Starting phenix.real_space_refine on Wed Sep 17 12:22:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n4b_0339/09_2025/6n4b_0339_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n4b_0339/09_2025/6n4b_0339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6n4b_0339/09_2025/6n4b_0339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n4b_0339/09_2025/6n4b_0339.map" model { file = "/net/cci-nas-00/data/ceres_data/6n4b_0339/09_2025/6n4b_0339_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n4b_0339/09_2025/6n4b_0339_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.030 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: 5 Type Number sf(0) Gaussians S 58 5.16 5 C 5423 2.51 5 N 1457 2.21 5 O 1514 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8453 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1646 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 8, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 72 Chain: "B" Number of atoms: 2553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2553 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 435 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 1988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 1988 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 8, 'TRANS': 267} Chain breaks: 2 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 269 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASN:plan1': 3, 'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 4, 'ASP:plan': 7, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 88 Chain: "S" Number of atoms: 1746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1746 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "R" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 85 Unusual residues: {'CLR': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Time building chain proxies: 2.10, per 1000 atoms: 0.25 Number of scatterers: 8453 At special positions: 0 Unit cell: (109.22, 122.98, 109.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 F 1 9.00 O 1514 8.00 N 1457 7.00 C 5423 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 257 " - pdb=" SG CYS R 264 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 350.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 14 sheets defined 35.1% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 6 through 28 removed outlier: 3.718A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 51 removed outlier: 3.937A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.453A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 removed outlier: 4.060A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.911A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.665A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.509A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.577A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.506A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR A 340 " --> pdb=" O PHE A 336 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N CYS A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 18 removed outlier: 3.550A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.803A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 22 removed outlier: 3.622A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU C 22 " --> pdb=" O GLN C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 34 through 39 Processing helix chain 'R' and resid 112 through 143 removed outlier: 4.519A pdb=" N VAL R 121 " --> pdb=" O LEU R 117 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU R 122 " --> pdb=" O ALA R 118 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER R 123 " --> pdb=" O ILE R 119 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL R 140 " --> pdb=" O LEU R 136 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE R 141 " --> pdb=" O VAL R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 179 removed outlier: 3.937A pdb=" N PHE R 155 " --> pdb=" O PRO R 151 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE R 156 " --> pdb=" O SER R 152 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA R 162 " --> pdb=" O SER R 158 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU R 164 " --> pdb=" O ALA R 160 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR R 172 " --> pdb=" O VAL R 168 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL R 179 " --> pdb=" O ILE R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 191 removed outlier: 4.288A pdb=" N LEU R 190 " --> pdb=" O ARG R 186 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE R 191 " --> pdb=" O ASN R 187 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 212 removed outlier: 3.622A pdb=" N ILE R 212 " --> pdb=" O PHE R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 212 through 220 removed outlier: 3.632A pdb=" N ILE R 216 " --> pdb=" O ILE R 212 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE R 218 " --> pdb=" O ARG R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 220 through 228 removed outlier: 4.523A pdb=" N LYS R 225 " --> pdb=" O PRO R 221 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ARG R 226 " --> pdb=" O LEU R 222 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL R 228 " --> pdb=" O TYR R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 249 Processing helix chain 'R' and resid 249 through 254 removed outlier: 4.183A pdb=" N LEU R 253 " --> pdb=" O VAL R 249 " (cutoff:3.500A) Processing helix chain 'R' and resid 272 through 277 Processing helix chain 'R' and resid 278 through 311 removed outlier: 3.693A pdb=" N VAL R 282 " --> pdb=" O PHE R 278 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE R 290 " --> pdb=" O LEU R 286 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET R 295 " --> pdb=" O VAL R 291 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE R 297 " --> pdb=" O ALA R 293 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE R 309 " --> pdb=" O ALA R 305 " (cutoff:3.500A) Processing helix chain 'R' and resid 336 through 355 removed outlier: 3.842A pdb=" N ALA R 342 " --> pdb=" O ASP R 338 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS R 343 " --> pdb=" O ILE R 339 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR R 344 " --> pdb=" O ARG R 340 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU R 347 " --> pdb=" O LYS R 343 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL R 351 " --> pdb=" O LEU R 347 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE R 353 " --> pdb=" O LEU R 349 " (cutoff:3.500A) Processing helix chain 'R' and resid 358 through 363 Processing helix chain 'R' and resid 374 through 399 removed outlier: 3.708A pdb=" N ALA R 380 " --> pdb=" O LYS R 376 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE R 381 " --> pdb=" O THR R 377 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET R 384 " --> pdb=" O ALA R 380 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU R 385 " --> pdb=" O PHE R 381 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N CYS R 386 " --> pdb=" O CYS R 382 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU R 387 " --> pdb=" O SER R 383 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU R 388 " --> pdb=" O MET R 384 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER R 390 " --> pdb=" O CYS R 386 " (cutoff:3.500A) Proline residue: R 394 - end of helix Processing helix chain 'R' and resid 401 through 410 removed outlier: 3.514A pdb=" N ARG R 405 " --> pdb=" O SER R 401 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.707A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 28 through 32' Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 7.273A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.489A 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: 3.601A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 328 " --> pdb=" O GLY B 319 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.918A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.568A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 4.012A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU B 152 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.730A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.765A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.908A 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: 3.775A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 4 through 7 removed outlier: 3.660A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.391A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU S 117 " --> pdb=" O ALA S 92 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA S 92 " --> pdb=" O LEU S 117 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP S 36 " --> pdb=" O ALA S 49 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.391A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU S 117 " --> pdb=" O ALA S 92 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA S 92 " --> pdb=" O LEU S 117 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'S' and resid 135 through 136 removed outlier: 6.100A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'S' and resid 174 through 177 removed outlier: 6.658A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 325 hydrogen bonds defined for protein. 936 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: 1.37 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.24: 1206 1.24 - 1.39: 2297 1.39 - 1.53: 4598 1.53 - 1.67: 451 1.67 - 1.81: 84 Bond restraints: 8636 Sorted by residual: bond pdb=" CAT KCA R 501 " pdb=" FAU KCA R 501 " ideal model delta sigma weight residual 1.342 1.101 0.241 2.00e-02 2.50e+03 1.45e+02 bond pdb=" CAB KCA R 501 " pdb=" CAM KCA R 501 " ideal model delta sigma weight residual 1.476 1.351 0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" CA TRP B 339 " pdb=" C TRP B 339 " ideal model delta sigma weight residual 1.523 1.457 0.067 1.18e-02 7.18e+03 3.19e+01 bond pdb=" CAP KCA R 501 " pdb=" CAQ KCA R 501 " ideal model delta sigma weight residual 1.507 1.395 0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" CA LEU B 336 " pdb=" C LEU B 336 " ideal model delta sigma weight residual 1.521 1.467 0.054 1.19e-02 7.06e+03 2.07e+01 ... (remaining 8631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.46: 11350 3.46 - 6.92: 352 6.92 - 10.39: 39 10.39 - 13.85: 6 13.85 - 17.31: 1 Bond angle restraints: 11748 Sorted by residual: angle pdb=" N PHE R 177 " pdb=" CA PHE R 177 " pdb=" C PHE R 177 " ideal model delta sigma weight residual 111.14 123.07 -11.93 1.08e+00 8.57e-01 1.22e+02 angle pdb=" C TYR S 223 " pdb=" N PRO S 224 " pdb=" CD PRO S 224 " ideal model delta sigma weight residual 120.60 137.91 -17.31 2.20e+00 2.07e-01 6.19e+01 angle pdb=" N TYR R 397 " pdb=" CA TYR R 397 " pdb=" C TYR R 397 " ideal model delta sigma weight residual 111.36 119.69 -8.33 1.09e+00 8.42e-01 5.84e+01 angle pdb=" N LEU R 193 " pdb=" CA LEU R 193 " pdb=" C LEU R 193 " ideal model delta sigma weight residual 114.39 103.36 11.03 1.45e+00 4.76e-01 5.78e+01 angle pdb=" N LEU S 225 " pdb=" CA LEU S 225 " pdb=" C LEU S 225 " ideal model delta sigma weight residual 111.17 121.84 -10.67 1.41e+00 5.03e-01 5.73e+01 ... (remaining 11743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 4939 17.03 - 34.07: 177 34.07 - 51.10: 34 51.10 - 68.14: 9 68.14 - 85.17: 2 Dihedral angle restraints: 5161 sinusoidal: 1911 harmonic: 3250 Sorted by residual: dihedral pdb=" N TYR S 178 " pdb=" C TYR S 178 " pdb=" CA TYR S 178 " pdb=" CB TYR S 178 " ideal model delta harmonic sigma weight residual 122.80 143.79 -20.99 0 2.50e+00 1.60e-01 7.05e+01 dihedral pdb=" C TYR S 178 " pdb=" N TYR S 178 " pdb=" CA TYR S 178 " pdb=" CB TYR S 178 " ideal model delta harmonic sigma weight residual -122.60 -142.31 19.71 0 2.50e+00 1.60e-01 6.21e+01 dihedral pdb=" C TRP R 241 " pdb=" N TRP R 241 " pdb=" CA TRP R 241 " pdb=" CB TRP R 241 " ideal model delta harmonic sigma weight residual -122.60 -139.20 16.60 0 2.50e+00 1.60e-01 4.41e+01 ... (remaining 5158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.187: 1319 0.187 - 0.374: 42 0.374 - 0.561: 7 0.561 - 0.749: 1 0.749 - 0.936: 1 Chirality restraints: 1370 Sorted by residual: 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 1.57 0.94 2.00e-01 2.50e+01 2.19e+01 chirality pdb=" CA TRP R 241 " pdb=" N TRP R 241 " pdb=" C TRP R 241 " pdb=" CB TRP R 241 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" CA LEU S 225 " pdb=" N LEU S 225 " pdb=" C LEU S 225 " pdb=" CB LEU S 225 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.56e+00 ... (remaining 1367 not shown) Planarity restraints: 1463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP S 111 " -0.032 2.00e-02 2.50e+03 2.56e-02 1.64e+01 pdb=" CG TRP S 111 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TRP S 111 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP S 111 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP S 111 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP S 111 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP S 111 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP S 111 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP S 111 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP S 111 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO R 394 " 0.020 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C PRO R 394 " -0.070 2.00e-02 2.50e+03 pdb=" O PRO R 394 " 0.025 2.00e-02 2.50e+03 pdb=" N ILE R 395 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 256 " 0.020 2.00e-02 2.50e+03 3.97e-02 1.57e+01 pdb=" CG ASN A 256 " -0.069 2.00e-02 2.50e+03 pdb=" OD1 ASN A 256 " 0.026 2.00e-02 2.50e+03 pdb=" ND2 ASN A 256 " 0.023 2.00e-02 2.50e+03 ... (remaining 1460 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 51 2.46 - 3.07: 5955 3.07 - 3.68: 11467 3.68 - 4.29: 16674 4.29 - 4.90: 28813 Nonbonded interactions: 62960 Sorted by model distance: nonbonded pdb=" CE MET R 371 " pdb=" CB ILE R 375 " model vdw 1.855 3.890 nonbonded pdb=" O ASP B 66 " pdb=" OG SER B 67 " model vdw 1.962 3.040 nonbonded pdb=" O ASP B 38 " pdb=" OD1 ASP B 38 " model vdw 1.981 3.040 nonbonded pdb=" O HIS S 220 " pdb=" ND1 HIS S 220 " model vdw 2.011 3.120 nonbonded pdb=" CD1 ILE S 126 " pdb=" OE2 GLU S 222 " model vdw 2.077 3.460 ... (remaining 62955 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.400 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 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 : 0.013 0.568 8638 Z= 0.859 Angle : 1.400 17.310 11750 Z= 0.876 Chirality : 0.091 0.936 1370 Planarity : 0.008 0.075 1463 Dihedral : 9.763 85.169 3058 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 20.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.84 % Allowed : 2.88 % Favored : 96.28 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.27 (0.23), residues: 1101 helix: -1.09 (0.27), residues: 320 sheet: -1.55 (0.30), residues: 253 loop : -1.65 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 314 TYR 0.049 0.005 TYR A 287 PHE 0.030 0.004 PHE A 196 TRP 0.068 0.005 TRP S 111 HIS 0.011 0.003 HIS R 143 Details of bonding type rmsd covalent geometry : bond 0.01127 ( 8636) covalent geometry : angle 1.40024 (11748) SS BOND : bond 0.00483 ( 1) SS BOND : angle 1.13652 ( 2) hydrogen bonds : bond 0.21552 ( 320) hydrogen bonds : angle 8.49648 ( 936) Misc. bond : bond 0.56806 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 224 time to evaluate : 0.331 Fit side-chains REVERT: A 14 GLU cc_start: 0.7919 (tt0) cc_final: 0.7571 (tt0) REVERT: B 13 GLN cc_start: 0.7174 (mt0) cc_final: 0.6929 (tt0) REVERT: C 18 GLN cc_start: 0.7284 (tp-100) cc_final: 0.7065 (tp-100) REVERT: R 186 ARG cc_start: 0.6786 (mtm180) cc_final: 0.5387 (ttt180) REVERT: R 347 LEU cc_start: 0.8691 (tp) cc_final: 0.8428 (tt) outliers start: 7 outliers final: 4 residues processed: 229 average time/residue: 0.5658 time to fit residues: 137.7828 Evaluate side-chains 140 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 136 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 264 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 255 ASN A 311 ASN B 91 HIS B 220 GLN B 259 GLN R 154 HIS R 178 HIS R 304 HIS S 3 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.148109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.117832 restraints weight = 11863.223| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.97 r_work: 0.3540 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8638 Z= 0.140 Angle : 0.659 9.793 11750 Z= 0.348 Chirality : 0.044 0.181 1370 Planarity : 0.004 0.041 1463 Dihedral : 7.199 70.361 1359 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.84 % Allowed : 13.33 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.24), residues: 1101 helix: -0.34 (0.28), residues: 349 sheet: -0.89 (0.30), residues: 269 loop : -1.69 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 62 TYR 0.022 0.002 TYR S 178 PHE 0.015 0.002 PHE R 289 TRP 0.017 0.002 TRP B 332 HIS 0.005 0.001 HIS R 143 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8636) covalent geometry : angle 0.65867 (11748) SS BOND : bond 0.00364 ( 1) SS BOND : angle 1.75799 ( 2) hydrogen bonds : bond 0.04796 ( 320) hydrogen bonds : angle 5.35613 ( 936) Misc. bond : bond 0.00116 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.285 Fit side-chains REVERT: A 333 GLN cc_start: 0.8276 (tp40) cc_final: 0.7674 (tm-30) REVERT: B 13 GLN cc_start: 0.6856 (mt0) cc_final: 0.6645 (tt0) REVERT: B 217 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8201 (pmm) REVERT: B 227 SER cc_start: 0.8854 (m) cc_final: 0.8161 (t) REVERT: B 292 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.8263 (m-80) REVERT: C 18 GLN cc_start: 0.6941 (tp-100) cc_final: 0.6686 (tp-100) REVERT: C 63 GLU cc_start: 0.6411 (tp30) cc_final: 0.6180 (tp30) REVERT: R 308 MET cc_start: 0.6635 (mmp) cc_final: 0.5720 (tmt) REVERT: R 353 ILE cc_start: 0.7304 (OUTLIER) cc_final: 0.7007 (tp) REVERT: S 60 TYR cc_start: 0.9135 (m-80) cc_final: 0.8912 (m-80) outliers start: 32 outliers final: 14 residues processed: 168 average time/residue: 0.4698 time to fit residues: 84.9459 Evaluate side-chains 138 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 264 CYS Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain R residue 353 ILE Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 105 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 178 HIS S 3 GLN S 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.139463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.109038 restraints weight = 11983.792| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.93 r_work: 0.3436 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 8638 Z= 0.248 Angle : 0.696 10.715 11750 Z= 0.370 Chirality : 0.047 0.194 1370 Planarity : 0.005 0.048 1463 Dihedral : 7.350 68.029 1355 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 5.28 % Allowed : 14.05 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.24), residues: 1101 helix: -0.29 (0.28), residues: 353 sheet: -0.77 (0.30), residues: 275 loop : -1.70 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 18 TYR 0.035 0.002 TYR S 178 PHE 0.021 0.002 PHE B 241 TRP 0.018 0.002 TRP R 279 HIS 0.010 0.002 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00585 ( 8636) covalent geometry : angle 0.69622 (11748) SS BOND : bond 0.00071 ( 1) SS BOND : angle 1.41994 ( 2) hydrogen bonds : bond 0.04998 ( 320) hydrogen bonds : angle 5.18374 ( 936) Misc. bond : bond 0.00096 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 136 time to evaluate : 0.329 Fit side-chains REVERT: A 308 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8235 (mt-10) REVERT: A 316 THR cc_start: 0.8798 (OUTLIER) cc_final: 0.8512 (p) REVERT: A 333 GLN cc_start: 0.8525 (tp40) cc_final: 0.7907 (tm-30) REVERT: B 217 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8208 (pmm) REVERT: B 292 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.8496 (m-80) REVERT: C 58 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7678 (pm20) REVERT: C 63 GLU cc_start: 0.6797 (tp30) cc_final: 0.6470 (tp30) REVERT: R 308 MET cc_start: 0.6740 (mmp) cc_final: 0.5779 (tmt) REVERT: R 353 ILE cc_start: 0.7420 (OUTLIER) cc_final: 0.7118 (tp) REVERT: S 128 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.7696 (mmm) outliers start: 44 outliers final: 24 residues processed: 163 average time/residue: 0.4808 time to fit residues: 84.3339 Evaluate side-chains 150 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain R residue 300 LYS Chi-restraints excluded: chain R residue 339 ILE Chi-restraints excluded: chain R residue 353 ILE Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 1.9990 chunk 78 optimal weight: 0.0980 chunk 4 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 82 optimal weight: 0.0170 chunk 53 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.2224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 HIS S 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.143265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.112400 restraints weight = 11990.232| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 3.01 r_work: 0.3502 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8638 Z= 0.121 Angle : 0.568 10.687 11750 Z= 0.299 Chirality : 0.041 0.219 1370 Planarity : 0.004 0.046 1463 Dihedral : 6.668 63.353 1354 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.44 % Allowed : 17.05 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.25), residues: 1101 helix: 0.07 (0.29), residues: 357 sheet: -0.61 (0.30), residues: 273 loop : -1.59 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 42 TYR 0.015 0.001 TYR S 178 PHE 0.026 0.001 PHE R 237 TRP 0.012 0.001 TRP R 279 HIS 0.005 0.001 HIS R 143 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 8636) covalent geometry : angle 0.56814 (11748) SS BOND : bond 0.00158 ( 1) SS BOND : angle 0.35831 ( 2) hydrogen bonds : bond 0.03869 ( 320) hydrogen bonds : angle 4.67887 ( 936) Misc. bond : bond 0.00028 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 0.337 Fit side-chains REVERT: A 276 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8571 (pp20) REVERT: A 308 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8054 (mt-10) REVERT: A 316 THR cc_start: 0.8676 (m) cc_final: 0.8415 (p) REVERT: A 333 GLN cc_start: 0.8378 (tp40) cc_final: 0.7385 (tm-30) REVERT: A 337 ASP cc_start: 0.8173 (t0) cc_final: 0.7833 (m-30) REVERT: B 217 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8134 (pmm) REVERT: B 292 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.8471 (m-10) REVERT: C 21 MET cc_start: 0.8272 (tpp) cc_final: 0.7941 (mpp) REVERT: C 58 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7719 (pm20) REVERT: C 63 GLU cc_start: 0.6590 (tp30) cc_final: 0.6190 (tp30) REVERT: R 308 MET cc_start: 0.6553 (mmp) cc_final: 0.5681 (tmt) REVERT: S 84 THR cc_start: 0.7988 (m) cc_final: 0.7603 (p) outliers start: 37 outliers final: 17 residues processed: 151 average time/residue: 0.5027 time to fit residues: 81.5032 Evaluate side-chains 146 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain R residue 411 MET Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 9.9990 chunk 28 optimal weight: 0.0980 chunk 73 optimal weight: 0.0870 chunk 80 optimal weight: 6.9990 chunk 17 optimal weight: 0.3980 chunk 101 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 HIS S 3 GLN S 182 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.144119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.113683 restraints weight = 11951.407| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.99 r_work: 0.3537 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8638 Z= 0.110 Angle : 0.541 11.025 11750 Z= 0.282 Chirality : 0.041 0.237 1370 Planarity : 0.003 0.045 1463 Dihedral : 6.338 61.817 1354 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.32 % Allowed : 17.89 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.25), residues: 1101 helix: 0.38 (0.29), residues: 356 sheet: -0.47 (0.30), residues: 273 loop : -1.44 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 42 TYR 0.014 0.001 TYR S 215 PHE 0.026 0.001 PHE R 237 TRP 0.012 0.001 TRP R 279 HIS 0.005 0.001 HIS R 143 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 8636) covalent geometry : angle 0.54133 (11748) SS BOND : bond 0.00099 ( 1) SS BOND : angle 0.42298 ( 2) hydrogen bonds : bond 0.03539 ( 320) hydrogen bonds : angle 4.39047 ( 936) Misc. bond : bond 0.00099 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 0.324 Fit side-chains REVERT: A 276 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8595 (pp20) REVERT: A 308 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8051 (mt-10) REVERT: A 316 THR cc_start: 0.8611 (m) cc_final: 0.8335 (p) REVERT: A 333 GLN cc_start: 0.8385 (tp40) cc_final: 0.7798 (tm-30) REVERT: B 217 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8177 (pmm) REVERT: C 11 GLN cc_start: 0.6933 (tm-30) cc_final: 0.6644 (tm-30) REVERT: C 21 MET cc_start: 0.8270 (tpp) cc_final: 0.7988 (mpp) REVERT: C 32 LYS cc_start: 0.7294 (ttpt) cc_final: 0.6968 (tttm) REVERT: C 58 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7630 (pm20) REVERT: S 84 THR cc_start: 0.8026 (m) cc_final: 0.7750 (p) outliers start: 36 outliers final: 19 residues processed: 166 average time/residue: 0.4608 time to fit residues: 82.0569 Evaluate side-chains 147 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 46 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 0.4980 chunk 81 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 HIS R 389 ASN S 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.144490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.114255 restraints weight = 11979.276| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.99 r_work: 0.3517 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8638 Z= 0.106 Angle : 0.549 11.549 11750 Z= 0.284 Chirality : 0.041 0.255 1370 Planarity : 0.003 0.044 1463 Dihedral : 6.073 60.014 1352 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.32 % Allowed : 19.21 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.25), residues: 1101 helix: 0.60 (0.29), residues: 356 sheet: -0.28 (0.31), residues: 280 loop : -1.34 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 24 TYR 0.014 0.001 TYR S 178 PHE 0.028 0.001 PHE R 237 TRP 0.010 0.001 TRP R 279 HIS 0.005 0.001 HIS R 143 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 8636) covalent geometry : angle 0.54901 (11748) SS BOND : bond 0.00060 ( 1) SS BOND : angle 0.29034 ( 2) hydrogen bonds : bond 0.03380 ( 320) hydrogen bonds : angle 4.28911 ( 936) Misc. bond : bond 0.00089 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 0.226 Fit side-chains REVERT: A 46 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8195 (mtpp) REVERT: A 276 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8597 (pp20) REVERT: A 316 THR cc_start: 0.8580 (m) cc_final: 0.8313 (p) REVERT: A 333 GLN cc_start: 0.8423 (tp40) cc_final: 0.7864 (tm-30) REVERT: B 217 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8185 (pmm) REVERT: B 234 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7680 (m-80) REVERT: C 21 MET cc_start: 0.8287 (tpp) cc_final: 0.7994 (mpp) REVERT: C 32 LYS cc_start: 0.7346 (ttpt) cc_final: 0.7027 (tttm) REVERT: C 58 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7670 (pm20) REVERT: S 2 VAL cc_start: 0.7499 (OUTLIER) cc_final: 0.7147 (p) REVERT: S 84 THR cc_start: 0.8081 (m) cc_final: 0.7672 (p) REVERT: S 128 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.7661 (mmm) outliers start: 36 outliers final: 21 residues processed: 153 average time/residue: 0.4647 time to fit residues: 76.4219 Evaluate side-chains 157 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain R residue 411 MET Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 66 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 82 optimal weight: 20.0000 chunk 89 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 12 optimal weight: 0.0270 overall best weight: 1.4844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN S 182 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.143295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.112861 restraints weight = 12095.319| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 3.00 r_work: 0.3513 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8638 Z= 0.123 Angle : 0.556 10.546 11750 Z= 0.288 Chirality : 0.041 0.269 1370 Planarity : 0.003 0.045 1463 Dihedral : 6.156 59.293 1352 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.96 % Allowed : 20.29 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.25), residues: 1101 helix: 0.72 (0.29), residues: 359 sheet: -0.26 (0.30), residues: 286 loop : -1.34 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 24 TYR 0.018 0.001 TYR S 178 PHE 0.025 0.001 PHE R 237 TRP 0.012 0.001 TRP S 47 HIS 0.005 0.001 HIS R 143 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8636) covalent geometry : angle 0.55582 (11748) SS BOND : bond 0.00032 ( 1) SS BOND : angle 0.35230 ( 2) hydrogen bonds : bond 0.03453 ( 320) hydrogen bonds : angle 4.31671 ( 936) Misc. bond : bond 0.00070 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 0.319 Fit side-chains REVERT: A 316 THR cc_start: 0.8670 (m) cc_final: 0.8388 (p) REVERT: A 333 GLN cc_start: 0.8492 (tp40) cc_final: 0.7913 (tm-30) REVERT: B 217 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8239 (pmm) REVERT: C 32 LYS cc_start: 0.7510 (ttpt) cc_final: 0.7207 (tttm) REVERT: C 58 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7743 (pm20) REVERT: S 84 THR cc_start: 0.8143 (m) cc_final: 0.7762 (p) REVERT: S 128 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.7694 (mmm) REVERT: S 201 THR cc_start: 0.9116 (p) cc_final: 0.8906 (t) REVERT: S 206 ARG cc_start: 0.8080 (ppt90) cc_final: 0.7128 (ptm160) outliers start: 33 outliers final: 20 residues processed: 150 average time/residue: 0.4678 time to fit residues: 75.5950 Evaluate side-chains 145 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 29 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 60 optimal weight: 20.0000 chunk 70 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 0.0050 chunk 61 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 overall best weight: 1.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN S 182 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.144067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.113986 restraints weight = 12017.593| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.95 r_work: 0.3491 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8638 Z= 0.125 Angle : 0.570 12.186 11750 Z= 0.293 Chirality : 0.041 0.277 1370 Planarity : 0.003 0.045 1463 Dihedral : 6.109 58.152 1352 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.20 % Allowed : 20.29 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.25), residues: 1101 helix: 0.84 (0.29), residues: 358 sheet: -0.22 (0.30), residues: 286 loop : -1.35 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 24 TYR 0.018 0.001 TYR S 178 PHE 0.027 0.001 PHE R 237 TRP 0.012 0.001 TRP S 47 HIS 0.005 0.001 HIS R 143 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8636) covalent geometry : angle 0.56965 (11748) SS BOND : bond 0.00036 ( 1) SS BOND : angle 0.33540 ( 2) hydrogen bonds : bond 0.03485 ( 320) hydrogen bonds : angle 4.33597 ( 936) Misc. bond : bond 0.00122 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 0.360 Fit side-chains REVERT: A 46 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8274 (mtpp) REVERT: A 316 THR cc_start: 0.8666 (m) cc_final: 0.8402 (p) REVERT: A 333 GLN cc_start: 0.8470 (tp40) cc_final: 0.7891 (tm-30) REVERT: B 217 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8217 (pmm) REVERT: C 21 MET cc_start: 0.8376 (tpp) cc_final: 0.8119 (mpp) REVERT: C 32 LYS cc_start: 0.7471 (ttpt) cc_final: 0.7156 (tttm) REVERT: C 58 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7739 (pm20) REVERT: S 84 THR cc_start: 0.8154 (m) cc_final: 0.7737 (p) REVERT: S 128 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.7686 (mmm) REVERT: S 189 ASP cc_start: 0.7801 (t0) cc_final: 0.7342 (m-30) REVERT: S 201 THR cc_start: 0.9096 (p) cc_final: 0.8887 (t) REVERT: S 206 ARG cc_start: 0.8082 (ppt90) cc_final: 0.7137 (ptm160) outliers start: 35 outliers final: 22 residues processed: 147 average time/residue: 0.4678 time to fit residues: 74.1269 Evaluate side-chains 148 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain R residue 339 ILE Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 69 optimal weight: 0.9980 chunk 23 optimal weight: 0.0070 chunk 1 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 62 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN S 182 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.143583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.113594 restraints weight = 11946.177| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.93 r_work: 0.3480 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8638 Z= 0.128 Angle : 0.565 8.591 11750 Z= 0.293 Chirality : 0.042 0.258 1370 Planarity : 0.003 0.045 1463 Dihedral : 6.107 57.304 1352 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.72 % Allowed : 20.77 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.25), residues: 1101 helix: 0.92 (0.29), residues: 358 sheet: -0.24 (0.30), residues: 286 loop : -1.34 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 24 TYR 0.018 0.001 TYR S 178 PHE 0.026 0.001 PHE R 237 TRP 0.013 0.001 TRP S 47 HIS 0.005 0.001 HIS R 143 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8636) covalent geometry : angle 0.56529 (11748) SS BOND : bond 0.00024 ( 1) SS BOND : angle 0.32483 ( 2) hydrogen bonds : bond 0.03479 ( 320) hydrogen bonds : angle 4.34685 ( 936) Misc. bond : bond 0.00095 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.341 Fit side-chains REVERT: A 46 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8298 (mtpp) REVERT: A 316 THR cc_start: 0.8694 (m) cc_final: 0.8430 (p) REVERT: A 333 GLN cc_start: 0.8444 (tp40) cc_final: 0.7870 (tm-30) REVERT: B 217 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8199 (pmm) REVERT: C 21 MET cc_start: 0.8373 (tpp) cc_final: 0.8106 (mpp) REVERT: C 32 LYS cc_start: 0.7489 (ttpt) cc_final: 0.7172 (tttm) REVERT: S 84 THR cc_start: 0.8184 (m) cc_final: 0.7758 (p) REVERT: S 128 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.7671 (mmm) REVERT: S 189 ASP cc_start: 0.7792 (t0) cc_final: 0.7326 (m-30) REVERT: S 201 THR cc_start: 0.9081 (p) cc_final: 0.8880 (t) REVERT: S 206 ARG cc_start: 0.8116 (ppt90) cc_final: 0.7186 (ptm160) outliers start: 31 outliers final: 23 residues processed: 145 average time/residue: 0.5057 time to fit residues: 78.7915 Evaluate side-chains 150 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain R residue 339 ILE Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 15 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN S 182 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.138388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.106058 restraints weight = 11846.786| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 3.00 r_work: 0.3278 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8638 Z= 0.119 Angle : 0.584 13.088 11750 Z= 0.297 Chirality : 0.041 0.236 1370 Planarity : 0.003 0.045 1463 Dihedral : 6.050 55.967 1352 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.00 % Allowed : 21.85 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.25), residues: 1101 helix: 1.00 (0.29), residues: 358 sheet: -0.24 (0.30), residues: 287 loop : -1.33 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 24 TYR 0.016 0.001 TYR S 178 PHE 0.029 0.001 PHE R 237 TRP 0.012 0.001 TRP S 47 HIS 0.005 0.001 HIS R 143 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8636) covalent geometry : angle 0.58380 (11748) SS BOND : bond 0.00031 ( 1) SS BOND : angle 0.27918 ( 2) hydrogen bonds : bond 0.03394 ( 320) hydrogen bonds : angle 4.32726 ( 936) Misc. bond : bond 0.00087 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8309 (mtpp) REVERT: A 316 THR cc_start: 0.8772 (m) cc_final: 0.8529 (p) REVERT: A 333 GLN cc_start: 0.8609 (tp40) cc_final: 0.8028 (tm-30) REVERT: B 217 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8372 (pmm) REVERT: C 21 MET cc_start: 0.8471 (tpp) cc_final: 0.8211 (mpp) REVERT: C 32 LYS cc_start: 0.7709 (ttpt) cc_final: 0.7397 (tttm) REVERT: C 58 GLU cc_start: 0.8202 (pm20) cc_final: 0.7482 (pm20) REVERT: S 2 VAL cc_start: 0.7782 (OUTLIER) cc_final: 0.7432 (p) REVERT: S 84 THR cc_start: 0.8385 (m) cc_final: 0.8031 (p) REVERT: S 128 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.7758 (mmm) REVERT: S 189 ASP cc_start: 0.7781 (t0) cc_final: 0.7360 (m-30) REVERT: S 206 ARG cc_start: 0.8165 (ppt90) cc_final: 0.7254 (ptm160) outliers start: 25 outliers final: 19 residues processed: 146 average time/residue: 0.5118 time to fit residues: 80.3253 Evaluate side-chains 149 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 19 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 13 optimal weight: 0.5980 chunk 35 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 60 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN S 182 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.139240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.108835 restraints weight = 11969.781| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.96 r_work: 0.3395 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8638 Z= 0.201 Angle : 0.637 9.224 11750 Z= 0.333 Chirality : 0.044 0.224 1370 Planarity : 0.004 0.046 1463 Dihedral : 6.533 59.186 1352 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.48 % Allowed : 21.61 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.25), residues: 1101 helix: 0.87 (0.29), residues: 356 sheet: -0.34 (0.30), residues: 284 loop : -1.48 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 24 TYR 0.028 0.002 TYR S 178 PHE 0.025 0.002 PHE R 237 TRP 0.020 0.002 TRP S 47 HIS 0.005 0.001 HIS R 304 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 8636) covalent geometry : angle 0.63664 (11748) SS BOND : bond 0.00015 ( 1) SS BOND : angle 0.58484 ( 2) hydrogen bonds : bond 0.04080 ( 320) hydrogen bonds : angle 4.63090 ( 936) Misc. bond : bond 0.00109 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2968.70 seconds wall clock time: 51 minutes 19.34 seconds (3079.34 seconds total)