Starting phenix.real_space_refine on Wed Feb 12 20:41:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t11_25587/02_2025/7t11_25587_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t11_25587/02_2025/7t11_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_25587/02_2025/7t11_25587.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t11_25587/02_2025/7t11_25587.map" model { file = "/net/cci-nas-00/data/ceres_data/7t11_25587/02_2025/7t11_25587_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t11_25587/02_2025/7t11_25587_neut.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 1, 'GLU:plan': 15, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 10} 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: {'GLN:plan1': 4, 'GLU:plan': 6, 'ARG:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 5} 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, 'GLU:plan': 5, 'ARG:plan': 2, '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, 'ARG:plan': 4, 'ASP:plan': 2} 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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 122 Time building chain proxies: 5.34, per 1000 atoms: 0.66 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: 2.12 Conformation dependent library (CDL) restraints added in 985.3 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: 0.82 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: 2.19 Time building geometry restraints manager: 2.41 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: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 21.240 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:12.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.550 ------------------------------------------------------------------------------- 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 8326 Z= 0.227 Angle : 0.610 9.947 11373 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (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 TRP 0.008 0.001 TRP R 188 HIS 0.004 0.001 HIS B 54 PHE 0.011 0.001 PHE B 234 TYR 0.013 0.001 TYR S 178 ARG 0.002 0.000 ARG S 67 *********************** 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 : 0.895 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: 1.0354 time to fit residues: 128.0014 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 : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.2980 chunk 82 optimal weight: 10.0000 chunk 45 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 55 optimal weight: 0.0070 chunk 44 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 304 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.217291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.181933 restraints weight = 8875.268| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 2.02 r_work: 0.3797 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3698 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8326 Z= 0.143 Angle : 0.508 6.869 11373 Z= 0.275 Chirality : 0.040 0.153 1353 Planarity : 0.004 0.061 1437 Dihedral : 4.355 35.332 1209 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.14 % Allowed : 7.21 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.25), residues: 1107 helix: 2.81 (0.27), residues: 383 sheet: 1.04 (0.32), residues: 261 loop : -0.73 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 108 HIS 0.006 0.001 HIS S 35 PHE 0.015 0.001 PHE R 98 TYR 0.010 0.001 TYR B 59 ARG 0.004 0.000 ARG A 312 *********************** 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 : 0.867 Fit side-chains REVERT: B 134 ARG cc_start: 0.8047 (ptp90) cc_final: 0.7816 (ptp90) REVERT: R 63 LEU cc_start: 0.5369 (tt) cc_final: 0.5146 (tp) REVERT: R 68 ILE cc_start: 0.6368 (OUTLIER) cc_final: 0.6023 (mp) REVERT: R 161 MET cc_start: 0.4467 (tmm) cc_final: 0.4246 (tmm) REVERT: R 278 SER cc_start: 0.6653 (p) cc_final: 0.6288 (p) outliers start: 16 outliers final: 3 residues processed: 90 average time/residue: 1.0377 time to fit residues: 100.5265 Evaluate side-chains 85 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR 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: 4.9990 chunk 40 optimal weight: 0.6980 chunk 54 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 13 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN S 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.213291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.177766 restraints weight = 8970.121| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 2.40 r_work: 0.3740 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3639 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8326 Z= 0.168 Angle : 0.526 6.962 11373 Z= 0.285 Chirality : 0.041 0.153 1353 Planarity : 0.004 0.054 1437 Dihedral : 4.367 37.402 1209 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.00 % Allowed : 9.61 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.25), residues: 1107 helix: 2.98 (0.27), residues: 376 sheet: 0.90 (0.31), residues: 263 loop : -0.71 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 297 HIS 0.005 0.001 HIS B 183 PHE 0.015 0.002 PHE B 151 TYR 0.014 0.001 TYR B 59 ARG 0.003 0.000 ARG A 312 *********************** 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: 15 poor density : 84 time to evaluate : 0.877 Fit side-chains REVERT: B 134 ARG cc_start: 0.8191 (ptp90) cc_final: 0.7372 (ppt170) REVERT: B 217 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8340 (pmt) REVERT: R 278 SER cc_start: 0.6569 (p) cc_final: 0.6212 (p) outliers start: 15 outliers final: 7 residues processed: 92 average time/residue: 1.0254 time to fit residues: 101.6926 Evaluate side-chains 88 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain R residue 87 ILE Chi-restraints excluded: chain R residue 135 VAL 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 62 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 65 optimal weight: 0.0570 chunk 59 optimal weight: 5.9990 chunk 107 optimal weight: 0.0980 chunk 55 optimal weight: 2.9990 chunk 105 optimal weight: 0.0670 chunk 106 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 overall best weight: 0.8440 ------------------------------------------------------------------------------- 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 = 0.4346 r_free = 0.4346 target = 0.212561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.177590 restraints weight = 8821.474| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 2.12 r_work: 0.3735 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8326 Z= 0.172 Angle : 0.519 6.719 11373 Z= 0.283 Chirality : 0.041 0.153 1353 Planarity : 0.004 0.050 1437 Dihedral : 4.372 37.866 1209 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.27 % Allowed : 10.95 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.25), residues: 1107 helix: 2.99 (0.27), residues: 376 sheet: 0.98 (0.31), residues: 261 loop : -0.79 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 36 HIS 0.005 0.001 HIS B 183 PHE 0.014 0.002 PHE A 196 TYR 0.012 0.001 TYR B 59 ARG 0.002 0.000 ARG S 98 *********************** 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 102 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.860 Fit side-chains REVERT: A 307 PHE cc_start: 0.7531 (OUTLIER) cc_final: 0.5892 (t80) REVERT: B 43 ILE cc_start: 0.5920 (OUTLIER) cc_final: 0.5260 (mp) REVERT: B 134 ARG cc_start: 0.8242 (ptp90) cc_final: 0.7510 (ppt170) REVERT: B 217 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8315 (pmt) REVERT: R 55 ILE cc_start: 0.6136 (pt) cc_final: 0.5877 (pp) REVERT: R 68 ILE cc_start: 0.6204 (OUTLIER) cc_final: 0.5878 (mp) REVERT: R 135 VAL cc_start: 0.7773 (OUTLIER) cc_final: 0.7505 (m) REVERT: R 278 SER cc_start: 0.6569 (p) cc_final: 0.6239 (p) outliers start: 17 outliers final: 7 residues processed: 92 average time/residue: 1.0443 time to fit residues: 103.4502 Evaluate side-chains 95 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 43 ILE 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 135 VAL 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 9 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 101 optimal weight: 20.0000 chunk 66 optimal weight: 0.0270 chunk 19 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 overall best weight: 1.1844 ------------------------------------------------------------------------------- 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 = 0.4325 r_free = 0.4325 target = 0.210256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.175600 restraints weight = 8736.817| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 2.15 r_work: 0.3695 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8326 Z= 0.218 Angle : 0.569 6.909 11373 Z= 0.309 Chirality : 0.042 0.156 1353 Planarity : 0.004 0.052 1437 Dihedral : 4.594 39.056 1209 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.00 % Allowed : 12.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.25), residues: 1107 helix: 2.88 (0.27), residues: 376 sheet: 0.89 (0.31), residues: 260 loop : -0.91 (0.25), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP S 36 HIS 0.005 0.002 HIS S 220 PHE 0.017 0.002 PHE A 196 TYR 0.013 0.002 TYR B 59 ARG 0.002 0.000 ARG S 87 *********************** 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 101 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.792 Fit side-chains REVERT: A 307 PHE cc_start: 0.7602 (OUTLIER) cc_final: 0.5985 (t80) REVERT: B 43 ILE cc_start: 0.5945 (OUTLIER) cc_final: 0.5616 (mm) REVERT: B 134 ARG cc_start: 0.8301 (ptp90) cc_final: 0.7541 (ppt170) REVERT: B 217 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8351 (pmt) REVERT: R 55 ILE cc_start: 0.6132 (pt) cc_final: 0.5888 (pp) REVERT: R 135 VAL cc_start: 0.7692 (OUTLIER) cc_final: 0.7430 (m) REVERT: R 278 SER cc_start: 0.6511 (p) cc_final: 0.6057 (p) outliers start: 15 outliers final: 7 residues processed: 92 average time/residue: 1.0359 time to fit residues: 102.6707 Evaluate side-chains 94 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 43 ILE 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 101 MET Chi-restraints excluded: chain R residue 135 VAL 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 4 optimal weight: 4.9990 chunk 39 optimal weight: 0.1980 chunk 46 optimal weight: 0.6980 chunk 102 optimal weight: 0.1980 chunk 51 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4328 r_free = 0.4328 target = 0.212061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.177038 restraints weight = 8879.774| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 2.10 r_work: 0.3721 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8326 Z= 0.139 Angle : 0.483 6.249 11373 Z= 0.263 Chirality : 0.040 0.147 1353 Planarity : 0.004 0.051 1437 Dihedral : 4.241 38.204 1209 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.54 % Allowed : 12.95 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.25), residues: 1107 helix: 3.10 (0.27), residues: 376 sheet: 0.95 (0.31), residues: 261 loop : -0.84 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 36 HIS 0.003 0.001 HIS S 35 PHE 0.015 0.001 PHE R 98 TYR 0.008 0.001 TYR R 211 ARG 0.001 0.000 ARG A 21 *********************** 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 106 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.880 Fit side-chains REVERT: A 307 PHE cc_start: 0.7593 (OUTLIER) cc_final: 0.5899 (t80) REVERT: B 43 ILE cc_start: 0.5895 (OUTLIER) cc_final: 0.5205 (mp) REVERT: B 134 ARG cc_start: 0.8260 (ptp90) cc_final: 0.7455 (ppt170) REVERT: B 217 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8272 (pmt) REVERT: R 55 ILE cc_start: 0.6219 (pt) cc_final: 0.5982 (pp) REVERT: R 68 ILE cc_start: 0.5980 (OUTLIER) cc_final: 0.5661 (mp) REVERT: R 135 VAL cc_start: 0.7601 (OUTLIER) cc_final: 0.7326 (m) REVERT: R 278 SER cc_start: 0.6132 (p) cc_final: 0.5626 (p) outliers start: 19 outliers final: 8 residues processed: 95 average time/residue: 1.0024 time to fit residues: 102.8339 Evaluate side-chains 98 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 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 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 135 VAL 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 91 optimal weight: 0.0570 chunk 45 optimal weight: 7.9990 chunk 57 optimal weight: 0.5980 chunk 19 optimal weight: 0.0050 chunk 47 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 72 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 34 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 overall best weight: 0.3512 ------------------------------------------------------------------------------- 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 = 0.4357 r_free = 0.4357 target = 0.215265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.180156 restraints weight = 8898.067| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 1.96 r_work: 0.3769 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3671 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8326 Z= 0.118 Angle : 0.446 6.240 11373 Z= 0.243 Chirality : 0.039 0.141 1353 Planarity : 0.003 0.049 1437 Dihedral : 3.891 36.800 1209 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.00 % Allowed : 13.08 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.25), residues: 1107 helix: 3.22 (0.27), residues: 376 sheet: 1.04 (0.30), residues: 282 loop : -0.67 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP S 36 HIS 0.003 0.001 HIS S 35 PHE 0.010 0.001 PHE B 199 TYR 0.006 0.001 TYR R 211 ARG 0.001 0.000 ARG B 251 *********************** 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 106 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.917 Fit side-chains REVERT: A 307 PHE cc_start: 0.7485 (OUTLIER) cc_final: 0.5796 (t80) REVERT: A 308 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7714 (mp0) REVERT: B 43 ILE cc_start: 0.5775 (OUTLIER) cc_final: 0.5146 (mp) REVERT: B 134 ARG cc_start: 0.8206 (ptp90) cc_final: 0.7409 (ppt170) REVERT: B 217 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8297 (pmt) REVERT: R 55 ILE cc_start: 0.6233 (pt) cc_final: 0.5983 (pp) REVERT: R 135 VAL cc_start: 0.7664 (OUTLIER) cc_final: 0.7365 (m) REVERT: R 278 SER cc_start: 0.5993 (p) cc_final: 0.5501 (p) outliers start: 15 outliers final: 7 residues processed: 101 average time/residue: 0.9797 time to fit residues: 106.8719 Evaluate side-chains 96 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 43 ILE 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 B residue 336 LEU Chi-restraints excluded: chain R residue 87 ILE Chi-restraints excluded: chain R residue 135 VAL 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 17 optimal weight: 3.9990 chunk 73 optimal weight: 20.0000 chunk 80 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.4320 r_free = 0.4320 target = 0.209471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.173249 restraints weight = 8776.650| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.32 r_work: 0.3695 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8326 Z= 0.234 Angle : 0.578 7.145 11373 Z= 0.314 Chirality : 0.042 0.157 1353 Planarity : 0.004 0.052 1437 Dihedral : 4.543 38.534 1209 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.14 % Allowed : 13.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.25), residues: 1107 helix: 3.03 (0.27), residues: 376 sheet: 0.95 (0.32), residues: 259 loop : -0.88 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 63 HIS 0.006 0.002 HIS S 220 PHE 0.018 0.002 PHE A 196 TYR 0.012 0.002 TYR R 211 ARG 0.002 0.000 ARG S 87 *********************** 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 102 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.839 Fit side-chains REVERT: A 307 PHE cc_start: 0.7591 (OUTLIER) cc_final: 0.5969 (t80) REVERT: B 43 ILE cc_start: 0.6001 (OUTLIER) cc_final: 0.5663 (mm) REVERT: B 134 ARG cc_start: 0.8325 (ptp90) cc_final: 0.7515 (ppt170) REVERT: B 217 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8317 (pmt) REVERT: R 55 ILE cc_start: 0.6300 (pt) cc_final: 0.6087 (pp) REVERT: R 135 VAL cc_start: 0.7687 (OUTLIER) cc_final: 0.7475 (m) REVERT: R 278 SER cc_start: 0.6162 (p) cc_final: 0.5666 (p) outliers start: 16 outliers final: 8 residues processed: 94 average time/residue: 1.0949 time to fit residues: 110.4001 Evaluate side-chains 96 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 135 VAL 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 15 optimal weight: 0.0980 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 54 optimal weight: 0.2980 chunk 102 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4332 r_free = 0.4332 target = 0.212354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.177344 restraints weight = 9018.955| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 2.12 r_work: 0.3728 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3627 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8326 Z= 0.134 Angle : 0.480 6.200 11373 Z= 0.262 Chirality : 0.040 0.145 1353 Planarity : 0.004 0.050 1437 Dihedral : 4.165 37.557 1209 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.74 % Allowed : 14.02 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.25), residues: 1107 helix: 3.17 (0.27), residues: 376 sheet: 1.06 (0.32), residues: 261 loop : -0.82 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 36 HIS 0.004 0.001 HIS S 35 PHE 0.011 0.001 PHE B 199 TYR 0.008 0.001 TYR R 211 ARG 0.001 0.000 ARG S 87 *********************** 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 99 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.991 Fit side-chains REVERT: A 307 PHE cc_start: 0.7590 (OUTLIER) cc_final: 0.5904 (t80) REVERT: B 43 ILE cc_start: 0.5855 (OUTLIER) cc_final: 0.5198 (mp) REVERT: B 134 ARG cc_start: 0.8305 (ptp90) cc_final: 0.7460 (ppt170) REVERT: B 217 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8299 (pmt) REVERT: R 55 ILE cc_start: 0.6259 (pt) cc_final: 0.6052 (pp) REVERT: R 135 VAL cc_start: 0.7642 (OUTLIER) cc_final: 0.7376 (m) REVERT: R 278 SER cc_start: 0.6016 (p) cc_final: 0.5522 (p) outliers start: 13 outliers final: 9 residues processed: 93 average time/residue: 1.0495 time to fit residues: 104.9956 Evaluate side-chains 98 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 135 VAL Chi-restraints excluded: chain R residue 136 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 87 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 57 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.4303 r_free = 0.4303 target = 0.207548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.173077 restraints weight = 8696.308| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.16 r_work: 0.3664 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8326 Z= 0.290 Angle : 0.644 8.065 11373 Z= 0.348 Chirality : 0.045 0.160 1353 Planarity : 0.004 0.054 1437 Dihedral : 4.891 40.043 1209 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.74 % Allowed : 14.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.25), residues: 1107 helix: 2.79 (0.26), residues: 376 sheet: 0.82 (0.31), residues: 264 loop : -1.07 (0.25), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP S 36 HIS 0.007 0.002 HIS S 220 PHE 0.022 0.002 PHE A 196 TYR 0.015 0.002 TYR B 59 ARG 0.003 0.001 ARG B 283 ********************** 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 98 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.864 Fit side-chains REVERT: A 307 PHE cc_start: 0.7711 (OUTLIER) cc_final: 0.6066 (t80) REVERT: B 43 ILE cc_start: 0.6150 (OUTLIER) cc_final: 0.5839 (mm) REVERT: B 134 ARG cc_start: 0.8376 (ptp90) cc_final: 0.7570 (ppt170) REVERT: B 217 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8354 (pmt) REVERT: R 55 ILE cc_start: 0.6211 (pt) cc_final: 0.5702 (mm) REVERT: R 135 VAL cc_start: 0.7830 (OUTLIER) cc_final: 0.7623 (m) REVERT: R 278 SER cc_start: 0.6397 (p) cc_final: 0.5899 (p) outliers start: 13 outliers final: 8 residues processed: 92 average time/residue: 1.1550 time to fit residues: 113.6183 Evaluate side-chains 94 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 135 VAL 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 99 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 63 optimal weight: 0.5980 chunk 82 optimal weight: 8.9990 chunk 84 optimal weight: 0.3980 chunk 11 optimal weight: 0.0170 chunk 31 optimal weight: 0.0770 chunk 23 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.3576 ------------------------------------------------------------------------------- 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 = 0.4336 r_free = 0.4336 target = 0.212840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.177974 restraints weight = 8916.393| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 2.03 r_work: 0.3735 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3638 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8326 Z= 0.128 Angle : 0.470 5.985 11373 Z= 0.258 Chirality : 0.040 0.140 1353 Planarity : 0.004 0.051 1437 Dihedral : 4.186 38.188 1209 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.74 % Allowed : 14.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.25), residues: 1107 helix: 3.17 (0.27), residues: 376 sheet: 0.96 (0.31), residues: 269 loop : -0.95 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 36 HIS 0.004 0.001 HIS S 35 PHE 0.018 0.001 PHE R 296 TYR 0.007 0.001 TYR B 59 ARG 0.001 0.000 ARG B 150 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6527.11 seconds wall clock time: 115 minutes 43.94 seconds (6943.94 seconds total)