Starting phenix.real_space_refine on Thu Sep 26 22:02:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2n_26316/09_2024/7u2n_26316_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2n_26316/09_2024/7u2n_26316.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2n_26316/09_2024/7u2n_26316.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2n_26316/09_2024/7u2n_26316.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2n_26316/09_2024/7u2n_26316_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2n_26316/09_2024/7u2n_26316_trim.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 2.345 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 9165 2.51 5 N 2255 2.21 5 O 2555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 14080 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2771 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'L2L': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, E, D, F, I, H, J Time building chain proxies: 6.26, per 1000 atoms: 0.44 Number of scatterers: 14080 At special positions: 0 Unit cell: (104.706, 106.368, 135.453, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 2555 8.00 N 2255 7.00 C 9165 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG F 1 " - " ASN A 54 " " NAG G 1 " - " ASN D 54 " " NAG H 1 " - " ASN B 54 " " NAG I 1 " - " ASN C 54 " " NAG J 1 " - " ASN E 54 " Time building additional restraints: 3.89 Conformation dependent library (CDL) restraints added in 1.8 seconds 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3310 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 30 sheets defined 40.3% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 25 through 35 removed outlier: 3.840A pdb=" N ASP A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 40 removed outlier: 4.200A pdb=" N TYR A 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 90 Processing helix chain 'A' and resid 102 through 108 removed outlier: 3.937A pdb=" N ASP A 107 " --> pdb=" O SER A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 244 through 257 removed outlier: 4.197A pdb=" N ILE A 250 " --> pdb=" O PRO A 246 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 287 removed outlier: 3.942A pdb=" N VAL A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 325 removed outlier: 3.575A pdb=" N ILE A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 307 " --> pdb=" O MET A 303 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 426 removed outlier: 4.253A pdb=" N LEU A 394 " --> pdb=" O GLU A 390 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A 399 " --> pdb=" O PHE A 395 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) Proline residue: A 411 - end of helix removed outlier: 4.162A pdb=" N LEU A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 35 removed outlier: 3.841A pdb=" N ASP D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 40 removed outlier: 4.201A pdb=" N TYR D 40 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 90 Processing helix chain 'D' and resid 102 through 108 removed outlier: 3.937A pdb=" N ASP D 107 " --> pdb=" O SER D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 237 No H-bonds generated for 'chain 'D' and resid 235 through 237' Processing helix chain 'D' and resid 238 through 243 Processing helix chain 'D' and resid 244 through 257 removed outlier: 4.197A pdb=" N ILE D 250 " --> pdb=" O PRO D 246 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP D 255 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 287 removed outlier: 3.942A pdb=" N VAL D 269 " --> pdb=" O ALA D 265 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG D 287 " --> pdb=" O SER D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 325 removed outlier: 3.576A pdb=" N ILE D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TRP D 302 " --> pdb=" O ALA D 298 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU D 307 " --> pdb=" O MET D 303 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL D 310 " --> pdb=" O CYS D 306 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA D 313 " --> pdb=" O PHE D 309 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA D 318 " --> pdb=" O LEU D 314 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA D 319 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 426 removed outlier: 4.253A pdb=" N LEU D 394 " --> pdb=" O GLU D 390 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER D 397 " --> pdb=" O LYS D 393 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA D 399 " --> pdb=" O PHE D 395 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE D 402 " --> pdb=" O ARG D 398 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL D 408 " --> pdb=" O THR D 404 " (cutoff:3.500A) Proline residue: D 411 - end of helix removed outlier: 4.161A pdb=" N LEU D 415 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TRP D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 35 removed outlier: 3.841A pdb=" N ASP B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 removed outlier: 4.201A pdb=" N TYR B 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 102 through 108 removed outlier: 3.937A pdb=" N ASP B 107 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 237 No H-bonds generated for 'chain 'B' and resid 235 through 237' Processing helix chain 'B' and resid 238 through 243 Processing helix chain 'B' and resid 244 through 257 removed outlier: 4.197A pdb=" N ILE B 250 " --> pdb=" O PRO B 246 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B 252 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 287 removed outlier: 3.941A pdb=" N VAL B 269 " --> pdb=" O ALA B 265 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 325 removed outlier: 3.576A pdb=" N ILE B 301 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TRP B 302 " --> pdb=" O ALA B 298 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B 307 " --> pdb=" O MET B 303 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL B 310 " --> pdb=" O CYS B 306 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA B 313 " --> pdb=" O PHE B 309 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA B 318 " --> pdb=" O LEU B 314 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA B 319 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 426 removed outlier: 4.253A pdb=" N LEU B 394 " --> pdb=" O GLU B 390 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B 397 " --> pdb=" O LYS B 393 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA B 399 " --> pdb=" O PHE B 395 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE B 402 " --> pdb=" O ARG B 398 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) Proline residue: B 411 - end of helix removed outlier: 4.163A pdb=" N LEU B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 35 removed outlier: 3.841A pdb=" N ASP C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 40 removed outlier: 4.201A pdb=" N TYR C 40 " --> pdb=" O VAL C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 90 Processing helix chain 'C' and resid 102 through 108 removed outlier: 3.936A pdb=" N ASP C 107 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 237 No H-bonds generated for 'chain 'C' and resid 235 through 237' Processing helix chain 'C' and resid 238 through 243 Processing helix chain 'C' and resid 244 through 257 removed outlier: 4.197A pdb=" N ILE C 250 " --> pdb=" O PRO C 246 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP C 255 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 287 removed outlier: 3.941A pdb=" N VAL C 269 " --> pdb=" O ALA C 265 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG C 287 " --> pdb=" O SER C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 325 removed outlier: 3.576A pdb=" N ILE C 301 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TRP C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 307 " --> pdb=" O MET C 303 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL C 310 " --> pdb=" O CYS C 306 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA C 313 " --> pdb=" O PHE C 309 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA C 318 " --> pdb=" O LEU C 314 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA C 319 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 426 removed outlier: 4.254A pdb=" N LEU C 394 " --> pdb=" O GLU C 390 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER C 397 " --> pdb=" O LYS C 393 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA C 399 " --> pdb=" O PHE C 395 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE C 402 " --> pdb=" O ARG C 398 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) Proline residue: C 411 - end of helix removed outlier: 4.162A pdb=" N LEU C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 35 removed outlier: 3.841A pdb=" N ASP E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 40 removed outlier: 4.200A pdb=" N TYR E 40 " --> pdb=" O VAL E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 90 Processing helix chain 'E' and resid 102 through 108 removed outlier: 3.936A pdb=" N ASP E 107 " --> pdb=" O SER E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 237 No H-bonds generated for 'chain 'E' and resid 235 through 237' Processing helix chain 'E' and resid 238 through 243 Processing helix chain 'E' and resid 244 through 257 removed outlier: 4.197A pdb=" N ILE E 250 " --> pdb=" O PRO E 246 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE E 252 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP E 255 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER E 257 " --> pdb=" O LEU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 287 removed outlier: 3.942A pdb=" N VAL E 269 " --> pdb=" O ALA E 265 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG E 287 " --> pdb=" O SER E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 325 removed outlier: 3.575A pdb=" N ILE E 301 " --> pdb=" O LYS E 297 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP E 302 " --> pdb=" O ALA E 298 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU E 307 " --> pdb=" O MET E 303 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL E 310 " --> pdb=" O CYS E 306 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA E 313 " --> pdb=" O PHE E 309 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA E 318 " --> pdb=" O LEU E 314 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA E 319 " --> pdb=" O LEU E 315 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL E 320 " --> pdb=" O GLU E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 426 removed outlier: 4.253A pdb=" N LEU E 394 " --> pdb=" O GLU E 390 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER E 397 " --> pdb=" O LYS E 393 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA E 399 " --> pdb=" O PHE E 395 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE E 402 " --> pdb=" O ARG E 398 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL E 408 " --> pdb=" O THR E 404 " (cutoff:3.500A) Proline residue: E 411 - end of helix removed outlier: 4.162A pdb=" N LEU E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 124 removed outlier: 3.713A pdb=" N TRP A 84 " --> pdb=" O VAL A 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 124 removed outlier: 6.299A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 116 Processing sheet with id=AA4, first strand: chain 'A' and resid 167 through 168 Processing sheet with id=AA5, first strand: chain 'A' and resid 211 through 213 Processing sheet with id=AA6, first strand: chain 'A' and resid 216 through 218 Processing sheet with id=AA7, first strand: chain 'D' and resid 122 through 124 removed outlier: 3.713A pdb=" N TRP D 84 " --> pdb=" O VAL D 142 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 122 through 124 removed outlier: 6.299A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 114 through 116 Processing sheet with id=AB1, first strand: chain 'D' and resid 167 through 168 Processing sheet with id=AB2, first strand: chain 'D' and resid 211 through 213 Processing sheet with id=AB3, first strand: chain 'D' and resid 216 through 218 Processing sheet with id=AB4, first strand: chain 'B' and resid 122 through 124 removed outlier: 3.714A pdb=" N TRP B 84 " --> pdb=" O VAL B 142 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 122 through 124 removed outlier: 6.300A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 114 through 116 Processing sheet with id=AB7, first strand: chain 'B' and resid 167 through 168 Processing sheet with id=AB8, first strand: chain 'B' and resid 211 through 213 Processing sheet with id=AB9, first strand: chain 'B' and resid 216 through 218 Processing sheet with id=AC1, first strand: chain 'C' and resid 122 through 124 removed outlier: 3.713A pdb=" N TRP C 84 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 122 through 124 removed outlier: 6.299A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 114 through 116 Processing sheet with id=AC4, first strand: chain 'C' and resid 167 through 168 Processing sheet with id=AC5, first strand: chain 'C' and resid 211 through 213 Processing sheet with id=AC6, first strand: chain 'C' and resid 216 through 218 Processing sheet with id=AC7, first strand: chain 'E' and resid 122 through 124 removed outlier: 3.714A pdb=" N TRP E 84 " --> pdb=" O VAL E 142 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 122 through 124 removed outlier: 6.298A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 114 through 116 Processing sheet with id=AD1, first strand: chain 'E' and resid 167 through 168 Processing sheet with id=AD2, first strand: chain 'E' and resid 211 through 213 Processing sheet with id=AD3, first strand: chain 'E' and resid 216 through 218 585 hydrogen bonds defined for protein. 1590 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: 4.34 Time building geometry restraints manager: 4.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4264 1.34 - 1.46: 3283 1.46 - 1.58: 6703 1.58 - 1.70: 0 1.70 - 1.82: 175 Bond restraints: 14425 Sorted by residual: bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.559 -0.040 2.00e-02 2.50e+03 4.07e+00 bond pdb=" C1 BMA I 3 " pdb=" C2 BMA I 3 " ideal model delta sigma weight residual 1.519 1.559 -0.040 2.00e-02 2.50e+03 4.03e+00 bond pdb=" C1 BMA J 3 " pdb=" C2 BMA J 3 " ideal model delta sigma weight residual 1.519 1.559 -0.040 2.00e-02 2.50e+03 3.96e+00 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.559 -0.040 2.00e-02 2.50e+03 3.96e+00 bond pdb=" C1 BMA H 3 " pdb=" C2 BMA H 3 " ideal model delta sigma weight residual 1.519 1.558 -0.039 2.00e-02 2.50e+03 3.90e+00 ... (remaining 14420 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 19171 2.21 - 4.43: 352 4.43 - 6.64: 62 6.64 - 8.85: 0 8.85 - 11.07: 5 Bond angle restraints: 19590 Sorted by residual: angle pdb=" N ASN B 261 " pdb=" CA ASN B 261 " pdb=" CB ASN B 261 " ideal model delta sigma weight residual 114.17 109.93 4.24 1.14e+00 7.69e-01 1.38e+01 angle pdb=" N ASN E 261 " pdb=" CA ASN E 261 " pdb=" CB ASN E 261 " ideal model delta sigma weight residual 114.17 109.93 4.24 1.14e+00 7.69e-01 1.38e+01 angle pdb=" N ASN A 261 " pdb=" CA ASN A 261 " pdb=" CB ASN A 261 " ideal model delta sigma weight residual 114.17 109.94 4.23 1.14e+00 7.69e-01 1.38e+01 angle pdb=" O04 L2L C 600 " pdb=" S03 L2L C 600 " pdb=" O05 L2L C 600 " ideal model delta sigma weight residual 112.97 101.90 11.07 3.00e+00 1.11e-01 1.36e+01 angle pdb=" N ASN D 261 " pdb=" CA ASN D 261 " pdb=" CB ASN D 261 " ideal model delta sigma weight residual 114.17 109.96 4.21 1.14e+00 7.69e-01 1.36e+01 ... (remaining 19585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 8447 17.68 - 35.35: 248 35.35 - 53.02: 21 53.02 - 70.70: 0 70.70 - 88.37: 70 Dihedral angle restraints: 8786 sinusoidal: 3686 harmonic: 5100 Sorted by residual: dihedral pdb=" CB CYS A 154 " pdb=" SG CYS A 154 " pdb=" SG CYS A 168 " pdb=" CB CYS A 168 " ideal model delta sinusoidal sigma weight residual 93.00 41.46 51.54 1 1.00e+01 1.00e-02 3.63e+01 dihedral pdb=" CA ASN A 160 " pdb=" C ASN A 160 " pdb=" N PHE A 161 " pdb=" CA PHE A 161 " ideal model delta harmonic sigma weight residual -180.00 -159.69 -20.31 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA ASN C 160 " pdb=" C ASN C 160 " pdb=" N PHE C 161 " pdb=" CA PHE C 161 " ideal model delta harmonic sigma weight residual -180.00 -159.70 -20.30 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 8783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1784 0.052 - 0.104: 390 0.104 - 0.157: 71 0.157 - 0.209: 5 0.209 - 0.261: 5 Chirality restraints: 2255 Sorted by residual: chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 2252 not shown) Planarity restraints: 2425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 151 " 0.012 2.00e-02 2.50e+03 2.31e-02 5.35e+00 pdb=" C VAL C 151 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL C 151 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU C 152 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 151 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.27e+00 pdb=" C VAL A 151 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL A 151 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU A 152 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 151 " 0.011 2.00e-02 2.50e+03 2.29e-02 5.22e+00 pdb=" C VAL E 151 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL E 151 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU E 152 " 0.013 2.00e-02 2.50e+03 ... (remaining 2422 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 198 2.61 - 3.18: 13283 3.18 - 3.75: 19880 3.75 - 4.33: 30405 4.33 - 4.90: 49011 Nonbonded interactions: 112777 Sorted by model distance: nonbonded pdb=" SG CYS D 154 " pdb=" SG CYS D 168 " model vdw 2.034 3.760 nonbonded pdb=" SG CYS B 154 " pdb=" SG CYS B 168 " model vdw 2.035 3.760 nonbonded pdb=" SG CYS E 154 " pdb=" SG CYS E 168 " model vdw 2.035 3.760 nonbonded pdb=" SG CYS C 154 " pdb=" SG CYS C 168 " model vdw 2.035 3.760 nonbonded pdb=" SG CYS C 214 " pdb=" SG CYS C 225 " model vdw 2.040 3.760 ... (remaining 112772 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 8.210 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: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.020 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 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 : 0.007 0.049 14425 Z= 0.475 Angle : 0.804 11.067 19590 Z= 0.431 Chirality : 0.048 0.261 2255 Planarity : 0.005 0.044 2420 Dihedral : 12.412 88.373 5470 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 23.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.23 (0.18), residues: 1705 helix: -2.95 (0.19), residues: 535 sheet: -3.24 (0.22), residues: 370 loop : -2.33 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 259 HIS 0.004 0.001 HIS D 217 PHE 0.021 0.002 PHE A 115 TYR 0.012 0.002 TYR A 74 ARG 0.007 0.001 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 481 time to evaluate : 2.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7857 (tp30) cc_final: 0.7503 (tp30) REVERT: A 96 ASP cc_start: 0.7708 (m-30) cc_final: 0.7261 (m-30) REVERT: A 108 SER cc_start: 0.8592 (t) cc_final: 0.8309 (t) REVERT: A 126 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7204 (pm20) REVERT: A 130 ASP cc_start: 0.8395 (m-30) cc_final: 0.8132 (m-30) REVERT: A 132 LYS cc_start: 0.8163 (mttm) cc_final: 0.7951 (mtmp) REVERT: A 189 LYS cc_start: 0.8608 (ptpt) cc_final: 0.8385 (ptpp) REVERT: A 206 LYS cc_start: 0.8349 (mtpt) cc_final: 0.7979 (mttt) REVERT: A 312 SER cc_start: 0.8172 (m) cc_final: 0.7819 (p) REVERT: D 63 SER cc_start: 0.8337 (t) cc_final: 0.7751 (p) REVERT: D 75 ARG cc_start: 0.7776 (ttm-80) cc_final: 0.7468 (ttm-80) REVERT: D 96 ASP cc_start: 0.7877 (m-30) cc_final: 0.7503 (m-30) REVERT: D 102 ASP cc_start: 0.8025 (t0) cc_final: 0.7811 (t0) REVERT: D 108 SER cc_start: 0.8729 (t) cc_final: 0.8529 (t) REVERT: D 126 GLU cc_start: 0.7362 (mt-10) cc_final: 0.6896 (pm20) REVERT: D 132 LYS cc_start: 0.8195 (mttm) cc_final: 0.7801 (mtmt) REVERT: D 189 LYS cc_start: 0.8581 (ptpt) cc_final: 0.8364 (ptpp) REVERT: D 206 LYS cc_start: 0.8334 (mtpt) cc_final: 0.7877 (mttm) REVERT: D 210 ASP cc_start: 0.8283 (m-30) cc_final: 0.7988 (m-30) REVERT: D 235 GLN cc_start: 0.8053 (mm110) cc_final: 0.7747 (mt0) REVERT: D 312 SER cc_start: 0.8196 (m) cc_final: 0.7911 (p) REVERT: B 28 GLU cc_start: 0.7877 (tp30) cc_final: 0.7590 (tp30) REVERT: B 31 ASP cc_start: 0.8304 (m-30) cc_final: 0.7894 (m-30) REVERT: B 96 ASP cc_start: 0.7720 (m-30) cc_final: 0.7142 (m-30) REVERT: B 108 SER cc_start: 0.8576 (t) cc_final: 0.8365 (t) REVERT: B 126 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7174 (pm20) REVERT: B 132 LYS cc_start: 0.8143 (mttm) cc_final: 0.7866 (mtmp) REVERT: B 206 LYS cc_start: 0.8347 (mtpt) cc_final: 0.7992 (mttm) REVERT: B 210 ASP cc_start: 0.8300 (m-30) cc_final: 0.8058 (m-30) REVERT: B 312 SER cc_start: 0.8159 (m) cc_final: 0.7845 (p) REVERT: C 28 GLU cc_start: 0.7845 (tp30) cc_final: 0.7550 (tp30) REVERT: C 96 ASP cc_start: 0.7756 (m-30) cc_final: 0.7356 (m-30) REVERT: C 108 SER cc_start: 0.8746 (t) cc_final: 0.8505 (t) REVERT: C 126 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7106 (pm20) REVERT: C 130 ASP cc_start: 0.8482 (m-30) cc_final: 0.8176 (m-30) REVERT: C 132 LYS cc_start: 0.8216 (mttm) cc_final: 0.7936 (mtmp) REVERT: C 189 LYS cc_start: 0.8559 (ptpt) cc_final: 0.8290 (ptpp) REVERT: C 206 LYS cc_start: 0.8311 (mtpt) cc_final: 0.7994 (mttm) REVERT: C 210 ASP cc_start: 0.8236 (m-30) cc_final: 0.7909 (m-30) REVERT: C 229 ARG cc_start: 0.7998 (mtt-85) cc_final: 0.7462 (mmm-85) REVERT: C 235 GLN cc_start: 0.7989 (mm110) cc_final: 0.7673 (mt0) REVERT: C 312 SER cc_start: 0.8218 (m) cc_final: 0.7936 (p) REVERT: E 28 GLU cc_start: 0.7947 (tp30) cc_final: 0.7647 (tp30) REVERT: E 75 ARG cc_start: 0.7874 (ttm-80) cc_final: 0.7614 (ttm-80) REVERT: E 96 ASP cc_start: 0.7711 (m-30) cc_final: 0.7202 (m-30) REVERT: E 108 SER cc_start: 0.8681 (t) cc_final: 0.8388 (t) REVERT: E 126 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7224 (pm20) REVERT: E 132 LYS cc_start: 0.8127 (mttm) cc_final: 0.7844 (mtmp) REVERT: E 189 LYS cc_start: 0.8466 (ptpt) cc_final: 0.8238 (ptpp) REVERT: E 210 ASP cc_start: 0.8281 (m-30) cc_final: 0.7933 (m-30) REVERT: E 235 GLN cc_start: 0.8057 (mm110) cc_final: 0.7851 (mm110) REVERT: E 312 SER cc_start: 0.8193 (m) cc_final: 0.7910 (p) outliers start: 0 outliers final: 0 residues processed: 481 average time/residue: 1.1709 time to fit residues: 622.4477 Evaluate side-chains 379 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 379 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 0.0970 chunk 128 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 68 optimal weight: 7.9990 chunk 133 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 77 ASN A 82 GLN A 141 ASN A 202 GLN A 231 HIS D 77 ASN D 82 GLN D 141 ASN D 202 GLN D 231 HIS D 418 ASN B 62 ASN B 77 ASN B 82 GLN B 141 ASN B 219 ASN B 231 HIS B 321 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 ASN C 77 ASN C 82 GLN C 141 ASN C 219 ASN C 231 HIS C 321 ASN E 62 ASN E 77 ASN E 82 GLN E 141 ASN E 171 GLN E 231 HIS E 321 ASN ** E 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14425 Z= 0.267 Angle : 0.752 6.063 19590 Z= 0.394 Chirality : 0.049 0.178 2255 Planarity : 0.006 0.061 2420 Dihedral : 12.354 78.737 2190 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.71 % Allowed : 13.33 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.19), residues: 1705 helix: -1.25 (0.21), residues: 560 sheet: -2.55 (0.24), residues: 370 loop : -1.80 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 259 HIS 0.003 0.001 HIS A 231 PHE 0.025 0.002 PHE D 414 TYR 0.014 0.002 TYR D 317 ARG 0.015 0.001 ARG E 229 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 400 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 TYR cc_start: 0.8397 (OUTLIER) cc_final: 0.8162 (t80) REVERT: A 104 SER cc_start: 0.8523 (t) cc_final: 0.7896 (p) REVERT: A 126 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7194 (pm20) REVERT: A 141 ASN cc_start: 0.8308 (m110) cc_final: 0.8027 (m110) REVERT: A 189 LYS cc_start: 0.8529 (ptpt) cc_final: 0.8303 (ptmm) REVERT: A 206 LYS cc_start: 0.8258 (mtpt) cc_final: 0.7941 (mttt) REVERT: A 235 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7855 (mt0) REVERT: D 49 LYS cc_start: 0.9019 (mmmt) cc_final: 0.8791 (mmmm) REVERT: D 63 SER cc_start: 0.8447 (t) cc_final: 0.7915 (p) REVERT: D 75 ARG cc_start: 0.7794 (ttm-80) cc_final: 0.7517 (ttm-80) REVERT: D 96 ASP cc_start: 0.7657 (m-30) cc_final: 0.7264 (m-30) REVERT: D 126 GLU cc_start: 0.7300 (mt-10) cc_final: 0.6800 (pm20) REVERT: D 130 ASP cc_start: 0.8422 (m-30) cc_final: 0.8216 (m-30) REVERT: D 132 LYS cc_start: 0.7986 (mttm) cc_final: 0.7622 (mtmt) REVERT: D 135 ARG cc_start: 0.7749 (ptp-170) cc_final: 0.7279 (ptp-170) REVERT: D 141 ASN cc_start: 0.8195 (m110) cc_final: 0.7799 (m110) REVERT: D 179 MET cc_start: 0.8087 (mmm) cc_final: 0.7830 (mmm) REVERT: D 189 LYS cc_start: 0.8472 (ptpt) cc_final: 0.8253 (ptpp) REVERT: D 206 LYS cc_start: 0.8248 (mtpt) cc_final: 0.7806 (mttm) REVERT: D 235 GLN cc_start: 0.7991 (mm110) cc_final: 0.7786 (mt0) REVERT: D 262 MET cc_start: 0.8296 (mpp) cc_final: 0.7079 (tmt) REVERT: B 126 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7168 (pm20) REVERT: B 135 ARG cc_start: 0.7789 (ptp-170) cc_final: 0.7544 (ptp-170) REVERT: B 179 MET cc_start: 0.8087 (mmm) cc_final: 0.7742 (mmm) REVERT: B 206 LYS cc_start: 0.8317 (mtpt) cc_final: 0.8042 (mttt) REVERT: B 219 ASN cc_start: 0.8349 (p0) cc_final: 0.8117 (p0) REVERT: B 235 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7852 (mt0) REVERT: B 262 MET cc_start: 0.8133 (mpp) cc_final: 0.7004 (tmt) REVERT: C 94 TYR cc_start: 0.8406 (OUTLIER) cc_final: 0.7195 (t80) REVERT: C 96 ASP cc_start: 0.7533 (m-30) cc_final: 0.7151 (m-30) REVERT: C 126 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7045 (pm20) REVERT: C 135 ARG cc_start: 0.7895 (ptp-170) cc_final: 0.7633 (ptp-170) REVERT: C 179 MET cc_start: 0.8134 (mmm) cc_final: 0.7915 (mmm) REVERT: C 189 LYS cc_start: 0.8497 (ptpt) cc_final: 0.8226 (ptpp) REVERT: C 206 LYS cc_start: 0.8201 (mtpt) cc_final: 0.7927 (mttm) REVERT: C 210 ASP cc_start: 0.8030 (m-30) cc_final: 0.7705 (m-30) REVERT: C 235 GLN cc_start: 0.8039 (mm110) cc_final: 0.7816 (mt0) REVERT: C 401 ARG cc_start: 0.8669 (mmm160) cc_final: 0.8324 (mmm-85) REVERT: E 28 GLU cc_start: 0.8006 (tp30) cc_final: 0.7740 (tp30) REVERT: E 62 ASN cc_start: 0.8044 (m-40) cc_final: 0.7839 (m-40) REVERT: E 75 ARG cc_start: 0.7865 (ttm-80) cc_final: 0.7596 (ttm-80) REVERT: E 105 MET cc_start: 0.7396 (tpp) cc_final: 0.7189 (tpp) REVERT: E 126 GLU cc_start: 0.7524 (mt-10) cc_final: 0.6984 (pm20) REVERT: E 132 LYS cc_start: 0.8010 (mttm) cc_final: 0.7796 (mtmp) REVERT: E 135 ARG cc_start: 0.7761 (ptp-170) cc_final: 0.7295 (ptp-170) REVERT: E 179 MET cc_start: 0.8122 (mmm) cc_final: 0.7920 (mmm) REVERT: E 189 LYS cc_start: 0.8388 (ptpt) cc_final: 0.8160 (ptpp) REVERT: E 210 ASP cc_start: 0.8086 (m-30) cc_final: 0.7764 (m-30) REVERT: E 235 GLN cc_start: 0.8031 (mm110) cc_final: 0.7643 (mt0) REVERT: E 262 MET cc_start: 0.8329 (mpp) cc_final: 0.7138 (tmt) outliers start: 41 outliers final: 18 residues processed: 410 average time/residue: 1.1250 time to fit residues: 509.6031 Evaluate side-chains 355 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 333 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 235 GLN Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 418 ASN Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 424 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 0.6980 chunk 47 optimal weight: 0.0170 chunk 128 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 154 optimal weight: 0.1980 chunk 167 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 chunk 153 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 202 GLN B 418 ASN C 62 ASN C 219 ASN E 418 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14425 Z= 0.196 Angle : 0.652 7.093 19590 Z= 0.339 Chirality : 0.044 0.138 2255 Planarity : 0.005 0.054 2420 Dihedral : 11.124 67.371 2190 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.50 % Allowed : 17.36 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.20), residues: 1705 helix: -0.16 (0.23), residues: 555 sheet: -2.17 (0.24), residues: 370 loop : -1.49 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 259 HIS 0.002 0.001 HIS A 231 PHE 0.016 0.001 PHE E 414 TYR 0.018 0.002 TYR C 317 ARG 0.007 0.000 ARG A 212 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 353 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 TYR cc_start: 0.8538 (OUTLIER) cc_final: 0.8219 (t80) REVERT: A 104 SER cc_start: 0.8377 (t) cc_final: 0.7830 (p) REVERT: A 126 GLU cc_start: 0.7398 (mt-10) cc_final: 0.7152 (pm20) REVERT: A 130 ASP cc_start: 0.8484 (m-30) cc_final: 0.8219 (m-30) REVERT: A 135 ARG cc_start: 0.7738 (ptp-170) cc_final: 0.7324 (ptp-170) REVERT: A 141 ASN cc_start: 0.8208 (m110) cc_final: 0.7868 (m110) REVERT: D 43 ARG cc_start: 0.8623 (mtm-85) cc_final: 0.8327 (mtm180) REVERT: D 49 LYS cc_start: 0.8968 (mmmt) cc_final: 0.8702 (mmmm) REVERT: D 63 SER cc_start: 0.8564 (t) cc_final: 0.8058 (p) REVERT: D 72 MET cc_start: 0.9196 (mtt) cc_final: 0.8990 (mmt) REVERT: D 75 ARG cc_start: 0.7808 (ttm-80) cc_final: 0.7489 (ttm-80) REVERT: D 126 GLU cc_start: 0.7347 (mt-10) cc_final: 0.6745 (pm20) REVERT: D 135 ARG cc_start: 0.7656 (ptp-170) cc_final: 0.7248 (ptp-170) REVERT: D 189 LYS cc_start: 0.8383 (ptpt) cc_final: 0.8169 (ptpp) REVERT: D 206 LYS cc_start: 0.8202 (mtpt) cc_final: 0.7821 (mttm) REVERT: D 212 ARG cc_start: 0.7681 (pmm-80) cc_final: 0.6992 (ptt90) REVERT: D 262 MET cc_start: 0.8243 (mpp) cc_final: 0.6836 (tmt) REVERT: B 32 LYS cc_start: 0.8303 (tmtt) cc_final: 0.8081 (tmtt) REVERT: B 126 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7055 (pm20) REVERT: B 135 ARG cc_start: 0.7718 (ptp-170) cc_final: 0.7494 (ptp-170) REVERT: B 179 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7794 (mmm) REVERT: B 206 LYS cc_start: 0.8293 (mtpt) cc_final: 0.8065 (mttp) REVERT: B 219 ASN cc_start: 0.8297 (p0) cc_final: 0.8062 (p0) REVERT: B 235 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7785 (mt0) REVERT: B 262 MET cc_start: 0.8020 (mpp) cc_final: 0.6685 (tmt) REVERT: C 94 TYR cc_start: 0.8402 (OUTLIER) cc_final: 0.7077 (t80) REVERT: C 96 ASP cc_start: 0.7398 (m-30) cc_final: 0.7096 (m-30) REVERT: C 126 GLU cc_start: 0.7431 (mt-10) cc_final: 0.6940 (pm20) REVERT: C 135 ARG cc_start: 0.7747 (ptp-170) cc_final: 0.7419 (ptp-170) REVERT: C 206 LYS cc_start: 0.8163 (mtpt) cc_final: 0.7942 (mttm) REVERT: C 229 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7990 (mmm-85) REVERT: C 243 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7358 (mtt) REVERT: C 401 ARG cc_start: 0.8660 (mmm160) cc_final: 0.8295 (mmm-85) REVERT: E 75 ARG cc_start: 0.7901 (ttm-80) cc_final: 0.7608 (ttm-80) REVERT: E 126 GLU cc_start: 0.7501 (mt-10) cc_final: 0.6935 (pm20) REVERT: E 132 LYS cc_start: 0.7968 (mttm) cc_final: 0.7745 (mtmp) REVERT: E 135 ARG cc_start: 0.7670 (ptp-170) cc_final: 0.7214 (ttp-170) REVERT: E 138 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8707 (mtmt) REVERT: E 179 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7835 (mmm) REVERT: E 210 ASP cc_start: 0.8151 (m-30) cc_final: 0.7830 (m-30) REVERT: E 235 GLN cc_start: 0.7943 (mm110) cc_final: 0.7697 (mt0) REVERT: E 262 MET cc_start: 0.8190 (mpp) cc_final: 0.6850 (tmt) outliers start: 53 outliers final: 23 residues processed: 372 average time/residue: 1.1515 time to fit residues: 470.2908 Evaluate side-chains 353 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 322 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 229 ARG Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 138 LYS Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain E residue 423 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 103 optimal weight: 0.0070 chunk 155 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 219 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 14425 Z= 0.331 Angle : 0.704 7.897 19590 Z= 0.365 Chirality : 0.046 0.136 2255 Planarity : 0.005 0.053 2420 Dihedral : 10.005 57.691 2190 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 5.15 % Allowed : 18.61 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.20), residues: 1705 helix: 0.42 (0.23), residues: 565 sheet: -1.89 (0.25), residues: 370 loop : -1.64 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 259 HIS 0.003 0.001 HIS B 217 PHE 0.016 0.002 PHE A 124 TYR 0.016 0.002 TYR C 317 ARG 0.005 0.000 ARG D 212 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 308 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7239 (pm20) REVERT: A 141 ASN cc_start: 0.8279 (m110) cc_final: 0.7967 (m110) REVERT: A 227 GLU cc_start: 0.8268 (pt0) cc_final: 0.8035 (pt0) REVERT: A 243 MET cc_start: 0.8289 (mpp) cc_final: 0.7669 (mtt) REVERT: A 312 SER cc_start: 0.7996 (OUTLIER) cc_final: 0.7549 (p) REVERT: A 391 MET cc_start: 0.4891 (pmm) cc_final: 0.3835 (ppp) REVERT: D 43 ARG cc_start: 0.8656 (mtm-85) cc_final: 0.8320 (mtm180) REVERT: D 75 ARG cc_start: 0.7833 (ttm-80) cc_final: 0.7495 (ttm-80) REVERT: D 81 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8245 (mpp80) REVERT: D 96 ASP cc_start: 0.8089 (p0) cc_final: 0.7760 (p0) REVERT: D 126 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7044 (pm20) REVERT: D 135 ARG cc_start: 0.7794 (ptp-170) cc_final: 0.7499 (ptp-170) REVERT: D 206 LYS cc_start: 0.8303 (mtpt) cc_final: 0.7928 (mttm) REVERT: D 227 GLU cc_start: 0.8216 (pt0) cc_final: 0.7902 (pt0) REVERT: D 262 MET cc_start: 0.8187 (mpp) cc_final: 0.6797 (tmt) REVERT: B 32 LYS cc_start: 0.8274 (tmtt) cc_final: 0.8032 (tmtt) REVERT: B 126 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7126 (pm20) REVERT: B 135 ARG cc_start: 0.7832 (ptp-170) cc_final: 0.7537 (ptp-170) REVERT: B 206 LYS cc_start: 0.8389 (mtpt) cc_final: 0.8166 (mttp) REVERT: B 235 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8131 (mt0) REVERT: B 262 MET cc_start: 0.8072 (mpp) cc_final: 0.6710 (tmt) REVERT: C 94 TYR cc_start: 0.8522 (OUTLIER) cc_final: 0.7424 (t80) REVERT: C 96 ASP cc_start: 0.7368 (m-30) cc_final: 0.7165 (m-30) REVERT: C 126 GLU cc_start: 0.7385 (mt-10) cc_final: 0.6964 (pm20) REVERT: C 135 ARG cc_start: 0.7845 (ptp-170) cc_final: 0.7489 (ptp-170) REVERT: C 206 LYS cc_start: 0.8204 (mtpt) cc_final: 0.7949 (mttm) REVERT: C 229 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8143 (mmm-85) REVERT: C 243 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7559 (mtt) REVERT: C 312 SER cc_start: 0.7933 (OUTLIER) cc_final: 0.7577 (p) REVERT: C 401 ARG cc_start: 0.8676 (mmm160) cc_final: 0.8304 (mmm-85) REVERT: E 75 ARG cc_start: 0.7941 (ttm-80) cc_final: 0.7629 (ttm-80) REVERT: E 126 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7104 (pm20) REVERT: E 132 LYS cc_start: 0.7978 (mttm) cc_final: 0.7722 (mtmp) REVERT: E 206 LYS cc_start: 0.8213 (mtpt) cc_final: 0.7832 (mttt) REVERT: E 210 ASP cc_start: 0.8189 (m-30) cc_final: 0.7852 (m-30) REVERT: E 219 ASN cc_start: 0.8308 (OUTLIER) cc_final: 0.8023 (p0) REVERT: E 235 GLN cc_start: 0.8119 (mm110) cc_final: 0.7821 (mt0) REVERT: E 262 MET cc_start: 0.8131 (mpp) cc_final: 0.6836 (tmt) REVERT: E 284 SER cc_start: 0.9217 (OUTLIER) cc_final: 0.9011 (p) REVERT: E 312 SER cc_start: 0.8010 (OUTLIER) cc_final: 0.7614 (p) outliers start: 78 outliers final: 41 residues processed: 336 average time/residue: 1.2099 time to fit residues: 445.9125 Evaluate side-chains 339 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 288 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 229 ARG Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 312 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 0.2980 chunk 93 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 219 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14425 Z= 0.247 Angle : 0.668 8.164 19590 Z= 0.343 Chirality : 0.045 0.172 2255 Planarity : 0.005 0.048 2420 Dihedral : 8.762 49.092 2190 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 5.02 % Allowed : 19.01 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.20), residues: 1705 helix: 0.64 (0.23), residues: 565 sheet: -1.70 (0.25), residues: 370 loop : -1.59 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 259 HIS 0.002 0.001 HIS D 217 PHE 0.015 0.002 PHE B 29 TYR 0.015 0.002 TYR C 317 ARG 0.005 0.000 ARG E 212 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 306 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 TYR cc_start: 0.8658 (OUTLIER) cc_final: 0.8082 (t80) REVERT: A 126 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7169 (pm20) REVERT: A 141 ASN cc_start: 0.8235 (m110) cc_final: 0.7924 (m110) REVERT: A 243 MET cc_start: 0.8344 (tpp) cc_final: 0.7618 (mtt) REVERT: A 312 SER cc_start: 0.8002 (OUTLIER) cc_final: 0.7588 (p) REVERT: A 391 MET cc_start: 0.4749 (pmm) cc_final: 0.4492 (pmm) REVERT: D 75 ARG cc_start: 0.7777 (ttm-80) cc_final: 0.7431 (ttm-80) REVERT: D 126 GLU cc_start: 0.7377 (mt-10) cc_final: 0.6804 (pm20) REVERT: D 135 ARG cc_start: 0.7774 (ptp-170) cc_final: 0.7459 (ptp-170) REVERT: D 179 MET cc_start: 0.8165 (mmm) cc_final: 0.7922 (mmm) REVERT: D 206 LYS cc_start: 0.8267 (mtpt) cc_final: 0.7896 (mttt) REVERT: D 227 GLU cc_start: 0.8168 (pt0) cc_final: 0.7934 (pt0) REVERT: D 243 MET cc_start: 0.8223 (tpp) cc_final: 0.7771 (mtt) REVERT: D 262 MET cc_start: 0.8156 (mpp) cc_final: 0.6722 (tmt) REVERT: B 126 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7124 (pm20) REVERT: B 206 LYS cc_start: 0.8356 (mtpt) cc_final: 0.8087 (mttt) REVERT: B 235 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8059 (mt0) REVERT: B 262 MET cc_start: 0.8013 (mpp) cc_final: 0.6766 (tmt) REVERT: C 94 TYR cc_start: 0.8505 (OUTLIER) cc_final: 0.7424 (t80) REVERT: C 96 ASP cc_start: 0.7397 (m-30) cc_final: 0.7175 (m-30) REVERT: C 126 GLU cc_start: 0.7347 (mt-10) cc_final: 0.6927 (pm20) REVERT: C 135 ARG cc_start: 0.7772 (ptp-170) cc_final: 0.7500 (ptp-170) REVERT: C 189 LYS cc_start: 0.8473 (ptpp) cc_final: 0.8037 (ptpp) REVERT: C 206 LYS cc_start: 0.8264 (mtpt) cc_final: 0.8036 (mttm) REVERT: C 229 ARG cc_start: 0.8379 (mmt90) cc_final: 0.8065 (mmm-85) REVERT: C 243 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7656 (mtt) REVERT: C 279 MET cc_start: 0.8707 (tpp) cc_final: 0.7107 (mpp) REVERT: C 401 ARG cc_start: 0.8676 (mmm160) cc_final: 0.8293 (mmm-85) REVERT: E 71 THR cc_start: 0.9315 (m) cc_final: 0.9073 (p) REVERT: E 75 ARG cc_start: 0.7919 (ttm-80) cc_final: 0.7541 (ttm-80) REVERT: E 126 GLU cc_start: 0.7478 (mt-10) cc_final: 0.6902 (pm20) REVERT: E 132 LYS cc_start: 0.7941 (mttm) cc_final: 0.7691 (mtmp) REVERT: E 135 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7457 (ptp-170) REVERT: E 206 LYS cc_start: 0.8205 (mtpt) cc_final: 0.7803 (mttt) REVERT: E 210 ASP cc_start: 0.8153 (m-30) cc_final: 0.7815 (m-30) REVERT: E 219 ASN cc_start: 0.8290 (OUTLIER) cc_final: 0.8005 (p0) REVERT: E 235 GLN cc_start: 0.8071 (mm110) cc_final: 0.7765 (mt0) REVERT: E 262 MET cc_start: 0.8112 (mpp) cc_final: 0.6787 (tmt) REVERT: E 312 SER cc_start: 0.7979 (m) cc_final: 0.7618 (p) outliers start: 76 outliers final: 40 residues processed: 332 average time/residue: 1.1734 time to fit residues: 428.7807 Evaluate side-chains 338 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 291 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 135 ARG Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 219 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 136 optimal weight: 0.0000 chunk 76 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 86 optimal weight: 0.0770 overall best weight: 0.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 321 ASN E 321 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14425 Z= 0.197 Angle : 0.657 8.829 19590 Z= 0.334 Chirality : 0.045 0.143 2255 Planarity : 0.004 0.041 2420 Dihedral : 7.165 36.224 2190 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.76 % Allowed : 20.26 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.20), residues: 1705 helix: 0.73 (0.23), residues: 570 sheet: -1.52 (0.25), residues: 370 loop : -1.52 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 186 HIS 0.002 0.001 HIS E 217 PHE 0.014 0.001 PHE E 322 TYR 0.015 0.001 TYR C 317 ARG 0.005 0.000 ARG E 212 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 303 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 TYR cc_start: 0.8557 (OUTLIER) cc_final: 0.8049 (t80) REVERT: A 126 GLU cc_start: 0.7361 (mt-10) cc_final: 0.7146 (pm20) REVERT: A 141 ASN cc_start: 0.8155 (m110) cc_final: 0.7869 (m110) REVERT: A 243 MET cc_start: 0.8292 (tpp) cc_final: 0.7539 (mtt) REVERT: A 312 SER cc_start: 0.7939 (OUTLIER) cc_final: 0.7546 (p) REVERT: D 63 SER cc_start: 0.8584 (t) cc_final: 0.8215 (p) REVERT: D 75 ARG cc_start: 0.7760 (ttm-80) cc_final: 0.7403 (ttm-80) REVERT: D 94 TYR cc_start: 0.8713 (OUTLIER) cc_final: 0.7891 (t80) REVERT: D 126 GLU cc_start: 0.7328 (mt-10) cc_final: 0.6796 (pm20) REVERT: D 135 ARG cc_start: 0.7737 (ptp-170) cc_final: 0.7415 (ptp-170) REVERT: D 179 MET cc_start: 0.8086 (mmm) cc_final: 0.7828 (mmm) REVERT: D 262 MET cc_start: 0.8050 (mpp) cc_final: 0.6652 (tmt) REVERT: B 126 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7100 (pm20) REVERT: B 179 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7873 (mmm) REVERT: B 206 LYS cc_start: 0.8316 (mtpt) cc_final: 0.8084 (mttp) REVERT: B 219 ASN cc_start: 0.8191 (OUTLIER) cc_final: 0.7902 (p0) REVERT: B 235 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8003 (mt0) REVERT: B 262 MET cc_start: 0.7953 (mpp) cc_final: 0.6769 (tmt) REVERT: C 94 TYR cc_start: 0.8462 (OUTLIER) cc_final: 0.7292 (t80) REVERT: C 126 GLU cc_start: 0.7302 (mt-10) cc_final: 0.6873 (pm20) REVERT: C 135 ARG cc_start: 0.7767 (ptp-170) cc_final: 0.7514 (ptp-170) REVERT: C 206 LYS cc_start: 0.8212 (mtpt) cc_final: 0.8012 (mttm) REVERT: C 229 ARG cc_start: 0.8358 (mmt90) cc_final: 0.8055 (mmm-85) REVERT: C 401 ARG cc_start: 0.8676 (mmm160) cc_final: 0.8292 (mmm-85) REVERT: E 49 LYS cc_start: 0.9116 (mmmt) cc_final: 0.8909 (mmmt) REVERT: E 71 THR cc_start: 0.9223 (OUTLIER) cc_final: 0.9008 (p) REVERT: E 94 TYR cc_start: 0.8523 (OUTLIER) cc_final: 0.8091 (t80) REVERT: E 126 GLU cc_start: 0.7455 (mt-10) cc_final: 0.6903 (pm20) REVERT: E 132 LYS cc_start: 0.7932 (mttm) cc_final: 0.7669 (mtmp) REVERT: E 135 ARG cc_start: 0.7628 (ptp-170) cc_final: 0.7421 (ptp-170) REVERT: E 210 ASP cc_start: 0.8132 (m-30) cc_final: 0.7793 (m-30) REVERT: E 219 ASN cc_start: 0.8252 (OUTLIER) cc_final: 0.7986 (p0) REVERT: E 235 GLN cc_start: 0.8039 (mm110) cc_final: 0.7748 (mt0) REVERT: E 262 MET cc_start: 0.8086 (mpp) cc_final: 0.6811 (tmt) REVERT: E 312 SER cc_start: 0.8001 (OUTLIER) cc_final: 0.7641 (p) outliers start: 57 outliers final: 28 residues processed: 322 average time/residue: 1.1479 time to fit residues: 406.7002 Evaluate side-chains 329 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 290 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 423 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 91 optimal weight: 0.0060 chunk 163 optimal weight: 0.8980 chunk 102 optimal weight: 0.0470 chunk 99 optimal weight: 6.9990 chunk 75 optimal weight: 0.0070 chunk 101 optimal weight: 0.6980 overall best weight: 0.2912 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 ASN C 321 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14425 Z= 0.175 Angle : 0.648 9.317 19590 Z= 0.328 Chirality : 0.044 0.139 2255 Planarity : 0.004 0.041 2420 Dihedral : 5.594 22.001 2190 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.17 % Allowed : 20.92 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.21), residues: 1705 helix: 1.00 (0.23), residues: 560 sheet: -1.29 (0.26), residues: 370 loop : -1.24 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 186 HIS 0.001 0.001 HIS E 217 PHE 0.015 0.001 PHE A 322 TYR 0.014 0.001 TYR C 317 ARG 0.004 0.000 ARG E 212 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 286 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 SER cc_start: 0.8574 (OUTLIER) cc_final: 0.8238 (p) REVERT: A 94 TYR cc_start: 0.8471 (OUTLIER) cc_final: 0.7974 (t80) REVERT: A 126 GLU cc_start: 0.7341 (mt-10) cc_final: 0.7094 (pm20) REVERT: A 135 ARG cc_start: 0.7743 (ptp-170) cc_final: 0.7193 (ptp-170) REVERT: A 141 ASN cc_start: 0.8102 (m110) cc_final: 0.7826 (m110) REVERT: A 243 MET cc_start: 0.8295 (tpp) cc_final: 0.7654 (mtt) REVERT: A 312 SER cc_start: 0.7922 (m) cc_final: 0.7529 (p) REVERT: D 63 SER cc_start: 0.8576 (t) cc_final: 0.8269 (p) REVERT: D 75 ARG cc_start: 0.7744 (ttm-80) cc_final: 0.7359 (ttm-80) REVERT: D 94 TYR cc_start: 0.8623 (OUTLIER) cc_final: 0.7703 (t80) REVERT: D 99 LEU cc_start: 0.6846 (mt) cc_final: 0.6626 (tp) REVERT: D 135 ARG cc_start: 0.7712 (ptp-170) cc_final: 0.7390 (ptp-170) REVERT: D 206 LYS cc_start: 0.8184 (mttp) cc_final: 0.7871 (mttp) REVERT: D 243 MET cc_start: 0.8235 (tpp) cc_final: 0.7779 (mtt) REVERT: D 262 MET cc_start: 0.7909 (mpp) cc_final: 0.6586 (tmt) REVERT: B 126 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7027 (pm20) REVERT: B 179 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7841 (mmm) REVERT: B 206 LYS cc_start: 0.8244 (mtpt) cc_final: 0.7871 (mttp) REVERT: B 219 ASN cc_start: 0.8130 (p0) cc_final: 0.7829 (p0) REVERT: B 235 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7976 (mt0) REVERT: B 262 MET cc_start: 0.7831 (mpp) cc_final: 0.6702 (tmt) REVERT: C 32 LYS cc_start: 0.8371 (ttpt) cc_final: 0.8119 (tmtt) REVERT: C 63 SER cc_start: 0.8674 (t) cc_final: 0.8373 (p) REVERT: C 72 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8634 (mmt) REVERT: C 94 TYR cc_start: 0.8348 (OUTLIER) cc_final: 0.7035 (t80) REVERT: C 126 GLU cc_start: 0.7270 (mt-10) cc_final: 0.6840 (pm20) REVERT: C 135 ARG cc_start: 0.7703 (ptp-170) cc_final: 0.7397 (ptp-170) REVERT: C 229 ARG cc_start: 0.8338 (mmt90) cc_final: 0.8036 (mmm-85) REVERT: C 312 SER cc_start: 0.7917 (m) cc_final: 0.7592 (p) REVERT: C 401 ARG cc_start: 0.8679 (mmm160) cc_final: 0.8287 (mmm-85) REVERT: E 63 SER cc_start: 0.8546 (OUTLIER) cc_final: 0.8225 (p) REVERT: E 94 TYR cc_start: 0.8464 (OUTLIER) cc_final: 0.7779 (t80) REVERT: E 132 LYS cc_start: 0.7897 (mttm) cc_final: 0.7645 (mtmp) REVERT: E 135 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7165 (ptp-170) REVERT: E 206 LYS cc_start: 0.8103 (mtpt) cc_final: 0.7786 (mttm) REVERT: E 210 ASP cc_start: 0.8119 (m-30) cc_final: 0.7899 (m-30) REVERT: E 235 GLN cc_start: 0.8003 (mm110) cc_final: 0.7752 (mt0) REVERT: E 262 MET cc_start: 0.8002 (mpp) cc_final: 0.6857 (tmt) REVERT: E 312 SER cc_start: 0.7985 (OUTLIER) cc_final: 0.7641 (p) REVERT: E 391 MET cc_start: 0.4654 (pmm) cc_final: 0.4281 (pmm) outliers start: 48 outliers final: 14 residues processed: 304 average time/residue: 1.1722 time to fit residues: 392.7939 Evaluate side-chains 299 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 274 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain E residue 135 ARG Chi-restraints excluded: chain E residue 312 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 111 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14425 Z= 0.286 Angle : 0.684 9.323 19590 Z= 0.347 Chirality : 0.045 0.138 2255 Planarity : 0.004 0.040 2420 Dihedral : 5.116 20.633 2190 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.04 % Allowed : 22.31 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.21), residues: 1705 helix: 1.19 (0.23), residues: 560 sheet: -1.36 (0.26), residues: 370 loop : -1.41 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 259 HIS 0.002 0.001 HIS E 217 PHE 0.016 0.002 PHE A 322 TYR 0.015 0.002 TYR B 317 ARG 0.003 0.000 ARG D 212 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 285 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 TYR cc_start: 0.8482 (OUTLIER) cc_final: 0.7743 (t80) REVERT: A 126 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7195 (pm20) REVERT: A 135 ARG cc_start: 0.7855 (ptp-170) cc_final: 0.7425 (ptp-170) REVERT: A 141 ASN cc_start: 0.8181 (m110) cc_final: 0.7888 (m110) REVERT: A 243 MET cc_start: 0.8378 (tpp) cc_final: 0.7671 (mtt) REVERT: A 312 SER cc_start: 0.7951 (OUTLIER) cc_final: 0.7555 (p) REVERT: D 63 SER cc_start: 0.8571 (OUTLIER) cc_final: 0.8200 (p) REVERT: D 75 ARG cc_start: 0.7786 (ttm-80) cc_final: 0.7419 (ttm-80) REVERT: D 94 TYR cc_start: 0.8630 (OUTLIER) cc_final: 0.7723 (t80) REVERT: D 126 GLU cc_start: 0.7325 (mt-10) cc_final: 0.6781 (pm20) REVERT: D 135 ARG cc_start: 0.7751 (ptp-170) cc_final: 0.7411 (ptp-170) REVERT: D 206 LYS cc_start: 0.8287 (mttp) cc_final: 0.7979 (mttp) REVERT: D 262 MET cc_start: 0.7958 (mpp) cc_final: 0.6650 (tmt) REVERT: B 63 SER cc_start: 0.8548 (OUTLIER) cc_final: 0.8164 (p) REVERT: B 126 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7083 (pm20) REVERT: B 189 LYS cc_start: 0.7914 (ptpp) cc_final: 0.7558 (ptpp) REVERT: B 206 LYS cc_start: 0.8341 (mtpt) cc_final: 0.8043 (mttm) REVERT: B 219 ASN cc_start: 0.8209 (OUTLIER) cc_final: 0.7892 (p0) REVERT: B 235 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8155 (mt0) REVERT: B 262 MET cc_start: 0.7833 (mpp) cc_final: 0.6504 (tmt) REVERT: B 312 SER cc_start: 0.7949 (OUTLIER) cc_final: 0.7572 (p) REVERT: B 391 MET cc_start: 0.4398 (pmm) cc_final: 0.3577 (ppp) REVERT: C 32 LYS cc_start: 0.8467 (ttpt) cc_final: 0.8210 (tmtt) REVERT: C 94 TYR cc_start: 0.8324 (OUTLIER) cc_final: 0.7046 (t80) REVERT: C 126 GLU cc_start: 0.7318 (mt-10) cc_final: 0.7011 (pm20) REVERT: C 135 ARG cc_start: 0.7797 (ptp-170) cc_final: 0.7515 (ptp-170) REVERT: C 229 ARG cc_start: 0.8406 (mmt90) cc_final: 0.7907 (mmm-85) REVERT: C 279 MET cc_start: 0.8692 (tpp) cc_final: 0.7073 (mpp) REVERT: C 312 SER cc_start: 0.7941 (OUTLIER) cc_final: 0.7606 (p) REVERT: E 94 TYR cc_start: 0.8547 (OUTLIER) cc_final: 0.7884 (t80) REVERT: E 126 GLU cc_start: 0.7485 (mt-10) cc_final: 0.6987 (pm20) REVERT: E 132 LYS cc_start: 0.7953 (mttm) cc_final: 0.7695 (mtmp) REVERT: E 206 LYS cc_start: 0.8169 (mtpt) cc_final: 0.7822 (mttm) REVERT: E 210 ASP cc_start: 0.8200 (m-30) cc_final: 0.7873 (m-30) REVERT: E 235 GLN cc_start: 0.8084 (mm110) cc_final: 0.7795 (mt0) REVERT: E 262 MET cc_start: 0.8027 (mpp) cc_final: 0.6839 (tmt) REVERT: E 312 SER cc_start: 0.7990 (OUTLIER) cc_final: 0.7641 (p) REVERT: E 391 MET cc_start: 0.4762 (pmm) cc_final: 0.3749 (ppp) outliers start: 46 outliers final: 19 residues processed: 302 average time/residue: 1.1460 time to fit residues: 380.7785 Evaluate side-chains 306 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 275 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 312 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 3.9990 chunk 143 optimal weight: 0.0870 chunk 152 optimal weight: 0.9980 chunk 91 optimal weight: 0.3980 chunk 66 optimal weight: 0.0050 chunk 119 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 overall best weight: 0.4974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14425 Z= 0.193 Angle : 0.659 9.609 19590 Z= 0.333 Chirality : 0.044 0.142 2255 Planarity : 0.004 0.039 2420 Dihedral : 4.751 18.199 2190 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.78 % Allowed : 23.43 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.20), residues: 1705 helix: 1.25 (0.23), residues: 560 sheet: -1.24 (0.25), residues: 370 loop : -1.41 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 186 HIS 0.002 0.001 HIS C 231 PHE 0.017 0.001 PHE A 322 TYR 0.014 0.001 TYR E 317 ARG 0.004 0.000 ARG E 135 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 285 time to evaluate : 1.526 Fit side-chains revert: symmetry clash REVERT: A 94 TYR cc_start: 0.8308 (OUTLIER) cc_final: 0.6968 (t80) REVERT: A 126 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7134 (pm20) REVERT: A 135 ARG cc_start: 0.7768 (ptp-170) cc_final: 0.7241 (ptp-170) REVERT: A 141 ASN cc_start: 0.8135 (m110) cc_final: 0.7856 (m110) REVERT: A 243 MET cc_start: 0.8347 (tpp) cc_final: 0.7695 (mtt) REVERT: A 312 SER cc_start: 0.7916 (m) cc_final: 0.7500 (p) REVERT: D 63 SER cc_start: 0.8571 (OUTLIER) cc_final: 0.8216 (p) REVERT: D 71 THR cc_start: 0.8898 (p) cc_final: 0.8573 (p) REVERT: D 75 ARG cc_start: 0.7751 (ttm-80) cc_final: 0.7382 (ttm-80) REVERT: D 94 TYR cc_start: 0.8581 (OUTLIER) cc_final: 0.7500 (t80) REVERT: D 135 ARG cc_start: 0.7772 (ptp-170) cc_final: 0.7415 (ptp-170) REVERT: D 206 LYS cc_start: 0.8242 (mttp) cc_final: 0.7986 (mttm) REVERT: D 262 MET cc_start: 0.7955 (mpp) cc_final: 0.6714 (tmt) REVERT: B 126 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6999 (pm20) REVERT: B 206 LYS cc_start: 0.8299 (mtpt) cc_final: 0.7994 (mttm) REVERT: B 219 ASN cc_start: 0.8142 (OUTLIER) cc_final: 0.7831 (p0) REVERT: B 235 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8117 (mt0) REVERT: B 262 MET cc_start: 0.7852 (mpp) cc_final: 0.6611 (tmt) REVERT: B 391 MET cc_start: 0.4209 (pmm) cc_final: 0.3340 (ppp) REVERT: C 72 MET cc_start: 0.9075 (OUTLIER) cc_final: 0.8708 (mmt) REVERT: C 94 TYR cc_start: 0.8204 (OUTLIER) cc_final: 0.6857 (t80) REVERT: C 126 GLU cc_start: 0.7265 (mt-10) cc_final: 0.6864 (pm20) REVERT: C 135 ARG cc_start: 0.7741 (ptp-170) cc_final: 0.7484 (ptp-170) REVERT: C 229 ARG cc_start: 0.8332 (mmt90) cc_final: 0.7991 (mmm-85) REVERT: C 279 MET cc_start: 0.8702 (tpp) cc_final: 0.7135 (mpp) REVERT: C 312 SER cc_start: 0.7913 (m) cc_final: 0.7575 (p) REVERT: C 391 MET cc_start: 0.5393 (pmm) cc_final: 0.4668 (ppp) REVERT: E 94 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.7648 (t80) REVERT: E 120 LYS cc_start: 0.8429 (tttp) cc_final: 0.8127 (tttt) REVERT: E 126 GLU cc_start: 0.7422 (mt-10) cc_final: 0.6878 (pm20) REVERT: E 132 LYS cc_start: 0.7903 (mttm) cc_final: 0.7654 (mtmp) REVERT: E 135 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7251 (ptp-170) REVERT: E 138 LYS cc_start: 0.8973 (ttpp) cc_final: 0.8603 (tttt) REVERT: E 171 GLN cc_start: 0.8624 (mt0) cc_final: 0.8342 (mt0) REVERT: E 206 LYS cc_start: 0.8140 (mtpt) cc_final: 0.7894 (mttm) REVERT: E 210 ASP cc_start: 0.8122 (m-30) cc_final: 0.7879 (m-30) REVERT: E 235 GLN cc_start: 0.8015 (mm110) cc_final: 0.7753 (mt0) REVERT: E 262 MET cc_start: 0.8032 (mpp) cc_final: 0.6915 (tmt) REVERT: E 312 SER cc_start: 0.7915 (m) cc_final: 0.7562 (p) REVERT: E 391 MET cc_start: 0.4745 (pmm) cc_final: 0.3750 (ppp) outliers start: 27 outliers final: 14 residues processed: 295 average time/residue: 1.1075 time to fit residues: 360.4328 Evaluate side-chains 303 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 280 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain E residue 135 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.3980 chunk 76 optimal weight: 0.0670 chunk 112 optimal weight: 3.9990 chunk 169 optimal weight: 0.6980 chunk 155 optimal weight: 0.6980 chunk 134 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 141 ASN C 321 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14425 Z= 0.192 Angle : 0.654 9.423 19590 Z= 0.329 Chirality : 0.044 0.138 2255 Planarity : 0.004 0.040 2420 Dihedral : 4.619 18.288 2190 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.52 % Allowed : 24.29 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.20), residues: 1705 helix: 1.35 (0.23), residues: 570 sheet: -1.18 (0.25), residues: 370 loop : -1.66 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 186 HIS 0.001 0.001 HIS E 217 PHE 0.017 0.001 PHE A 322 TYR 0.014 0.001 TYR A 317 ARG 0.006 0.000 ARG D 392 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 280 time to evaluate : 1.475 Fit side-chains revert: symmetry clash REVERT: A 63 SER cc_start: 0.8527 (OUTLIER) cc_final: 0.8182 (p) REVERT: A 94 TYR cc_start: 0.8277 (OUTLIER) cc_final: 0.7025 (t80) REVERT: A 126 GLU cc_start: 0.7368 (mt-10) cc_final: 0.7113 (pm20) REVERT: A 135 ARG cc_start: 0.7748 (ptp-170) cc_final: 0.7210 (ptp-170) REVERT: A 141 ASN cc_start: 0.8113 (m110) cc_final: 0.7818 (m110) REVERT: A 156 MET cc_start: 0.9050 (mmt) cc_final: 0.8440 (mmt) REVERT: A 243 MET cc_start: 0.8350 (tpp) cc_final: 0.7700 (mtt) REVERT: D 63 SER cc_start: 0.8561 (OUTLIER) cc_final: 0.8222 (p) REVERT: D 71 THR cc_start: 0.8902 (p) cc_final: 0.8566 (p) REVERT: D 75 ARG cc_start: 0.7745 (ttm-80) cc_final: 0.7367 (ttm-80) REVERT: D 94 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.7426 (t80) REVERT: D 135 ARG cc_start: 0.7736 (ptp-170) cc_final: 0.7408 (ptp-170) REVERT: D 206 LYS cc_start: 0.8226 (mttp) cc_final: 0.7983 (mttm) REVERT: D 262 MET cc_start: 0.8036 (mpp) cc_final: 0.6749 (tmt) REVERT: B 63 SER cc_start: 0.8617 (OUTLIER) cc_final: 0.8269 (p) REVERT: B 94 TYR cc_start: 0.8277 (OUTLIER) cc_final: 0.7829 (t80) REVERT: B 126 GLU cc_start: 0.7344 (mt-10) cc_final: 0.6937 (pm20) REVERT: B 206 LYS cc_start: 0.8239 (mtpt) cc_final: 0.7895 (mttp) REVERT: B 219 ASN cc_start: 0.8136 (OUTLIER) cc_final: 0.7820 (p0) REVERT: B 235 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8099 (mt0) REVERT: B 262 MET cc_start: 0.7870 (mpp) cc_final: 0.6609 (tmt) REVERT: B 391 MET cc_start: 0.4206 (pmm) cc_final: 0.3268 (ppp) REVERT: C 63 SER cc_start: 0.8624 (OUTLIER) cc_final: 0.8311 (p) REVERT: C 72 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8700 (mmt) REVERT: C 94 TYR cc_start: 0.8101 (OUTLIER) cc_final: 0.6724 (t80) REVERT: C 126 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6817 (pm20) REVERT: C 135 ARG cc_start: 0.7736 (ptp-170) cc_final: 0.7501 (ptp-170) REVERT: C 229 ARG cc_start: 0.8343 (mmt90) cc_final: 0.8027 (mmm-85) REVERT: C 279 MET cc_start: 0.8696 (tpp) cc_final: 0.7124 (mpp) REVERT: C 312 SER cc_start: 0.7953 (m) cc_final: 0.7608 (p) REVERT: C 391 MET cc_start: 0.5566 (pmm) cc_final: 0.4741 (ppp) REVERT: E 63 SER cc_start: 0.8530 (OUTLIER) cc_final: 0.8195 (p) REVERT: E 94 TYR cc_start: 0.8368 (OUTLIER) cc_final: 0.7533 (t80) REVERT: E 120 LYS cc_start: 0.8422 (tttp) cc_final: 0.8123 (tttt) REVERT: E 126 GLU cc_start: 0.7439 (mt-10) cc_final: 0.6907 (pm20) REVERT: E 132 LYS cc_start: 0.7910 (mttm) cc_final: 0.7670 (mtmp) REVERT: E 138 LYS cc_start: 0.8974 (ttpp) cc_final: 0.8612 (tttt) REVERT: E 171 GLN cc_start: 0.8650 (mt0) cc_final: 0.8372 (mt0) REVERT: E 206 LYS cc_start: 0.8131 (mtpt) cc_final: 0.7888 (mttm) REVERT: E 210 ASP cc_start: 0.8143 (m-30) cc_final: 0.7911 (m-30) REVERT: E 235 GLN cc_start: 0.7976 (mm110) cc_final: 0.7747 (mt0) REVERT: E 243 MET cc_start: 0.8203 (mtt) cc_final: 0.7969 (mtt) REVERT: E 262 MET cc_start: 0.8123 (mpp) cc_final: 0.6952 (tmt) REVERT: E 312 SER cc_start: 0.7925 (m) cc_final: 0.7559 (p) REVERT: E 391 MET cc_start: 0.4699 (pmm) cc_final: 0.3725 (ppp) outliers start: 23 outliers final: 6 residues processed: 288 average time/residue: 1.1011 time to fit residues: 350.2741 Evaluate side-chains 291 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 272 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 94 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 135 optimal weight: 0.0980 chunk 56 optimal weight: 0.9980 chunk 138 optimal weight: 0.0060 chunk 17 optimal weight: 0.0870 chunk 24 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.4374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.166936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.117127 restraints weight = 16461.152| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.92 r_work: 0.3152 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14425 Z= 0.177 Angle : 0.640 9.209 19590 Z= 0.321 Chirality : 0.044 0.136 2255 Planarity : 0.004 0.038 2420 Dihedral : 4.506 17.679 2190 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.52 % Allowed : 24.49 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.20), residues: 1705 helix: 1.49 (0.23), residues: 570 sheet: -1.10 (0.25), residues: 370 loop : -1.65 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 186 HIS 0.001 0.001 HIS A 231 PHE 0.018 0.001 PHE A 322 TYR 0.014 0.001 TYR A 317 ARG 0.002 0.000 ARG E 212 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6810.23 seconds wall clock time: 121 minutes 9.77 seconds (7269.77 seconds total)