0.8052 (m) cc_final: 0.7581 (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: 0.2477 time to fit residues: 95.5019 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 : 0.939 ------------------------------------------------------------------------------- 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 104 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 52 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 = 0.3351 r_free = 0.3351 target = 0.112101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.094659 restraints weight = 15517.413| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.07 r_work: 0.2940 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9769 Z= 0.246 Angle : 0.582 9.584 13299 Z= 0.304 Chirality : 0.043 0.159 1539 Planarity : 0.004 0.059 1672 Dihedral : 5.078 57.847 1406 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.84 % Allowed : 14.41 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.24), residues: 1255 helix: 1.09 (0.28), residues: 373 sheet: 0.57 (0.28), residues: 311 loop : -1.41 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 47 HIS 0.006 0.002 HIS A 220 PHE 0.022 0.002 PHE S 29 TYR 0.018 0.002 TYR S 235 ARG 0.005 0.000 ARG R 130 *********************** 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 284 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 257 time to evaluate : 0.949 Fit side-chains REVERT: A 60 MET cc_start: 0.8268 (mmm) cc_final: 0.7679 (tpp) REVERT: A 221 MET cc_start: 0.8476 (ttm) cc_final: 0.8237 (ttp) REVERT: B 72 SER cc_start: 0.8334 (t) cc_final: 0.7929 (p) REVERT: B 212 ASP cc_start: 0.7704 (t0) cc_final: 0.7368 (t0) REVERT: R 73 SER cc_start: 0.8658 (t) cc_final: 0.8450 (t) REVERT: R 158 PHE cc_start: 0.8434 (t80) cc_final: 0.8222 (t80) REVERT: S 71 SER cc_start: 0.7966 (m) cc_final: 0.7537 (p) REVERT: S 76 LYS cc_start: 0.8576 (mttp) cc_final: 0.8315 (mttp) REVERT: S 230 MET cc_start: 0.7902 (mmm) cc_final: 0.7532 (ttm) REVERT: N 98 ARG cc_start: 0.8528 (ttp80) cc_final: 0.8147 (ttt-90) outliers start: 27 outliers final: 22 residues processed: 270 average time/residue: 0.2576 time to fit residues: 92.0584 Evaluate side-chains 271 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 249 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 238 THR 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 49 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 97 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 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 = 0.3379 r_free = 0.3379 target = 0.114150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.096458 restraints weight = 15642.288| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.21 r_work: 0.2970 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9769 Z= 0.151 Angle : 0.509 8.737 13299 Z= 0.263 Chirality : 0.041 0.151 1539 Planarity : 0.004 0.060 1672 Dihedral : 4.595 57.421 1398 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.52 % Allowed : 17.77 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.24), residues: 1255 helix: 1.47 (0.29), residues: 373 sheet: 0.74 (0.28), residues: 314 loop : -1.38 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 47 HIS 0.004 0.001 HIS R 108 PHE 0.018 0.001 PHE S 29 TYR 0.012 0.001 TYR S 235 ARG 0.004 0.000 ARG B 68 *********************** 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 284 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 260 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: A 59 GLN cc_start: 0.8094 (mm-40) cc_final: 0.7551 (mm-40) REVERT: A 60 MET cc_start: 0.8142 (mmm) cc_final: 0.7678 (tpp) REVERT: B 72 SER cc_start: 0.8346 (t) cc_final: 0.7931 (p) REVERT: B 212 ASP cc_start: 0.7731 (t0) cc_final: 0.7398 (t0) REVERT: R 73 SER cc_start: 0.8658 (t) cc_final: 0.8443 (t) REVERT: R 158 PHE cc_start: 0.8439 (t80) cc_final: 0.8237 (t80) REVERT: S 71 SER cc_start: 0.7950 (m) cc_final: 0.7366 (p) REVERT: S 76 LYS cc_start: 0.8548 (mttp) cc_final: 0.8275 (mttp) REVERT: S 228 TYR cc_start: 0.8440 (m-80) cc_final: 0.8177 (m-80) REVERT: S 230 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7516 (ttm) REVERT: N 98 ARG cc_start: 0.8522 (ttp80) cc_final: 0.8216 (ttt-90) outliers start: 24 outliers final: 19 residues processed: 271 average time/residue: 0.2463 time to fit residues: 89.1215 Evaluate side-chains 266 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 246 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE 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 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 253 GLU Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 268 LEU 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 S residue 243 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 54 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 109 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 = 0.3373 r_free = 0.3373 target = 0.113678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.095979 restraints weight = 15397.544| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.18 r_work: 0.2938 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9769 Z= 0.158 Angle : 0.510 8.587 13299 Z= 0.263 Chirality : 0.041 0.169 1539 Planarity : 0.004 0.064 1672 Dihedral : 4.254 57.437 1396 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.58 % Allowed : 19.14 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.24), residues: 1255 helix: 1.63 (0.29), residues: 374 sheet: 0.81 (0.28), residues: 311 loop : -1.39 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 47 HIS 0.004 0.001 HIS S 35 PHE 0.015 0.001 PHE S 29 TYR 0.012 0.001 TYR S 235 ARG 0.004 0.000 ARG B 68 *********************** 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 296 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 262 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: A 59 GLN cc_start: 0.8109 (mm-40) cc_final: 0.7454 (mm-40) REVERT: A 60 MET cc_start: 0.8098 (mmm) cc_final: 0.7515 (tmm) REVERT: B 72 SER cc_start: 0.8334 (t) cc_final: 0.7914 (p) REVERT: R 73 SER cc_start: 0.8681 (t) cc_final: 0.8470 (t) REVERT: R 158 PHE cc_start: 0.8428 (t80) cc_final: 0.8217 (t80) REVERT: R 314 PHE cc_start: 0.8643 (t80) cc_final: 0.8430 (t80) REVERT: S 71 SER cc_start: 0.7965 (m) cc_final: 0.7365 (p) REVERT: S 76 LYS cc_start: 0.8560 (mttp) cc_final: 0.8299 (mttp) REVERT: S 228 TYR cc_start: 0.8475 (m-80) cc_final: 0.8203 (m-80) REVERT: S 230 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.7497 (ttm) REVERT: N 98 ARG cc_start: 0.8514 (ttp80) cc_final: 0.8296 (ttt-90) outliers start: 34 outliers final: 24 residues processed: 278 average time/residue: 0.2377 time to fit residues: 88.5410 Evaluate side-chains 275 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 250 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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 43 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 269 ILE Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 76 CYS 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 260 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 243 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 41 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 118 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 61 optimal weight: 40.0000 chunk 108 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 R 108 HIS R 196 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.109394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.092520 restraints weight = 15266.989| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.05 r_work: 0.2916 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 9769 Z= 0.429 Angle : 0.651 8.750 13299 Z= 0.345 Chirality : 0.046 0.194 1539 Planarity : 0.005 0.065 1672 Dihedral : 4.996 54.300 1396 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 4.31 % Allowed : 20.50 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.24), residues: 1255 helix: 1.26 (0.28), residues: 373 sheet: 0.61 (0.28), residues: 324 loop : -1.56 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP N 47 HIS 0.006 0.002 HIS R 122 PHE 0.026 0.002 PHE N 108 TYR 0.025 0.002 TYR S 190 ARG 0.007 0.001 ARG B 68 *********************** 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 320 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 279 time to evaluate : 1.037 Fit side-chains REVERT: A 59 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7728 (mm-40) REVERT: A 60 MET cc_start: 0.8147 (mmm) cc_final: 0.7723 (tpp) REVERT: A 221 MET cc_start: 0.8372 (ttm) cc_final: 0.8151 (ttp) REVERT: A 369 THR cc_start: 0.8908 (p) cc_final: 0.8455 (t) REVERT: B 59 TYR cc_start: 0.8444 (OUTLIER) cc_final: 0.8194 (t80) REVERT: B 72 SER cc_start: 0.8345 (t) cc_final: 0.7881 (p) REVERT: R 73 SER cc_start: 0.8669 (t) cc_final: 0.8454 (t) REVERT: R 86 MET cc_start: 0.8752 (ttm) cc_final: 0.8536 (ttm) REVERT: S 30 SER cc_start: 0.8864 (p) cc_final: 0.8561 (t) REVERT: S 71 SER cc_start: 0.8035 (m) cc_final: 0.7635 (p) REVERT: S 76 LYS cc_start: 0.8607 (mttp) cc_final: 0.8334 (mttp) REVERT: S 168 SER cc_start: 0.8336 (p) cc_final: 0.8058 (p) REVERT: S 230 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7737 (ttm) REVERT: N 91 THR cc_start: 0.8332 (OUTLIER) cc_final: 0.8096 (t) outliers start: 41 outliers final: 32 residues processed: 300 average time/residue: 0.2664 time to fit residues: 107.3307 Evaluate side-chains 308 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 273 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR 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 39 LEU Chi-restraints excluded: chain R residue 47 VAL 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 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 275 ILE Chi-restraints excluded: chain R residue 288 THR Chi-restraints excluded: chain R residue 298 TRP Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 78 THR 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 70 ILE 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 72 optimal weight: 0.9980 chunk 33 optimal weight: 0.0980 chunk 102 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 78 optimal weight: 0.0970 chunk 90 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 384 GLN B 156 GLN S 35 HIS S 232 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.113652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.096600 restraints weight = 15128.988| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.04 r_work: 0.2992 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9769 Z= 0.135 Angle : 0.519 8.700 13299 Z= 0.268 Chirality : 0.041 0.179 1539 Planarity : 0.004 0.063 1672 Dihedral : 4.404 56.503 1396 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.26 % Allowed : 22.08 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.24), residues: 1255 helix: 1.64 (0.29), residues: 375 sheet: 0.62 (0.29), residues: 309 loop : -1.37 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 47 HIS 0.006 0.001 HIS A 220 PHE 0.015 0.001 PHE R 267 TYR 0.010 0.001 TYR S 60 ARG 0.006 0.000 ARG B 68 *********************** 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 301 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 270 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.8049 (mmm) cc_final: 0.7713 (tpp) REVERT: A 221 MET cc_start: 0.8355 (ttm) cc_final: 0.8069 (ttp) REVERT: A 384 GLN cc_start: 0.8299 (tt0) cc_final: 0.8055 (tt0) REVERT: B 50 THR cc_start: 0.8488 (m) cc_final: 0.8252 (t) REVERT: B 61 MET cc_start: 0.7862 (ppp) cc_final: 0.7580 (ppp) REVERT: B 241 PHE cc_start: 0.8490 (p90) cc_final: 0.8180 (p90) REVERT: B 283 ARG cc_start: 0.8341 (tpt-90) cc_final: 0.7992 (tpt90) REVERT: R 73 SER cc_start: 0.8697 (t) cc_final: 0.8482 (t) REVERT: R 81 VAL cc_start: 0.9034 (OUTLIER) cc_final: 0.8790 (t) REVERT: R 260 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7721 (mt) REVERT: S 71 SER cc_start: 0.7949 (m) cc_final: 0.7349 (p) REVERT: S 76 LYS cc_start: 0.8601 (mttp) cc_final: 0.8344 (mttp) REVERT: S 168 SER cc_start: 0.8270 (p) cc_final: 0.7979 (p) REVERT: S 228 TYR cc_start: 0.8446 (m-80) cc_final: 0.8226 (m-80) REVERT: S 230 MET cc_start: 0.7746 (OUTLIER) cc_final: 0.7457 (mmm) REVERT: N 98 ARG cc_start: 0.8399 (ttp80) cc_final: 0.8174 (ttt-90) outliers start: 31 outliers final: 20 residues processed: 289 average time/residue: 0.2388 time to fit residues: 92.4321 Evaluate side-chains 288 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 265 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 207 ILE 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 R residue 47 VAL Chi-restraints excluded: chain R residue 76 CYS Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 119 SER 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 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 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 61 optimal weight: 30.0000 chunk 48 optimal weight: 0.9980 chunk 62 optimal weight: 8.9990 chunk 118 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 109 optimal weight: 9.9990 chunk 80 optimal weight: 0.7980 chunk 43 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN S 232 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.113161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.095923 restraints weight = 15255.619| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.08 r_work: 0.2975 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9769 Z= 0.178 Angle : 0.528 8.403 13299 Z= 0.275 Chirality : 0.041 0.188 1539 Planarity : 0.004 0.065 1672 Dihedral : 4.378 56.030 1396 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.15 % Allowed : 22.82 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.24), residues: 1255 helix: 1.66 (0.29), residues: 375 sheet: 0.56 (0.29), residues: 320 loop : -1.31 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 47 HIS 0.005 0.001 HIS A 220 PHE 0.015 0.001 PHE R 158 TYR 0.021 0.001 TYR A 391 ARG 0.007 0.000 ARG B 68 *********************** 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 305 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 275 time to evaluate : 2.141 Fit side-chains REVERT: A 59 GLN cc_start: 0.8141 (mm-40) cc_final: 0.7772 (mm-40) REVERT: A 60 MET cc_start: 0.8054 (mmm) cc_final: 0.7711 (tpp) REVERT: A 221 MET cc_start: 0.8361 (ttm) cc_final: 0.8078 (ttp) REVERT: A 384 GLN cc_start: 0.8310 (tt0) cc_final: 0.8078 (tt0) REVERT: B 50 THR cc_start: 0.8511 (m) cc_final: 0.8258 (t) REVERT: B 72 SER cc_start: 0.8315 (t) cc_final: 0.7884 (p) REVERT: B 283 ARG cc_start: 0.8386 (tpt-90) cc_final: 0.8030 (tpt90) REVERT: R 73 SER cc_start: 0.8692 (t) cc_final: 0.8483 (t) REVERT: S 71 SER cc_start: 0.8026 (m) cc_final: 0.7415 (p) REVERT: S 76 LYS cc_start: 0.8625 (mttp) cc_final: 0.8367 (mttp) REVERT: S 168 SER cc_start: 0.8267 (p) cc_final: 0.7972 (p) REVERT: S 228 TYR cc_start: 0.8502 (m-80) cc_final: 0.8245 (m-80) REVERT: S 230 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7454 (ttt) outliers start: 30 outliers final: 23 residues processed: 291 average time/residue: 0.2952 time to fit residues: 115.1867 Evaluate side-chains 294 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 270 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 B residue 18 ILE Chi-restraints excluded: chain B residue 43 ILE 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 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 269 VAL Chi-restraints excluded: chain R residue 288 THR Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain S residue 78 THR 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 N residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 84 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 70 optimal weight: 0.1980 chunk 45 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN S 232 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.113220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.095922 restraints weight = 15245.903| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.13 r_work: 0.2966 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9769 Z= 0.187 Angle : 0.540 8.453 13299 Z= 0.280 Chirality : 0.042 0.194 1539 Planarity : 0.004 0.064 1672 Dihedral : 4.391 55.432 1396 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.05 % Allowed : 24.40 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.24), residues: 1255 helix: 1.69 (0.29), residues: 375 sheet: 0.58 (0.29), residues: 320 loop : -1.34 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 47 HIS 0.004 0.001 HIS S 35 PHE 0.019 0.001 PHE R 267 TYR 0.029 0.001 TYR A 391 ARG 0.007 0.000 ARG B 68 *********************** 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 293 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 264 time to evaluate : 1.432 Fit side-chains REVERT: A 59 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7773 (mm-40) REVERT: A 60 MET cc_start: 0.8043 (mmm) cc_final: 0.7721 (tpp) REVERT: A 221 MET cc_start: 0.8384 (ttm) cc_final: 0.8088 (ttp) REVERT: A 384 GLN cc_start: 0.8311 (tt0) cc_final: 0.8074 (tt0) REVERT: B 72 SER cc_start: 0.8336 (t) cc_final: 0.7898 (p) REVERT: B 283 ARG cc_start: 0.8398 (tpt-90) cc_final: 0.8022 (tpt90) REVERT: R 73 SER cc_start: 0.8699 (t) cc_final: 0.8490 (t) REVERT: S 71 SER cc_start: 0.7988 (m) cc_final: 0.7340 (p) REVERT: S 76 LYS cc_start: 0.8615 (mttp) cc_final: 0.8357 (mttp) REVERT: S 168 SER cc_start: 0.8305 (p) cc_final: 0.8012 (p) REVERT: S 228 TYR cc_start: 0.8453 (m-80) cc_final: 0.8169 (m-80) outliers start: 29 outliers final: 26 residues processed: 278 average time/residue: 0.3934 time to fit residues: 147.4814 Evaluate side-chains 288 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 262 time to evaluate : 1.599 ------------------------------------------------------------------------------- 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 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 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 119 SER 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 288 THR Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain S residue 78 THR 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 N residue 52 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 99 optimal weight: 1.9990 chunk 5 optimal weight: 0.0770 chunk 98 optimal weight: 4.9990 chunk 87 optimal weight: 0.0470 chunk 60 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 88 optimal weight: 0.6980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN R 68 ASN S 232 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.115919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.098702 restraints weight = 15258.020| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.08 r_work: 0.3024 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9769 Z= 0.125 Angle : 0.508 8.807 13299 Z= 0.259 Chirality : 0.040 0.175 1539 Planarity : 0.004 0.064 1672 Dihedral : 4.098 56.350 1396 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.52 % Allowed : 23.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.24), residues: 1255 helix: 1.85 (0.29), residues: 373 sheet: 0.79 (0.29), residues: 309 loop : -1.32 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 47 HIS 0.004 0.001 HIS S 35 PHE 0.018 0.001 PHE R 158 TYR 0.017 0.001 TYR A 391 ARG 0.007 0.000 ARG R 130 *********************** 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 295 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 271 time to evaluate : 1.047 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.7988 (mmm) cc_final: 0.7754 (mmm) REVERT: A 384 GLN cc_start: 0.8305 (tt0) cc_final: 0.8079 (tt0) REVERT: B 50 THR cc_start: 0.8454 (m) cc_final: 0.8237 (t) REVERT: B 61 MET cc_start: 0.7758 (ppp) cc_final: 0.7375 (ppp) REVERT: B 283 ARG cc_start: 0.8341 (tpt-90) cc_final: 0.8067 (tpt170) REVERT: C 46 LYS cc_start: 0.8723 (mmpt) cc_final: 0.8480 (mmpt) REVERT: R 73 SER cc_start: 0.8667 (t) cc_final: 0.8456 (t) REVERT: R 269 VAL cc_start: 0.8838 (OUTLIER) cc_final: 0.8630 (t) REVERT: S 71 SER cc_start: 0.7804 (m) cc_final: 0.7110 (p) REVERT: S 76 LYS cc_start: 0.8618 (mttp) cc_final: 0.8347 (mttp) REVERT: S 178 LEU cc_start: 0.8679 (tp) cc_final: 0.8466 (tt) REVERT: S 228 TYR cc_start: 0.8420 (m-80) cc_final: 0.8144 (m-80) outliers start: 24 outliers final: 16 residues processed: 284 average time/residue: 0.2385 time to fit residues: 90.6081 Evaluate side-chains 284 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 267 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 187 VAL 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 119 SER 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 299 CYS Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 122 optimal weight: 0.5980 chunk 98 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 76 optimal weight: 20.0000 chunk 123 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 267 GLN B 156 GLN S 232 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.114918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.097651 restraints weight = 15360.826| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.08 r_work: 0.3005 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9769 Z= 0.144 Angle : 0.520 8.024 13299 Z= 0.265 Chirality : 0.040 0.194 1539 Planarity : 0.004 0.065 1672 Dihedral : 3.818 55.351 1394 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.79 % Allowed : 25.45 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.24), residues: 1255 helix: 1.85 (0.29), residues: 373 sheet: 0.80 (0.29), residues: 310 loop : -1.33 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 47 HIS 0.005 0.001 HIS A 220 PHE 0.025 0.001 PHE B 241 TYR 0.021 0.001 TYR A 391 ARG 0.008 0.000 ARG R 130 ********************** 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 286 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 269 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: A 59 GLN cc_start: 0.8119 (mm-40) cc_final: 0.7754 (mm-40) REVERT: A 60 MET cc_start: 0.8020 (mmm) cc_final: 0.7718 (mmm) REVERT: B 50 THR cc_start: 0.8499 (m) cc_final: 0.8254 (t) REVERT: B 262 MET cc_start: 0.7992 (tpp) cc_final: 0.7772 (tpp) REVERT: B 283 ARG cc_start: 0.8352 (tpt-90) cc_final: 0.7981 (tpt90) REVERT: C 46 LYS cc_start: 0.8751 (mmpt) cc_final: 0.8494 (mmpt) REVERT: R 73 SER cc_start: 0.8689 (t) cc_final: 0.8481 (t) REVERT: R 269 VAL cc_start: 0.8849 (OUTLIER) cc_final: 0.8645 (t) REVERT: S 71 SER cc_start: 0.7854 (m) cc_final: 0.7176 (p) REVERT: S 76 LYS cc_start: 0.8622 (mttp) cc_final: 0.8351 (mttp) REVERT: S 168 SER cc_start: 0.8289 (p) cc_final: 0.8041 (p) REVERT: S 228 TYR cc_start: 0.8417 (m-80) cc_final: 0.8069 (m-80) outliers start: 17 outliers final: 14 residues processed: 280 average time/residue: 0.2394 time to fit residues: 89.2250 Evaluate side-chains 281 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 266 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 SER 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 119 SER 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 78 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 51 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 117 optimal weight: 0.4980 chunk 75 optimal weight: 0.1980 chunk 91 optimal weight: 0.9990 chunk 122 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 384 GLN B 156 GLN S 232 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.115582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.098279 restraints weight = 15281.116| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.08 r_work: 0.3028 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9769 Z= 0.128 Angle : 0.521 10.181 13299 Z= 0.261 Chirality : 0.040 0.182 1539 Planarity : 0.004 0.062 1672 Dihedral : 3.736 55.436 1394 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.00 % Allowed : 25.45 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.24), residues: 1255 helix: 1.91 (0.28), residues: 373 sheet: 0.90 (0.29), residues: 303 loop : -1.28 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 47 HIS 0.006 0.001 HIS A 220 PHE 0.024 0.001 PHE B 241 TYR 0.012 0.001 TYR A 391 ARG 0.007 0.000 ARG B 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5360.03 seconds wall clock time: 95 minutes 11.58 seconds (5711.58 seconds total)