Starting phenix.real_space_refine on Tue Mar 3 19:29:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t11_25587/03_2026/7t11_25587_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t11_25587/03_2026/7t11_25587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t11_25587/03_2026/7t11_25587.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t11_25587/03_2026/7t11_25587.map" model { file = "/net/cci-nas-00/data/ceres_data/7t11_25587/03_2026/7t11_25587_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t11_25587/03_2026/7t11_25587_neut.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.097 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 58 5.16 5 C 5245 2.51 5 N 1383 2.21 5 O 1465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8151 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1563 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 245 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLU:plan': 15, 'ASP:plan': 10, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 112 Chain: "B" Number of atoms: 2490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2490 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 5, 'GLN:plan1': 4, 'ARG:plan': 6, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 91 Chain: "C" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 362 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "S" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1642 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 217} Chain breaks: 3 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASP:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 58 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Classifications: {'peptide': 3} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 2} Chain: "P" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {'THO': 1} Classifications: {'peptide': 4, 'undetermined': 1} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 4} Chain: "R" Number of atoms: 2023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2023 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 11, 'TRANS': 273} Unresolved non-hydrogen bonds: 253 Unresolved non-hydrogen angles: 309 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASN:plan1': 3, 'PHE:plan': 4, 'ARG:plan': 9, 'TYR:plan': 1, 'TRP:plan': 2, 'GLN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 122 Time building chain proxies: 1.72, per 1000 atoms: 0.21 Number of scatterers: 8151 At special positions: 0 Unit cell: (99.6957, 121.85, 113.329, 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 58 16.00 O 1465 8.00 N 1383 7.00 C 5245 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 Simple disulfide: pdb=" SG CYS P 2 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 115 " - pdb=" SG CYS R 193 " 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 Links applied TRANS " DTR P 4 " - " PHE P 3 " Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 241.8 milliseconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DPN P 1 " pdb=" CB DTR P 4 " Number of C-beta restraints generated: 2116 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 15 sheets defined 37.8% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.513A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.199A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.769A pdb=" N ALA A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.886A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.010A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 329 through 352 removed outlier: 3.528A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 8 through 24 removed outlier: 3.593A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 43 removed outlier: 3.671A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU C 42 " --> pdb=" O MET C 38 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA C 43 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 48 removed outlier: 3.520A pdb=" N GLU C 47 " --> pdb=" O HIS C 44 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 44 through 48' Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.641A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 71 removed outlier: 3.600A pdb=" N ILE R 49 " --> pdb=" O VAL R 45 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR R 50 " --> pdb=" O LEU R 46 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE R 51 " --> pdb=" O THR R 47 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N CYS R 54 " --> pdb=" O TYR R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 94 Processing helix chain 'R' and resid 95 through 105 removed outlier: 4.318A pdb=" N LEU R 99 " --> pdb=" O GLY R 95 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET R 101 " --> pdb=" O PRO R 97 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN R 102 " --> pdb=" O PHE R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 146 removed outlier: 3.635A pdb=" N CYS R 115 " --> pdb=" O GLY R 111 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR R 120 " --> pdb=" O ARG R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 154 removed outlier: 4.058A pdb=" N LYS R 152 " --> pdb=" O LYS R 149 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG R 154 " --> pdb=" O ALA R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 174 removed outlier: 3.553A pdb=" N MET R 164 " --> pdb=" O LYS R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 180 removed outlier: 3.540A pdb=" N MET R 178 " --> pdb=" O ILE R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 201 through 215 removed outlier: 3.720A pdb=" N TYR R 205 " --> pdb=" O SER R 201 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU R 215 " --> pdb=" O TYR R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 236 Processing helix chain 'R' and resid 244 through 280 removed outlier: 4.014A pdb=" N LYS R 253 " --> pdb=" O ARG R 249 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL R 254 " --> pdb=" O ASN R 250 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR R 255 " --> pdb=" O LEU R 251 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE R 265 " --> pdb=" O VAL R 261 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE R 266 " --> pdb=" O VAL R 262 " (cutoff:3.500A) Proline residue: R 271 - end of helix Processing helix chain 'R' and resid 287 through 304 removed outlier: 3.939A pdb=" N VAL R 299 " --> pdb=" O ASP R 295 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU R 300 " --> pdb=" O PHE R 296 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR R 301 " --> pdb=" O VAL R 297 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR R 302 " --> pdb=" O VAL R 298 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN R 304 " --> pdb=" O LEU R 300 " (cutoff:3.500A) Processing helix chain 'R' and resid 307 through 313 Processing helix chain 'R' and resid 316 through 327 removed outlier: 3.755A pdb=" N GLN R 324 " --> pdb=" O LYS R 320 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN R 325 " --> pdb=" O LYS R 321 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL R 326 " --> pdb=" O SER R 322 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.569A pdb=" N VAL A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 9.098A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.628A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.873A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.926A 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: 7.046A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.718A 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 151 removed outlier: 3.855A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.992A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.477A 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: 6.627A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 6.516A 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: 6.567A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.829A 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: 3.866A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.199A 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: 6.051A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.051A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129 removed outlier: 3.538A pdb=" N VAL S 143 " --> pdb=" O ILE S 204 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE S 200 " --> pdb=" O CYS S 147 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER S 194 " --> pdb=" O THR S 201 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 174 through 177 removed outlier: 6.751A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'P' and resid 2 through 3 Processing sheet with id=AB6, first strand: chain 'R' and resid 182 through 185 401 hydrogen bonds defined for protein. 1143 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: 1.17 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1297 1.31 - 1.44: 2327 1.44 - 1.56: 4621 1.56 - 1.69: 0 1.69 - 1.82: 81 Bond restraints: 8326 Sorted by residual: bond pdb=" C THO P 8 " pdb=" O THO P 8 " ideal model delta sigma weight residual 1.231 1.410 -0.179 2.00e-02 2.50e+03 8.00e+01 bond pdb=" C ILE S 177 " pdb=" O ILE S 177 " ideal model delta sigma weight residual 1.236 1.195 0.041 9.90e-03 1.02e+04 1.74e+01 bond pdb=" CA ASN S 182 " pdb=" C ASN S 182 " ideal model delta sigma weight residual 1.525 1.464 0.061 2.10e-02 2.27e+03 8.45e+00 bond pdb=" C TYR S 178 " pdb=" O TYR S 178 " ideal model delta sigma weight residual 1.234 1.199 0.035 1.26e-02 6.30e+03 7.88e+00 bond pdb=" C LEU S 183 " pdb=" O LEU S 183 " ideal model delta sigma weight residual 1.234 1.201 0.033 1.22e-02 6.72e+03 7.48e+00 ... (remaining 8321 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 11199 1.99 - 3.98: 149 3.98 - 5.97: 20 5.97 - 7.96: 2 7.96 - 9.95: 3 Bond angle restraints: 11373 Sorted by residual: angle pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta sigma weight residual 121.70 131.65 -9.95 1.80e+00 3.09e-01 3.05e+01 angle pdb=" CA THO P 8 " pdb=" C THO P 8 " pdb=" O THO P 8 " ideal model delta sigma weight residual 120.80 112.17 8.63 1.70e+00 3.46e-01 2.58e+01 angle pdb=" CA ILE S 177 " pdb=" C ILE S 177 " pdb=" N TYR S 178 " ideal model delta sigma weight residual 116.18 120.44 -4.26 1.24e+00 6.50e-01 1.18e+01 angle pdb=" N GLN R 187 " pdb=" CA GLN R 187 " pdb=" C GLN R 187 " ideal model delta sigma weight residual 110.35 105.62 4.73 1.38e+00 5.25e-01 1.17e+01 angle pdb=" N ARG R 190 " pdb=" CA ARG R 190 " pdb=" C ARG R 190 " ideal model delta sigma weight residual 108.38 112.70 -4.32 1.35e+00 5.49e-01 1.02e+01 ... (remaining 11368 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 4582 17.38 - 34.75: 192 34.75 - 52.13: 38 52.13 - 69.51: 4 69.51 - 86.89: 4 Dihedral angle restraints: 4820 sinusoidal: 1539 harmonic: 3281 Sorted by residual: dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 159.64 20.36 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" N MET S 180 " pdb=" C MET S 180 " pdb=" CA MET S 180 " pdb=" CB MET S 180 " ideal model delta harmonic sigma weight residual 122.80 131.98 -9.18 0 2.50e+00 1.60e-01 1.35e+01 dihedral pdb=" CA PHE S 32 " pdb=" C PHE S 32 " pdb=" N GLY S 33 " pdb=" CA GLY S 33 " ideal model delta harmonic sigma weight residual 180.00 163.55 16.45 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 4817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1254 0.082 - 0.164: 96 0.164 - 0.245: 1 0.245 - 0.327: 1 0.327 - 0.409: 1 Chirality restraints: 1353 Sorted by residual: chirality pdb=" CA MET S 180 " pdb=" N MET S 180 " pdb=" C MET S 180 " pdb=" CB MET S 180 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" CA ARG S 179 " pdb=" N ARG S 179 " pdb=" C ARG S 179 " pdb=" CB ARG S 179 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA TYR S 178 " pdb=" N TYR S 178 " pdb=" C TYR S 178 " pdb=" CB TYR S 178 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1350 not shown) Planarity restraints: 1438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " -0.054 5.00e-02 4.00e+02 8.16e-02 1.07e+01 pdb=" N PRO S 75 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 175 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO R 176 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO R 176 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 176 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO B 236 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.021 5.00e-02 4.00e+02 ... (remaining 1435 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 72 2.67 - 3.22: 7151 3.22 - 3.78: 11434 3.78 - 4.34: 15404 4.34 - 4.90: 27139 Nonbonded interactions: 61200 Sorted by model distance: nonbonded pdb=" O LEU S 176 " pdb=" CD1 ILE S 177 " model vdw 2.107 3.460 nonbonded pdb=" ND2 ASN R 186 " pdb=" O ARG R 190 " model vdw 2.199 3.120 nonbonded pdb=" OE2 GLU A 308 " pdb=" OG1 THR A 321 " model vdw 2.288 3.040 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.346 3.040 nonbonded pdb=" O THR B 181 " pdb=" OG1 THR B 181 " model vdw 2.392 3.040 ... (remaining 61195 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: 3.760 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.210 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.179 8330 Z= 0.206 Angle : 0.611 9.947 11382 Z= 0.364 Chirality : 0.043 0.409 1353 Planarity : 0.004 0.082 1437 Dihedral : 10.837 86.887 2692 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.27 % Allowed : 0.13 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.25), residues: 1107 helix: 2.20 (0.28), residues: 378 sheet: 0.87 (0.30), residues: 286 loop : -0.92 (0.26), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 67 TYR 0.013 0.001 TYR S 178 PHE 0.011 0.001 PHE B 234 TRP 0.008 0.001 TRP R 188 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 8326) covalent geometry : angle 0.61022 (11373) SS BOND : bond 0.00285 ( 3) SS BOND : angle 1.23594 ( 6) hydrogen bonds : bond 0.22436 ( 397) hydrogen bonds : angle 6.09920 ( 1143) link_TRANS : bond 0.00073 ( 1) link_TRANS : angle 0.20089 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 113 time to evaluate : 0.284 Fit side-chains REVERT: B 101 MET cc_start: 0.7918 (mtt) cc_final: 0.7706 (mtt) REVERT: S 128 MET cc_start: 0.5487 (mmt) cc_final: 0.5152 (mmp) REVERT: R 135 VAL cc_start: 0.7954 (p) cc_final: 0.7685 (m) outliers start: 2 outliers final: 0 residues processed: 115 average time/residue: 0.4722 time to fit residues: 58.1372 Evaluate side-chains 84 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.212874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.177429 restraints weight = 8834.886| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 2.24 r_work: 0.3733 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3633 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8330 Z= 0.156 Angle : 0.575 7.202 11382 Z= 0.312 Chirality : 0.042 0.160 1353 Planarity : 0.005 0.063 1437 Dihedral : 4.683 36.369 1209 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.14 % Allowed : 7.74 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.25), residues: 1107 helix: 2.77 (0.27), residues: 376 sheet: 0.80 (0.32), residues: 261 loop : -0.77 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 312 TYR 0.016 0.001 TYR B 59 PHE 0.015 0.002 PHE A 196 TRP 0.011 0.001 TRP R 108 HIS 0.006 0.002 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8326) covalent geometry : angle 0.57476 (11373) SS BOND : bond 0.00622 ( 3) SS BOND : angle 1.20865 ( 6) hydrogen bonds : bond 0.05900 ( 397) hydrogen bonds : angle 4.32105 ( 1143) link_TRANS : bond 0.00128 ( 1) link_TRANS : angle 0.11573 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.358 Fit side-chains REVERT: A 307 PHE cc_start: 0.7352 (OUTLIER) cc_final: 0.5394 (t80) REVERT: B 134 ARG cc_start: 0.8201 (ptp90) cc_final: 0.7934 (ptp90) REVERT: B 217 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8249 (pmt) REVERT: R 63 LEU cc_start: 0.5184 (tt) cc_final: 0.4966 (tp) REVERT: R 135 VAL cc_start: 0.7704 (p) cc_final: 0.7409 (m) REVERT: R 278 SER cc_start: 0.6762 (p) cc_final: 0.6389 (p) outliers start: 16 outliers final: 4 residues processed: 90 average time/residue: 0.4664 time to fit residues: 45.0970 Evaluate side-chains 85 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain R residue 68 ILE Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 214 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 37 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 0.2980 chunk 10 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 95 optimal weight: 8.9990 chunk 41 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN R 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.213180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.178202 restraints weight = 8796.652| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.14 r_work: 0.3739 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3639 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8330 Z= 0.127 Angle : 0.515 6.907 11382 Z= 0.279 Chirality : 0.041 0.152 1353 Planarity : 0.004 0.055 1437 Dihedral : 4.385 38.848 1209 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.74 % Allowed : 10.41 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.25), residues: 1107 helix: 2.90 (0.27), residues: 376 sheet: 0.85 (0.31), residues: 263 loop : -0.77 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 312 TYR 0.011 0.001 TYR B 59 PHE 0.014 0.001 PHE B 151 TRP 0.009 0.001 TRP B 297 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 8326) covalent geometry : angle 0.51513 (11373) SS BOND : bond 0.00530 ( 3) SS BOND : angle 0.95394 ( 6) hydrogen bonds : bond 0.05077 ( 397) hydrogen bonds : angle 4.01063 ( 1143) link_TRANS : bond 0.00055 ( 1) link_TRANS : angle 0.05423 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.308 Fit side-chains REVERT: A 307 PHE cc_start: 0.7443 (OUTLIER) cc_final: 0.5759 (t80) REVERT: B 134 ARG cc_start: 0.8216 (ptp90) cc_final: 0.7422 (ppt170) REVERT: B 217 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8212 (pmt) REVERT: R 135 VAL cc_start: 0.7701 (p) cc_final: 0.7457 (m) REVERT: R 278 SER cc_start: 0.6640 (p) cc_final: 0.6286 (p) outliers start: 13 outliers final: 7 residues processed: 93 average time/residue: 0.4862 time to fit residues: 48.4161 Evaluate side-chains 89 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 87 ILE Chi-restraints excluded: chain R residue 192 SER Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 214 ILE Chi-restraints excluded: chain R residue 299 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 64 optimal weight: 1.9990 chunk 17 optimal weight: 0.0770 chunk 106 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.213109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.178432 restraints weight = 8996.920| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 2.41 r_work: 0.3739 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3636 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8330 Z= 0.122 Angle : 0.503 6.667 11382 Z= 0.274 Chirality : 0.041 0.151 1353 Planarity : 0.004 0.050 1437 Dihedral : 4.321 38.480 1209 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.54 % Allowed : 11.48 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.25), residues: 1107 helix: 2.96 (0.27), residues: 376 sheet: 0.88 (0.31), residues: 263 loop : -0.77 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 21 TYR 0.010 0.001 TYR B 59 PHE 0.013 0.001 PHE R 98 TRP 0.009 0.001 TRP B 297 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 8326) covalent geometry : angle 0.50267 (11373) SS BOND : bond 0.00489 ( 3) SS BOND : angle 0.91534 ( 6) hydrogen bonds : bond 0.04782 ( 397) hydrogen bonds : angle 3.92571 ( 1143) link_TRANS : bond 0.00038 ( 1) link_TRANS : angle 0.07208 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.293 Fit side-chains REVERT: A 307 PHE cc_start: 0.7550 (OUTLIER) cc_final: 0.5999 (t80) REVERT: B 134 ARG cc_start: 0.8238 (ptp90) cc_final: 0.7464 (ppt170) REVERT: B 217 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8185 (pmt) REVERT: R 55 ILE cc_start: 0.6069 (pt) cc_final: 0.5816 (pp) REVERT: R 68 ILE cc_start: 0.5961 (OUTLIER) cc_final: 0.5661 (mp) REVERT: R 135 VAL cc_start: 0.7615 (p) cc_final: 0.7373 (m) REVERT: R 278 SER cc_start: 0.6469 (p) cc_final: 0.6136 (p) outliers start: 19 outliers final: 6 residues processed: 94 average time/residue: 0.4791 time to fit residues: 48.3970 Evaluate side-chains 91 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 68 ILE Chi-restraints excluded: chain R residue 87 ILE Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 299 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 15 optimal weight: 0.0770 chunk 91 optimal weight: 0.0270 chunk 70 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 overall best weight: 1.0202 ------------------------------------------------------------------------------- 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 = 0.4334 r_free = 0.4334 target = 0.211122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.176673 restraints weight = 8859.360| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 2.23 r_work: 0.3720 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3621 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8330 Z= 0.145 Angle : 0.545 6.785 11382 Z= 0.296 Chirality : 0.042 0.154 1353 Planarity : 0.004 0.052 1437 Dihedral : 4.488 39.277 1209 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.27 % Allowed : 12.95 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.25), residues: 1107 helix: 2.90 (0.27), residues: 376 sheet: 0.88 (0.31), residues: 262 loop : -0.88 (0.25), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 116 TYR 0.012 0.001 TYR B 59 PHE 0.015 0.002 PHE A 196 TRP 0.010 0.001 TRP S 36 HIS 0.005 0.001 HIS S 220 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8326) covalent geometry : angle 0.54468 (11373) SS BOND : bond 0.00551 ( 3) SS BOND : angle 1.25335 ( 6) hydrogen bonds : bond 0.05351 ( 397) hydrogen bonds : angle 4.04433 ( 1143) link_TRANS : bond 0.00020 ( 1) link_TRANS : angle 0.08691 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.330 Fit side-chains REVERT: A 307 PHE cc_start: 0.7608 (OUTLIER) cc_final: 0.5984 (t80) REVERT: B 43 ILE cc_start: 0.5961 (OUTLIER) cc_final: 0.5655 (mm) REVERT: B 134 ARG cc_start: 0.8299 (ptp90) cc_final: 0.7542 (ppt170) REVERT: B 217 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8155 (pmt) REVERT: R 55 ILE cc_start: 0.6163 (pt) cc_final: 0.5915 (pp) REVERT: R 135 VAL cc_start: 0.7680 (p) cc_final: 0.7459 (m) REVERT: R 278 SER cc_start: 0.6473 (p) cc_final: 0.6014 (p) outliers start: 17 outliers final: 10 residues processed: 96 average time/residue: 0.4407 time to fit residues: 45.8196 Evaluate side-chains 96 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 87 ILE Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 192 SER Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 299 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 88 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 70 optimal weight: 0.0870 chunk 25 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 81 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 7 optimal weight: 0.4980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.213716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.178897 restraints weight = 8832.843| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 1.96 r_work: 0.3750 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8330 Z= 0.110 Angle : 0.479 6.457 11382 Z= 0.261 Chirality : 0.040 0.146 1353 Planarity : 0.004 0.050 1437 Dihedral : 4.182 38.482 1209 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.40 % Allowed : 13.22 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.25), residues: 1107 helix: 3.07 (0.27), residues: 376 sheet: 0.95 (0.31), residues: 263 loop : -0.80 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG S 87 TYR 0.007 0.001 TYR R 211 PHE 0.014 0.001 PHE R 98 TRP 0.010 0.001 TRP S 36 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 8326) covalent geometry : angle 0.47894 (11373) SS BOND : bond 0.00412 ( 3) SS BOND : angle 0.89480 ( 6) hydrogen bonds : bond 0.04326 ( 397) hydrogen bonds : angle 3.82742 ( 1143) link_TRANS : bond 0.00015 ( 1) link_TRANS : angle 0.06200 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.215 Fit side-chains REVERT: A 307 PHE cc_start: 0.7642 (OUTLIER) cc_final: 0.5868 (t80) REVERT: B 134 ARG cc_start: 0.8252 (ptp90) cc_final: 0.7489 (ppt170) REVERT: B 217 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.8169 (pmt) REVERT: R 55 ILE cc_start: 0.6215 (pt) cc_final: 0.5973 (pp) REVERT: R 135 VAL cc_start: 0.7649 (p) cc_final: 0.7441 (m) REVERT: R 278 SER cc_start: 0.6176 (p) cc_final: 0.5674 (p) outliers start: 18 outliers final: 8 residues processed: 97 average time/residue: 0.4594 time to fit residues: 47.9104 Evaluate side-chains 92 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 87 ILE Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 299 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 40 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 91 optimal weight: 0.0060 chunk 47 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 26 optimal weight: 0.0030 chunk 28 optimal weight: 0.2980 overall best weight: 0.3006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.215434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.180454 restraints weight = 8981.811| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 2.09 r_work: 0.3774 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3672 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8330 Z= 0.091 Angle : 0.441 6.294 11382 Z= 0.240 Chirality : 0.039 0.140 1353 Planarity : 0.003 0.048 1437 Dihedral : 3.897 37.207 1209 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.47 % Allowed : 14.55 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.25), residues: 1107 helix: 3.22 (0.27), residues: 376 sheet: 1.08 (0.30), residues: 282 loop : -0.69 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 15 TYR 0.006 0.001 TYR R 180 PHE 0.015 0.001 PHE R 296 TRP 0.008 0.001 TRP S 36 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00175 ( 8326) covalent geometry : angle 0.44107 (11373) SS BOND : bond 0.00351 ( 3) SS BOND : angle 0.70959 ( 6) hydrogen bonds : bond 0.03537 ( 397) hydrogen bonds : angle 3.64518 ( 1143) link_TRANS : bond 0.00027 ( 1) link_TRANS : angle 0.06784 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.321 Fit side-chains REVERT: A 307 PHE cc_start: 0.7490 (OUTLIER) cc_final: 0.5821 (t80) REVERT: B 134 ARG cc_start: 0.8213 (ptp90) cc_final: 0.7398 (ppt170) REVERT: B 217 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.8134 (pmt) REVERT: R 55 ILE cc_start: 0.6216 (pt) cc_final: 0.5965 (pp) REVERT: R 135 VAL cc_start: 0.7501 (p) cc_final: 0.7248 (m) REVERT: R 278 SER cc_start: 0.5836 (p) cc_final: 0.5351 (p) outliers start: 11 outliers final: 6 residues processed: 94 average time/residue: 0.4983 time to fit residues: 50.2146 Evaluate side-chains 93 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 87 ILE Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 299 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 21 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 70 optimal weight: 0.0570 chunk 62 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.211846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.176655 restraints weight = 8856.880| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 1.99 r_work: 0.3722 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8330 Z= 0.122 Angle : 0.501 6.480 11382 Z= 0.272 Chirality : 0.041 0.148 1353 Planarity : 0.004 0.051 1437 Dihedral : 4.125 37.347 1209 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.87 % Allowed : 14.29 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.25), residues: 1107 helix: 3.16 (0.27), residues: 376 sheet: 1.02 (0.32), residues: 263 loop : -0.71 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 134 TYR 0.009 0.001 TYR R 211 PHE 0.015 0.001 PHE R 98 TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS S 220 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 8326) covalent geometry : angle 0.50082 (11373) SS BOND : bond 0.00464 ( 3) SS BOND : angle 0.99593 ( 6) hydrogen bonds : bond 0.04500 ( 397) hydrogen bonds : angle 3.81088 ( 1143) link_TRANS : bond 0.00015 ( 1) link_TRANS : angle 0.09621 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.241 Fit side-chains REVERT: A 307 PHE cc_start: 0.7542 (OUTLIER) cc_final: 0.5855 (t80) REVERT: B 134 ARG cc_start: 0.8281 (ptp90) cc_final: 0.7474 (ppt170) REVERT: B 217 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.8131 (pmt) REVERT: R 55 ILE cc_start: 0.6243 (pt) cc_final: 0.6027 (pp) REVERT: R 135 VAL cc_start: 0.7599 (p) cc_final: 0.7375 (m) REVERT: R 278 SER cc_start: 0.5967 (p) cc_final: 0.5473 (p) outliers start: 14 outliers final: 8 residues processed: 92 average time/residue: 0.4915 time to fit residues: 48.4817 Evaluate side-chains 92 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 87 ILE Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 299 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 57 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 77 optimal weight: 0.1980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.212103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.176932 restraints weight = 8830.476| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 1.96 r_work: 0.3731 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3632 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8330 Z= 0.116 Angle : 0.491 6.343 11382 Z= 0.268 Chirality : 0.040 0.146 1353 Planarity : 0.004 0.050 1437 Dihedral : 4.117 37.232 1209 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.47 % Allowed : 14.42 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.25), residues: 1107 helix: 3.20 (0.27), residues: 376 sheet: 0.98 (0.32), residues: 265 loop : -0.72 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 116 TYR 0.008 0.001 TYR R 211 PHE 0.018 0.001 PHE R 296 TRP 0.008 0.001 TRP S 36 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 8326) covalent geometry : angle 0.49007 (11373) SS BOND : bond 0.00439 ( 3) SS BOND : angle 1.43364 ( 6) hydrogen bonds : bond 0.04400 ( 397) hydrogen bonds : angle 3.80598 ( 1143) link_TRANS : bond 0.00008 ( 1) link_TRANS : angle 0.07550 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.582 Fit side-chains REVERT: A 307 PHE cc_start: 0.7524 (OUTLIER) cc_final: 0.5850 (t80) REVERT: B 134 ARG cc_start: 0.8321 (ptp90) cc_final: 0.7473 (ppt170) REVERT: B 217 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.8134 (pmt) REVERT: R 55 ILE cc_start: 0.6236 (pt) cc_final: 0.6029 (pp) REVERT: R 278 SER cc_start: 0.5995 (p) cc_final: 0.5500 (p) outliers start: 11 outliers final: 8 residues processed: 91 average time/residue: 0.5030 time to fit residues: 49.4346 Evaluate side-chains 93 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 87 ILE Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 299 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 60 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 chunk 34 optimal weight: 0.0270 chunk 59 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.211763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.176680 restraints weight = 8813.441| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 1.99 r_work: 0.3723 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8330 Z= 0.119 Angle : 0.499 6.393 11382 Z= 0.272 Chirality : 0.040 0.146 1353 Planarity : 0.004 0.050 1437 Dihedral : 4.138 37.171 1209 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.34 % Allowed : 14.95 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.25), residues: 1107 helix: 3.14 (0.27), residues: 376 sheet: 1.04 (0.32), residues: 263 loop : -0.74 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG S 87 TYR 0.009 0.001 TYR R 211 PHE 0.021 0.001 PHE R 296 TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 8326) covalent geometry : angle 0.49864 (11373) SS BOND : bond 0.00441 ( 3) SS BOND : angle 1.30619 ( 6) hydrogen bonds : bond 0.04496 ( 397) hydrogen bonds : angle 3.83475 ( 1143) link_TRANS : bond 0.00007 ( 1) link_TRANS : angle 0.08253 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.370 Fit side-chains REVERT: A 307 PHE cc_start: 0.7535 (OUTLIER) cc_final: 0.5891 (t80) REVERT: B 134 ARG cc_start: 0.8329 (ptp90) cc_final: 0.7477 (ppt170) REVERT: B 217 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.8161 (pmt) REVERT: R 55 ILE cc_start: 0.6204 (pt) cc_final: 0.5700 (mm) REVERT: R 278 SER cc_start: 0.5931 (p) cc_final: 0.5432 (p) outliers start: 10 outliers final: 8 residues processed: 90 average time/residue: 0.5010 time to fit residues: 48.2392 Evaluate side-chains 95 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 87 ILE Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 299 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 23 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 94 optimal weight: 0.0070 chunk 36 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 21 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN R 276 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.210026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.175346 restraints weight = 8796.760| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 2.15 r_work: 0.3694 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8330 Z= 0.156 Angle : 0.567 6.917 11382 Z= 0.308 Chirality : 0.042 0.154 1353 Planarity : 0.004 0.052 1437 Dihedral : 4.512 38.488 1209 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.60 % Allowed : 14.69 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.25), residues: 1107 helix: 3.02 (0.27), residues: 376 sheet: 0.94 (0.32), residues: 262 loop : -0.88 (0.25), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 283 TYR 0.012 0.002 TYR R 211 PHE 0.021 0.002 PHE R 296 TRP 0.010 0.001 TRP B 63 HIS 0.006 0.002 HIS S 220 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 8326) covalent geometry : angle 0.56593 (11373) SS BOND : bond 0.00521 ( 3) SS BOND : angle 1.49604 ( 6) hydrogen bonds : bond 0.05515 ( 397) hydrogen bonds : angle 4.06642 ( 1143) link_TRANS : bond 0.00006 ( 1) link_TRANS : angle 0.15236 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3426.84 seconds wall clock time: 58 minutes 45.88 seconds (3525.88 seconds total)