Starting phenix.real_space_refine on Fri Aug 22 20:30:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iw4_35762/08_2025/8iw4_35762_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iw4_35762/08_2025/8iw4_35762.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iw4_35762/08_2025/8iw4_35762.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iw4_35762/08_2025/8iw4_35762.map" model { file = "/net/cci-nas-00/data/ceres_data/8iw4_35762/08_2025/8iw4_35762_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iw4_35762/08_2025/8iw4_35762_neut.cif" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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 49 5.16 5 C 5077 2.51 5 N 1338 2.21 5 O 1436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7900 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1408 Classifications: {'peptide': 179} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 1, 'TRANS': 177} Chain breaks: 6 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 7, 'GLN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 66 Chain: "B" Number of atoms: 2230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2230 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 5, 'TRANS': 296} Chain breaks: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 5, 'ASP:plan': 4, 'ASN:plan1': 3, 'GLU:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "C" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 239 Classifications: {'peptide': 35} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 30} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "R" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2226 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 12, 'TRANS': 283} Chain breaks: 2 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'TYR:plan': 2, 'TRP:plan': 1, 'ARG:plan': 2, 'GLU:plan': 5, 'ASP:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 65 Chain: "S" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1787 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Chain: "R" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'SPD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.22, per 1000 atoms: 0.28 Number of scatterers: 7900 At special positions: 0 Unit cell: (91.086, 113.411, 113.411, 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 49 16.00 O 1436 8.00 N 1338 7.00 C 5077 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 R 105 " - pdb=" SG CYS R 190 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 515.6 milliseconds Enol-peptide restraints added in 1.2 microseconds 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1946 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 13 sheets defined 32.5% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 6 through 38 removed outlier: 3.546A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 52 removed outlier: 4.309A pdb=" N GLY A 52 " --> pdb=" O ASP A 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 49 through 52' Processing helix chain 'A' and resid 57 through 61 Processing helix chain 'A' and resid 269 through 278 Processing helix chain 'A' and resid 336 through 352 removed outlier: 3.826A pdb=" N PHE A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.681A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 removed outlier: 3.966A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'R' and resid 35 through 57 removed outlier: 4.975A pdb=" N LEU R 41 " --> pdb=" O GLY R 37 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLY R 42 " --> pdb=" O VAL R 38 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA R 43 " --> pdb=" O LEU R 39 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASN R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL R 53 " --> pdb=" O GLY R 49 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE R 55 " --> pdb=" O LEU R 51 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA R 56 " --> pdb=" O LEU R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 85 removed outlier: 4.114A pdb=" N VAL R 71 " --> pdb=" O THR R 67 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL R 81 " --> pdb=" O ALA R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 96 Processing helix chain 'R' and resid 104 through 136 removed outlier: 3.657A pdb=" N THR R 109 " --> pdb=" O CYS R 105 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N CYS R 110 " --> pdb=" O LYS R 106 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP R 112 " --> pdb=" O HIS R 108 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR R 113 " --> pdb=" O THR R 109 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER R 114 " --> pdb=" O CYS R 110 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE R 117 " --> pdb=" O THR R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 144 removed outlier: 3.735A pdb=" N LYS R 143 " --> pdb=" O THR R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 169 removed outlier: 3.776A pdb=" N PHE R 158 " --> pdb=" O ALA R 154 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER R 164 " --> pdb=" O SER R 160 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER R 166 " --> pdb=" O THR R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 195 through 232 removed outlier: 4.340A pdb=" N LEU R 200 " --> pdb=" O GLN R 196 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU R 201 " --> pdb=" O ASN R 197 " (cutoff:3.500A) Proline residue: R 209 - end of helix removed outlier: 3.991A pdb=" N VAL R 212 " --> pdb=" O LEU R 208 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N MET R 213 " --> pdb=" O PRO R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 246 through 283 removed outlier: 4.395A pdb=" N LYS R 251 " --> pdb=" O GLU R 247 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG R 252 " --> pdb=" O ARG R 248 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR R 259 " --> pdb=" O LYS R 255 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU R 260 " --> pdb=" O ALA R 256 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA R 263 " --> pdb=" O THR R 259 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER R 270 " --> pdb=" O ALA R 266 " (cutoff:3.500A) Proline residue: R 273 - end of helix removed outlier: 3.772A pdb=" N ALA R 282 " --> pdb=" O ALA R 278 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TYR R 283 " --> pdb=" O VAL R 279 " (cutoff:3.500A) Processing helix chain 'R' and resid 289 through 312 removed outlier: 3.610A pdb=" N TYR R 293 " --> pdb=" O PRO R 289 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU R 294 " --> pdb=" O ALA R 290 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE R 295 " --> pdb=" O TYR R 291 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL R 300 " --> pdb=" O LEU R 296 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN R 303 " --> pdb=" O CYS R 299 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N SER R 304 " --> pdb=" O VAL R 300 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA R 305 " --> pdb=" O TYR R 301 " (cutoff:3.500A) Proline residue: R 308 - end of helix Processing helix chain 'R' and resid 315 through 327 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.535A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.523A pdb=" N HIS A 41 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 50 removed outlier: 6.856A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.275A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.031A 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: 7.074A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 153 removed outlier: 6.602A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.698A 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: 7.009A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TRP B 211 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.395A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.379A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TYR B 289 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (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 11 through 12 removed outlier: 3.814A pdb=" N VAL S 12 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.814A pdb=" N VAL S 12 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG S 98 " --> pdb=" O PHE S 110 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 141 through 142 Processing sheet with id=AB4, first strand: chain 'S' and resid 194 through 195 removed outlier: 3.545A pdb=" N TYR S 190 " --> pdb=" O ASN S 194 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR S 175 " --> pdb=" O MET S 230 " (cutoff:3.500A) 338 hydrogen bonds defined for protein. 960 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.40 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1372 1.33 - 1.45: 2261 1.45 - 1.57: 4380 1.57 - 1.70: 0 1.70 - 1.82: 68 Bond restraints: 8081 Sorted by residual: bond pdb=" CA ASN A 271 " pdb=" C ASN A 271 " ideal model delta sigma weight residual 1.522 1.445 0.077 1.36e-02 5.41e+03 3.24e+01 bond pdb=" C TYR A 360 " pdb=" O TYR A 360 " ideal model delta sigma weight residual 1.249 1.222 0.027 8.50e-03 1.38e+04 9.82e+00 bond pdb=" C VAL R 94 " pdb=" O VAL R 94 " ideal model delta sigma weight residual 1.236 1.202 0.034 1.23e-02 6.61e+03 7.83e+00 bond pdb=" N GLN A 267 " pdb=" CA GLN A 267 " ideal model delta sigma weight residual 1.460 1.488 -0.028 1.28e-02 6.10e+03 4.92e+00 bond pdb=" CA VAL R 94 " pdb=" CB VAL R 94 " ideal model delta sigma weight residual 1.540 1.510 0.030 1.37e-02 5.33e+03 4.72e+00 ... (remaining 8076 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 10762 2.56 - 5.12: 184 5.12 - 7.68: 29 7.68 - 10.25: 6 10.25 - 12.81: 2 Bond angle restraints: 10983 Sorted by residual: angle pdb=" N HIS A 357 " pdb=" CA HIS A 357 " pdb=" C HIS A 357 " ideal model delta sigma weight residual 111.14 123.05 -11.91 1.08e+00 8.57e-01 1.22e+02 angle pdb=" N TYR A 358 " pdb=" CA TYR A 358 " pdb=" C TYR A 358 " ideal model delta sigma weight residual 111.30 124.11 -12.81 1.36e+00 5.41e-01 8.87e+01 angle pdb=" N ASN R 303 " pdb=" CA ASN R 303 " pdb=" C ASN R 303 " ideal model delta sigma weight residual 112.38 103.43 8.95 1.22e+00 6.72e-01 5.38e+01 angle pdb=" N CYS A 359 " pdb=" CA CYS A 359 " pdb=" C CYS A 359 " ideal model delta sigma weight residual 110.24 119.64 -9.40 1.30e+00 5.92e-01 5.23e+01 angle pdb=" N ALA A 269 " pdb=" CA ALA A 269 " pdb=" C ALA A 269 " ideal model delta sigma weight residual 113.41 104.60 8.81 1.22e+00 6.72e-01 5.22e+01 ... (remaining 10978 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 4141 17.16 - 34.31: 421 34.31 - 51.47: 101 51.47 - 68.62: 14 68.62 - 85.78: 6 Dihedral angle restraints: 4683 sinusoidal: 1663 harmonic: 3020 Sorted by residual: dihedral pdb=" C VAL R 279 " pdb=" N VAL R 279 " pdb=" CA VAL R 279 " pdb=" CB VAL R 279 " ideal model delta harmonic sigma weight residual -122.00 -137.52 15.52 0 2.50e+00 1.60e-01 3.85e+01 dihedral pdb=" N GLN A 267 " pdb=" C GLN A 267 " pdb=" CA GLN A 267 " pdb=" CB GLN A 267 " ideal model delta harmonic sigma weight residual 122.80 133.97 -11.17 0 2.50e+00 1.60e-01 2.00e+01 dihedral pdb=" C GLN A 267 " pdb=" N GLN A 267 " pdb=" CA GLN A 267 " pdb=" CB GLN A 267 " ideal model delta harmonic sigma weight residual -122.60 -133.05 10.45 0 2.50e+00 1.60e-01 1.75e+01 ... (remaining 4680 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 1154 0.102 - 0.205: 75 0.205 - 0.307: 16 0.307 - 0.410: 6 0.410 - 0.512: 2 Chirality restraints: 1253 Sorted by residual: chirality pdb=" CA TYR A 358 " pdb=" N TYR A 358 " pdb=" C TYR A 358 " pdb=" CB TYR A 358 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.55e+00 chirality pdb=" CA VAL R 279 " pdb=" N VAL R 279 " pdb=" C VAL R 279 " pdb=" CB VAL R 279 " both_signs ideal model delta sigma weight residual False 2.44 1.99 0.45 2.00e-01 2.50e+01 5.04e+00 chirality pdb=" CA LYS A 216 " pdb=" N LYS A 216 " pdb=" C LYS A 216 " pdb=" CB LYS A 216 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.63e+00 ... (remaining 1250 not shown) Planarity restraints: 1381 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR R 301 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.25e+00 pdb=" C TYR R 301 " 0.053 2.00e-02 2.50e+03 pdb=" O TYR R 301 " -0.020 2.00e-02 2.50e+03 pdb=" N TYR R 302 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 351 " 0.010 2.00e-02 2.50e+03 2.10e-02 4.40e+00 pdb=" C ALA A 351 " -0.036 2.00e-02 2.50e+03 pdb=" O ALA A 351 " 0.014 2.00e-02 2.50e+03 pdb=" N SER A 352 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER R 147 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.30e+00 pdb=" C SER R 147 " -0.036 2.00e-02 2.50e+03 pdb=" O SER R 147 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL R 148 " 0.012 2.00e-02 2.50e+03 ... (remaining 1378 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 195 2.69 - 3.25: 7248 3.25 - 3.80: 11631 3.80 - 4.35: 15289 4.35 - 4.90: 26177 Nonbonded interactions: 60540 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.143 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.180 3.040 nonbonded pdb=" OD2 ASP A 215 " pdb=" NH1 ARG A 373 " model vdw 2.224 3.120 nonbonded pdb=" ND2 ASN B 119 " pdb=" O GLY B 144 " model vdw 2.234 3.120 nonbonded pdb=" O SER S 105 " pdb=" NH2 ARG S 191 " model vdw 2.258 3.120 ... (remaining 60535 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: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.750 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 8084 Z= 0.227 Angle : 0.813 12.808 10989 Z= 0.543 Chirality : 0.063 0.512 1253 Planarity : 0.004 0.033 1381 Dihedral : 14.913 85.776 2728 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.39 % Allowed : 8.07 % Favored : 90.54 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.27), residues: 1013 helix: 0.78 (0.33), residues: 288 sheet: -0.04 (0.32), residues: 265 loop : -1.41 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.018 0.001 TYR S 235 PHE 0.012 0.001 PHE A 219 TRP 0.013 0.001 TRP R 317 HIS 0.002 0.001 HIS S 232 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 8081) covalent geometry : angle 0.81295 (10983) SS BOND : bond 0.00551 ( 3) SS BOND : angle 0.84460 ( 6) hydrogen bonds : bond 0.15817 ( 334) hydrogen bonds : angle 6.07224 ( 960) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.286 Fit side-chains REVERT: R 94 VAL cc_start: 0.7301 (t) cc_final: 0.6964 (p) REVERT: R 98 TRP cc_start: 0.5655 (t-100) cc_final: 0.4917 (t-100) REVERT: R 128 ILE cc_start: 0.6476 (OUTLIER) cc_final: 0.6256 (mt) REVERT: R 264 MET cc_start: 0.5059 (mmp) cc_final: 0.4741 (mmt) REVERT: S 6 GLU cc_start: 0.4100 (mm-30) cc_final: 0.3409 (mm-30) REVERT: S 160 ARG cc_start: 0.7064 (ttp80) cc_final: 0.6732 (ttp80) outliers start: 11 outliers final: 4 residues processed: 124 average time/residue: 0.1135 time to fit residues: 18.2743 Evaluate side-chains 96 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain R residue 128 ILE Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.0170 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 218 ASN A 236 GLN B 142 HIS B 225 HIS ** R 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 232 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.157977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.133272 restraints weight = 8971.522| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.22 r_work: 0.3419 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8084 Z= 0.124 Angle : 0.529 5.706 10989 Z= 0.278 Chirality : 0.043 0.147 1253 Planarity : 0.004 0.032 1381 Dihedral : 4.980 52.550 1136 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.14 % Allowed : 12.23 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.28), residues: 1013 helix: 1.15 (0.32), residues: 306 sheet: 0.10 (0.32), residues: 271 loop : -1.31 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 251 TYR 0.024 0.002 TYR S 235 PHE 0.019 0.001 PHE S 68 TRP 0.015 0.001 TRP R 317 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8081) covalent geometry : angle 0.52808 (10983) SS BOND : bond 0.00590 ( 3) SS BOND : angle 1.12584 ( 6) hydrogen bonds : bond 0.03859 ( 334) hydrogen bonds : angle 4.53172 ( 960) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.305 Fit side-chains REVERT: B 312 ASP cc_start: 0.6899 (t70) cc_final: 0.6655 (t0) REVERT: R 52 LEU cc_start: 0.7932 (mt) cc_final: 0.7579 (mt) REVERT: R 277 ASP cc_start: 0.7611 (t0) cc_final: 0.7164 (t0) outliers start: 17 outliers final: 11 residues processed: 115 average time/residue: 0.0940 time to fit residues: 14.6163 Evaluate side-chains 109 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 191 GLN Chi-restraints excluded: chain S residue 81 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 91 optimal weight: 0.0970 chunk 26 optimal weight: 0.0980 chunk 45 optimal weight: 0.0980 chunk 28 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN C 44 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.171462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.156401 restraints weight = 8748.179| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 0.73 r_work: 0.3467 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8084 Z= 0.090 Angle : 0.473 5.477 10989 Z= 0.247 Chirality : 0.041 0.143 1253 Planarity : 0.003 0.047 1381 Dihedral : 4.604 53.196 1130 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.77 % Allowed : 15.13 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.28), residues: 1013 helix: 1.37 (0.32), residues: 308 sheet: 0.19 (0.33), residues: 266 loop : -1.28 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 251 TYR 0.020 0.001 TYR S 235 PHE 0.017 0.001 PHE S 68 TRP 0.010 0.001 TRP R 98 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00194 ( 8081) covalent geometry : angle 0.47308 (10983) SS BOND : bond 0.00367 ( 3) SS BOND : angle 0.74416 ( 6) hydrogen bonds : bond 0.03015 ( 334) hydrogen bonds : angle 4.17858 ( 960) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.333 Fit side-chains REVERT: B 61 MET cc_start: 0.8631 (ppp) cc_final: 0.8399 (ppp) REVERT: B 66 ASP cc_start: 0.7218 (p0) cc_final: 0.7017 (p0) REVERT: B 163 ASP cc_start: 0.7654 (OUTLIER) cc_final: 0.7453 (p0) REVERT: R 165 PHE cc_start: 0.6743 (t80) cc_final: 0.4890 (m-80) REVERT: R 277 ASP cc_start: 0.7476 (t0) cc_final: 0.7160 (t0) REVERT: S 113 GLN cc_start: 0.6924 (mm110) cc_final: 0.6117 (pt0) REVERT: S 230 MET cc_start: 0.7961 (tpt) cc_final: 0.7211 (tpt) outliers start: 14 outliers final: 8 residues processed: 119 average time/residue: 0.0968 time to fit residues: 15.4720 Evaluate side-chains 111 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 110 CYS Chi-restraints excluded: chain R residue 191 GLN Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain S residue 81 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 61 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 101 optimal weight: 0.2980 chunk 79 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 5 optimal weight: 0.0000 chunk 85 optimal weight: 0.9980 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN B 88 ASN ** R 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.164297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 118)---------------| | r_work = 0.3515 r_free = 0.3515 target = 0.140150 restraints weight = 8886.401| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.18 r_work: 0.3339 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8084 Z= 0.092 Angle : 0.468 5.510 10989 Z= 0.245 Chirality : 0.041 0.141 1253 Planarity : 0.003 0.039 1381 Dihedral : 4.532 53.507 1130 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.64 % Allowed : 16.52 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.28), residues: 1013 helix: 1.51 (0.32), residues: 308 sheet: 0.18 (0.33), residues: 268 loop : -1.30 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 18 TYR 0.020 0.001 TYR S 235 PHE 0.014 0.001 PHE S 68 TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00203 ( 8081) covalent geometry : angle 0.46771 (10983) SS BOND : bond 0.00335 ( 3) SS BOND : angle 0.74776 ( 6) hydrogen bonds : bond 0.03013 ( 334) hydrogen bonds : angle 4.06232 ( 960) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.297 Fit side-chains REVERT: B 66 ASP cc_start: 0.7268 (p0) cc_final: 0.7042 (p0) REVERT: B 163 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.7530 (p0) REVERT: R 52 LEU cc_start: 0.8080 (mt) cc_final: 0.7763 (mt) REVERT: R 277 ASP cc_start: 0.7572 (t0) cc_final: 0.7288 (t0) REVERT: S 113 GLN cc_start: 0.7025 (mm110) cc_final: 0.6040 (pt0) REVERT: S 230 MET cc_start: 0.8030 (tpt) cc_final: 0.7330 (tpt) outliers start: 13 outliers final: 8 residues processed: 113 average time/residue: 0.0937 time to fit residues: 14.3487 Evaluate side-chains 108 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain R residue 110 CYS Chi-restraints excluded: chain R residue 191 GLN Chi-restraints excluded: chain R residue 329 LYS Chi-restraints excluded: chain S residue 81 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 59 optimal weight: 1.9990 chunk 47 optimal weight: 20.0000 chunk 50 optimal weight: 30.0000 chunk 66 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 35 optimal weight: 20.0000 chunk 99 optimal weight: 0.0170 chunk 17 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 overall best weight: 3.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN C 44 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.156244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.139297 restraints weight = 9045.321| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 0.88 r_work: 0.3295 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8084 Z= 0.212 Angle : 0.612 6.429 10989 Z= 0.323 Chirality : 0.045 0.163 1253 Planarity : 0.004 0.041 1381 Dihedral : 5.280 56.598 1130 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.90 % Allowed : 17.78 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.27), residues: 1013 helix: 1.01 (0.31), residues: 303 sheet: -0.05 (0.31), residues: 280 loop : -1.52 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 314 TYR 0.034 0.002 TYR S 235 PHE 0.020 0.002 PHE R 117 TRP 0.011 0.002 TRP B 82 HIS 0.006 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00515 ( 8081) covalent geometry : angle 0.61171 (10983) SS BOND : bond 0.00638 ( 3) SS BOND : angle 1.27778 ( 6) hydrogen bonds : bond 0.05057 ( 334) hydrogen bonds : angle 4.48400 ( 960) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7961 (ttmt) cc_final: 0.7154 (ttmm) REVERT: B 66 ASP cc_start: 0.7201 (p0) cc_final: 0.6803 (p0) REVERT: R 204 LEU cc_start: 0.8332 (mt) cc_final: 0.7935 (mt) REVERT: S 113 GLN cc_start: 0.7054 (mm110) cc_final: 0.6154 (mm110) REVERT: S 230 MET cc_start: 0.8189 (tpt) cc_final: 0.7699 (tpt) outliers start: 23 outliers final: 21 residues processed: 123 average time/residue: 0.0884 time to fit residues: 14.8696 Evaluate side-chains 123 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 110 CYS Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 191 GLN Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 329 LYS Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 159 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.155988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.134608 restraints weight = 8962.791| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 0.94 r_work: 0.3301 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8084 Z= 0.132 Angle : 0.531 6.849 10989 Z= 0.278 Chirality : 0.042 0.161 1253 Planarity : 0.004 0.037 1381 Dihedral : 5.047 55.362 1130 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.90 % Allowed : 18.03 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.27), residues: 1013 helix: 1.12 (0.31), residues: 308 sheet: -0.08 (0.31), residues: 282 loop : -1.47 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 129 TYR 0.026 0.001 TYR S 235 PHE 0.014 0.001 PHE S 68 TRP 0.013 0.001 TRP B 82 HIS 0.007 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8081) covalent geometry : angle 0.53110 (10983) SS BOND : bond 0.00436 ( 3) SS BOND : angle 0.87364 ( 6) hydrogen bonds : bond 0.03902 ( 334) hydrogen bonds : angle 4.25788 ( 960) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7869 (ttmt) cc_final: 0.7189 (ttmm) REVERT: S 113 GLN cc_start: 0.7011 (mm110) cc_final: 0.6073 (mm110) REVERT: S 230 MET cc_start: 0.8121 (tpt) cc_final: 0.7590 (tpt) outliers start: 23 outliers final: 15 residues processed: 119 average time/residue: 0.0886 time to fit residues: 14.4342 Evaluate side-chains 116 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 110 CYS Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 191 GLN Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 329 LYS Chi-restraints excluded: chain S residue 81 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 98 optimal weight: 0.0060 chunk 24 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.157412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 116)---------------| | r_work = 0.3465 r_free = 0.3465 target = 0.135377 restraints weight = 9042.355| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 0.97 r_work: 0.3293 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8084 Z= 0.140 Angle : 0.536 6.072 10989 Z= 0.281 Chirality : 0.043 0.156 1253 Planarity : 0.004 0.036 1381 Dihedral : 5.081 55.211 1130 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.40 % Allowed : 18.41 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.27), residues: 1013 helix: 1.19 (0.31), residues: 308 sheet: -0.14 (0.31), residues: 282 loop : -1.48 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 129 TYR 0.026 0.001 TYR S 235 PHE 0.016 0.001 PHE B 241 TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 8081) covalent geometry : angle 0.53563 (10983) SS BOND : bond 0.00473 ( 3) SS BOND : angle 0.92267 ( 6) hydrogen bonds : bond 0.04025 ( 334) hydrogen bonds : angle 4.26680 ( 960) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7882 (ttmt) cc_final: 0.7214 (ttmm) REVERT: S 113 GLN cc_start: 0.7032 (mm110) cc_final: 0.5972 (mm110) REVERT: S 230 MET cc_start: 0.8105 (tpt) cc_final: 0.7549 (tpt) REVERT: S 234 GLU cc_start: 0.7726 (tt0) cc_final: 0.7510 (tt0) outliers start: 27 outliers final: 24 residues processed: 119 average time/residue: 0.0853 time to fit residues: 13.7400 Evaluate side-chains 126 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 110 CYS Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 191 GLN Chi-restraints excluded: chain R residue 287 ILE Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 329 LYS Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 159 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 79 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 92 optimal weight: 0.0030 chunk 47 optimal weight: 6.9990 overall best weight: 2.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.152113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.3389 r_free = 0.3389 target = 0.129401 restraints weight = 9003.103| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 0.98 r_work: 0.3277 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8084 Z= 0.158 Angle : 0.551 5.768 10989 Z= 0.290 Chirality : 0.043 0.163 1253 Planarity : 0.004 0.036 1381 Dihedral : 5.174 58.125 1130 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.40 % Allowed : 19.17 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.27), residues: 1013 helix: 1.14 (0.31), residues: 309 sheet: -0.21 (0.31), residues: 282 loop : -1.53 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 129 TYR 0.028 0.002 TYR S 235 PHE 0.015 0.002 PHE R 117 TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 8081) covalent geometry : angle 0.55093 (10983) SS BOND : bond 0.00502 ( 3) SS BOND : angle 0.98260 ( 6) hydrogen bonds : bond 0.04253 ( 334) hydrogen bonds : angle 4.32025 ( 960) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7928 (ttmt) cc_final: 0.7238 (ttmm) REVERT: S 113 GLN cc_start: 0.7027 (mm110) cc_final: 0.5933 (mm110) REVERT: S 230 MET cc_start: 0.8149 (tpt) cc_final: 0.7642 (tpt) outliers start: 27 outliers final: 25 residues processed: 118 average time/residue: 0.0883 time to fit residues: 14.1417 Evaluate side-chains 122 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 110 CYS Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 191 GLN Chi-restraints excluded: chain R residue 287 ILE Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 329 LYS Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 159 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 47 optimal weight: 20.0000 chunk 4 optimal weight: 0.0070 chunk 43 optimal weight: 9.9990 chunk 51 optimal weight: 0.0000 chunk 2 optimal weight: 0.5980 chunk 101 optimal weight: 10.0000 chunk 73 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 overall best weight: 0.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.163004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.142542 restraints weight = 8884.795| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 0.92 r_work: 0.3355 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8084 Z= 0.085 Angle : 0.469 5.811 10989 Z= 0.243 Chirality : 0.041 0.138 1253 Planarity : 0.003 0.032 1381 Dihedral : 4.689 57.667 1130 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.77 % Allowed : 20.55 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.28), residues: 1013 helix: 1.74 (0.32), residues: 303 sheet: 0.08 (0.32), residues: 268 loop : -1.36 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 129 TYR 0.018 0.001 TYR S 235 PHE 0.012 0.001 PHE S 68 TRP 0.013 0.001 TRP R 98 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00183 ( 8081) covalent geometry : angle 0.46930 (10983) SS BOND : bond 0.00262 ( 3) SS BOND : angle 0.62002 ( 6) hydrogen bonds : bond 0.02678 ( 334) hydrogen bonds : angle 4.00489 ( 960) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.281 Fit side-chains REVERT: B 163 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7429 (p0) REVERT: B 234 PHE cc_start: 0.7873 (OUTLIER) cc_final: 0.6407 (m-80) REVERT: R 232 GLU cc_start: 0.7090 (mm-30) cc_final: 0.6790 (mm-30) REVERT: S 113 GLN cc_start: 0.6953 (mm110) cc_final: 0.5746 (mm110) REVERT: S 230 MET cc_start: 0.7908 (tpt) cc_final: 0.7317 (tpt) outliers start: 14 outliers final: 9 residues processed: 113 average time/residue: 0.0896 time to fit residues: 13.8785 Evaluate side-chains 112 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 110 CYS Chi-restraints excluded: chain R residue 191 GLN Chi-restraints excluded: chain S residue 81 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 96 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 chunk 83 optimal weight: 0.0060 chunk 18 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 HIS ** R 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.159869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.3494 r_free = 0.3494 target = 0.138028 restraints weight = 8901.454| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 0.97 r_work: 0.3327 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8084 Z= 0.114 Angle : 0.500 5.972 10989 Z= 0.260 Chirality : 0.042 0.148 1253 Planarity : 0.003 0.032 1381 Dihedral : 4.833 56.865 1130 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.89 % Allowed : 20.93 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.27), residues: 1013 helix: 1.62 (0.32), residues: 307 sheet: -0.02 (0.32), residues: 275 loop : -1.34 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 129 TYR 0.020 0.001 TYR S 235 PHE 0.012 0.001 PHE B 241 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8081) covalent geometry : angle 0.49924 (10983) SS BOND : bond 0.00441 ( 3) SS BOND : angle 1.03827 ( 6) hydrogen bonds : bond 0.03527 ( 334) hydrogen bonds : angle 4.06912 ( 960) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.300 Fit side-chains REVERT: B 120 ILE cc_start: 0.8162 (mm) cc_final: 0.7948 (mm) REVERT: B 234 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.6489 (m-80) REVERT: R 232 GLU cc_start: 0.7346 (mm-30) cc_final: 0.6881 (mm-30) REVERT: S 113 GLN cc_start: 0.6928 (mm110) cc_final: 0.5823 (mm110) REVERT: S 230 MET cc_start: 0.8033 (tpt) cc_final: 0.7462 (tpt) outliers start: 15 outliers final: 10 residues processed: 110 average time/residue: 0.1016 time to fit residues: 15.1346 Evaluate side-chains 112 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 110 CYS Chi-restraints excluded: chain R residue 191 GLN Chi-restraints excluded: chain S residue 81 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 73 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.161085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.139239 restraints weight = 8851.659| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 0.99 r_work: 0.3291 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8084 Z= 0.102 Angle : 0.487 5.608 10989 Z= 0.253 Chirality : 0.041 0.142 1253 Planarity : 0.003 0.033 1381 Dihedral : 4.753 54.734 1130 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.02 % Allowed : 20.81 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.28), residues: 1013 helix: 1.75 (0.32), residues: 304 sheet: 0.10 (0.32), residues: 269 loop : -1.30 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 129 TYR 0.019 0.001 TYR S 235 PHE 0.011 0.001 PHE B 241 TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 8081) covalent geometry : angle 0.48612 (10983) SS BOND : bond 0.00332 ( 3) SS BOND : angle 0.95886 ( 6) hydrogen bonds : bond 0.03244 ( 334) hydrogen bonds : angle 4.01725 ( 960) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1918.34 seconds wall clock time: 33 minutes 39.16 seconds (2019.16 seconds total)