Starting phenix.real_space_refine on Wed Mar 4 15:03:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6plx_20379/03_2026/6plx_20379.cif Found real_map, /net/cci-nas-00/data/ceres_data/6plx_20379/03_2026/6plx_20379.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6plx_20379/03_2026/6plx_20379.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6plx_20379/03_2026/6plx_20379.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6plx_20379/03_2026/6plx_20379.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6plx_20379/03_2026/6plx_20379.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.061 sd= 2.930 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 100 5.16 5 C 9270 2.51 5 N 2290 2.21 5 O 2580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14240 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" 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: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E, G, H, I, J Time building chain proxies: 2.42, per 1000 atoms: 0.17 Number of scatterers: 14240 At special positions: 0 Unit cell: (107.813, 105.344, 136.618, 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 100 16.00 O 2580 8.00 N 2290 7.00 C 9270 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 168 " distance=2.04 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.04 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 168 " distance=2.04 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 168 " distance=2.04 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 168 " distance=2.04 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 168 " distance=2.04 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.04 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.04 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.04 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 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 B 54 " " NAG H 1 " - " ASN C 54 " " NAG I 1 " - " ASN D 54 " " NAG J 1 " - " ASN E 54 " Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 479.5 milliseconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 25 sheets defined 37.6% alpha, 40.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 25 through 35 removed outlier: 3.530A pdb=" N LYS A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 40 removed outlier: 4.010A pdb=" N GLY A 39 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N TYR A 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 36 through 40' Processing helix chain 'A' and resid 87 through 90 Processing helix chain 'A' and resid 102 through 106 removed outlier: 3.619A pdb=" N LEU A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 163 Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 245 through 254 removed outlier: 3.810A pdb=" N ILE A 250 " --> pdb=" O PRO A 246 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 285 removed outlier: 3.540A pdb=" N VAL A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N VAL A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 299 through 325 removed outlier: 4.304A pdb=" N VAL A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 402 removed outlier: 3.587A pdb=" N LYS A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU A 394 " --> pdb=" O GLU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.783A pdb=" N PHE A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 425 removed outlier: 3.924A pdb=" N TRP A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 35 removed outlier: 3.530A pdb=" N LYS B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 removed outlier: 4.009A pdb=" N GLY B 39 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N TYR B 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 36 through 40' Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 102 through 106 removed outlier: 3.619A pdb=" N LEU B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 163 Processing helix chain 'B' and resid 238 through 243 Processing helix chain 'B' and resid 245 through 254 removed outlier: 3.810A pdb=" N ILE B 250 " --> pdb=" O PRO B 246 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE B 252 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 285 removed outlier: 3.540A pdb=" N VAL B 269 " --> pdb=" O ALA B 265 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR B 280 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 299 through 325 removed outlier: 4.305A pdb=" N VAL B 305 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 310 " --> pdb=" O CYS B 306 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE B 322 " --> pdb=" O ALA B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 402 removed outlier: 3.588A pdb=" N LYS B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU B 394 " --> pdb=" O GLU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.784A pdb=" N PHE B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 425 removed outlier: 3.924A pdb=" N TRP B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR B 424 " --> pdb=" O PHE B 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 35 removed outlier: 3.531A pdb=" N LYS C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 40 removed outlier: 4.009A pdb=" N GLY C 39 " --> pdb=" O LYS C 36 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR C 40 " --> pdb=" O VAL C 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 36 through 40' Processing helix chain 'C' and resid 87 through 90 Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.619A pdb=" N LEU C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 163 Processing helix chain 'C' and resid 238 through 243 Processing helix chain 'C' and resid 245 through 254 removed outlier: 3.809A pdb=" N ILE C 250 " --> pdb=" O PRO C 246 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 285 removed outlier: 3.540A pdb=" N VAL C 269 " --> pdb=" O ALA C 265 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N VAL C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR C 280 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 299 through 325 removed outlier: 4.305A pdb=" N VAL C 305 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C 310 " --> pdb=" O CYS C 306 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE C 322 " --> pdb=" O ALA C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 402 removed outlier: 3.588A pdb=" N LYS C 393 " --> pdb=" O GLU C 389 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU C 394 " --> pdb=" O GLU C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.783A pdb=" N PHE C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 425 removed outlier: 3.923A pdb=" N TRP C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 35 removed outlier: 3.531A pdb=" N LYS D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 40 removed outlier: 4.008A pdb=" N GLY D 39 " --> pdb=" O LYS D 36 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N TYR D 40 " --> pdb=" O VAL D 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 36 through 40' Processing helix chain 'D' and resid 87 through 90 Processing helix chain 'D' and resid 102 through 106 removed outlier: 3.619A pdb=" N LEU D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 163 Processing helix chain 'D' and resid 238 through 243 Processing helix chain 'D' and resid 245 through 254 removed outlier: 3.809A pdb=" N ILE D 250 " --> pdb=" O PRO D 246 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 285 removed outlier: 3.539A pdb=" N VAL D 269 " --> pdb=" O ALA D 265 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL D 276 " --> pdb=" O GLY D 272 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR D 280 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR D 281 " --> pdb=" O LEU D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 299 through 325 removed outlier: 4.303A pdb=" N VAL D 305 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL D 310 " --> pdb=" O CYS D 306 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR D 317 " --> pdb=" O ALA D 313 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 402 removed outlier: 3.588A pdb=" N LYS D 393 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU D 394 " --> pdb=" O GLU D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 removed outlier: 3.783A pdb=" N PHE D 410 " --> pdb=" O SER D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 425 removed outlier: 3.924A pdb=" N TRP D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR D 424 " --> pdb=" O PHE D 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 35 removed outlier: 3.531A pdb=" N LYS E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 40 removed outlier: 4.009A pdb=" N GLY E 39 " --> pdb=" O LYS E 36 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N TYR E 40 " --> pdb=" O VAL E 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 36 through 40' Processing helix chain 'E' and resid 87 through 90 Processing helix chain 'E' and resid 102 through 106 removed outlier: 3.619A pdb=" N LEU E 106 " --> pdb=" O PRO E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 163 Processing helix chain 'E' and resid 238 through 243 Processing helix chain 'E' and resid 245 through 254 removed outlier: 3.809A pdb=" N ILE E 250 " --> pdb=" O PRO E 246 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE E 252 " --> pdb=" O LEU E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 285 removed outlier: 3.540A pdb=" N VAL E 269 " --> pdb=" O ALA E 265 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL E 276 " --> pdb=" O GLY E 272 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR E 280 " --> pdb=" O VAL E 276 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR E 281 " --> pdb=" O LEU E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 299 through 325 removed outlier: 4.305A pdb=" N VAL E 305 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU E 308 " --> pdb=" O ALA E 304 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL E 310 " --> pdb=" O CYS E 306 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR E 317 " --> pdb=" O ALA E 313 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE E 322 " --> pdb=" O ALA E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 402 removed outlier: 3.588A pdb=" N LYS E 393 " --> pdb=" O GLU E 389 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU E 394 " --> pdb=" O GLU E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 removed outlier: 3.784A pdb=" N PHE E 410 " --> pdb=" O SER E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 425 removed outlier: 3.924A pdb=" N TRP E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR E 424 " --> pdb=" O PHE E 420 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.661A pdb=" N ASN A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 124 removed outlier: 6.346A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N GLN A 193 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE A 59 " --> pdb=" O GLN A 193 " (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 114 through 116 Processing sheet with id=AA5, first strand: chain 'A' and resid 216 through 217 Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.661A pdb=" N ASN B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 122 through 124 removed outlier: 6.345A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N GLN B 193 " --> pdb=" O CYS B 57 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE B 59 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 114 through 116 Processing sheet with id=AA9, first strand: chain 'B' and resid 114 through 116 Processing sheet with id=AB1, first strand: chain 'B' and resid 216 through 217 Processing sheet with id=AB2, first strand: chain 'C' and resid 98 through 100 removed outlier: 4.660A pdb=" N ASN C 141 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 122 through 124 removed outlier: 6.346A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N GLN C 193 " --> pdb=" O CYS C 57 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE C 59 " --> pdb=" O GLN C 193 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 114 through 116 Processing sheet with id=AB5, first strand: chain 'C' and resid 114 through 116 Processing sheet with id=AB6, first strand: chain 'C' and resid 216 through 217 Processing sheet with id=AB7, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.661A pdb=" N ASN D 141 " --> pdb=" O SER D 137 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 122 through 124 removed outlier: 6.346A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N GLN D 193 " --> pdb=" O CYS D 57 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE D 59 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 114 through 116 Processing sheet with id=AC1, first strand: chain 'D' and resid 114 through 116 Processing sheet with id=AC2, first strand: chain 'D' and resid 216 through 217 Processing sheet with id=AC3, first strand: chain 'E' and resid 98 through 100 removed outlier: 4.661A pdb=" N ASN E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 122 through 124 removed outlier: 6.345A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N GLN E 193 " --> pdb=" O CYS E 57 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE E 59 " --> pdb=" O GLN E 193 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 114 through 116 Processing sheet with id=AC6, first strand: chain 'E' and resid 114 through 116 Processing sheet with id=AC7, first strand: chain 'E' and resid 216 through 217 695 hydrogen bonds defined for protein. 2010 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.32 Time building geometry restraints manager: 1.32 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: 4296 1.34 - 1.46: 3614 1.46 - 1.58: 6505 1.58 - 1.70: 0 1.70 - 1.83: 170 Bond restraints: 14585 Sorted by residual: bond pdb=" CB ARG C 234 " pdb=" CG ARG C 234 " ideal model delta sigma weight residual 1.520 1.458 0.062 3.00e-02 1.11e+03 4.22e+00 bond pdb=" CB ARG A 234 " pdb=" CG ARG A 234 " ideal model delta sigma weight residual 1.520 1.459 0.061 3.00e-02 1.11e+03 4.20e+00 bond pdb=" CB ARG B 234 " pdb=" CG ARG B 234 " ideal model delta sigma weight residual 1.520 1.459 0.061 3.00e-02 1.11e+03 4.19e+00 bond pdb=" CB ARG D 234 " pdb=" CG ARG D 234 " ideal model delta sigma weight residual 1.520 1.459 0.061 3.00e-02 1.11e+03 4.18e+00 bond pdb=" CB ARG E 234 " pdb=" CG ARG E 234 " ideal model delta sigma weight residual 1.520 1.459 0.061 3.00e-02 1.11e+03 4.11e+00 ... (remaining 14580 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 19044 2.59 - 5.18: 571 5.18 - 7.77: 140 7.77 - 10.36: 15 10.36 - 12.96: 5 Bond angle restraints: 19775 Sorted by residual: angle pdb=" C VAL C 127 " pdb=" N THR C 128 " pdb=" CA THR C 128 " ideal model delta sigma weight residual 121.54 134.50 -12.96 1.91e+00 2.74e-01 4.60e+01 angle pdb=" C VAL D 127 " pdb=" N THR D 128 " pdb=" CA THR D 128 " ideal model delta sigma weight residual 121.54 134.46 -12.92 1.91e+00 2.74e-01 4.57e+01 angle pdb=" C VAL E 127 " pdb=" N THR E 128 " pdb=" CA THR E 128 " ideal model delta sigma weight residual 121.54 134.44 -12.90 1.91e+00 2.74e-01 4.56e+01 angle pdb=" C VAL A 127 " pdb=" N THR A 128 " pdb=" CA THR A 128 " ideal model delta sigma weight residual 121.54 134.44 -12.90 1.91e+00 2.74e-01 4.56e+01 angle pdb=" C VAL B 127 " pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta sigma weight residual 121.54 134.42 -12.88 1.91e+00 2.74e-01 4.54e+01 ... (remaining 19770 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.20: 8637 21.20 - 42.40: 218 42.40 - 63.61: 20 63.61 - 84.81: 35 84.81 - 106.01: 20 Dihedral angle restraints: 8930 sinusoidal: 3815 harmonic: 5115 Sorted by residual: dihedral pdb=" CA ASN B 160 " pdb=" C ASN B 160 " pdb=" N PHE B 161 " pdb=" CA PHE B 161 " ideal model delta harmonic sigma weight residual -180.00 -152.19 -27.81 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ASN D 160 " pdb=" C ASN D 160 " pdb=" N PHE D 161 " pdb=" CA PHE D 161 " ideal model delta harmonic sigma weight residual -180.00 -152.24 -27.76 0 5.00e+00 4.00e-02 3.08e+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 -152.25 -27.75 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 8927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1580 0.059 - 0.118: 556 0.118 - 0.178: 99 0.178 - 0.237: 15 0.237 - 0.296: 15 Chirality restraints: 2265 Sorted by residual: chirality pdb=" C5 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C6 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.19e+00 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 -2.57 0.29 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 2262 not shown) Planarity restraints: 2455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 102 " -0.042 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO B 103 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 103 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 103 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 102 " 0.042 5.00e-02 4.00e+02 6.30e-02 6.36e+00 pdb=" N PRO E 103 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO E 103 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 103 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 102 " 0.042 5.00e-02 4.00e+02 6.29e-02 6.33e+00 pdb=" N PRO D 103 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.035 5.00e-02 4.00e+02 ... (remaining 2452 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 4509 2.83 - 3.35: 12052 3.35 - 3.87: 22648 3.87 - 4.38: 27134 4.38 - 4.90: 46038 Nonbonded interactions: 112381 Sorted by model distance: nonbonded pdb=" OE2 GLU D 69 " pdb=" NH2 ARG D 234 " model vdw 2.316 3.120 nonbonded pdb=" OE2 GLU B 69 " pdb=" NH2 ARG B 234 " model vdw 2.316 3.120 nonbonded pdb=" OE2 GLU A 69 " pdb=" NH2 ARG A 234 " model vdw 2.317 3.120 nonbonded pdb=" OE2 GLU C 69 " pdb=" NH2 ARG C 234 " model vdw 2.317 3.120 nonbonded pdb=" OE2 GLU E 69 " pdb=" NH2 ARG E 234 " model vdw 2.317 3.120 ... (remaining 112376 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: 0.04 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: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.440 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 : 0.011 0.076 14610 Z= 0.435 Angle : 1.160 12.956 19840 Z= 0.584 Chirality : 0.065 0.296 2265 Planarity : 0.008 0.063 2450 Dihedral : 13.133 106.011 5580 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.10 (0.15), residues: 1710 helix: -4.69 (0.08), residues: 585 sheet: -2.54 (0.22), residues: 395 loop : -2.48 (0.18), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG A 135 TYR 0.017 0.003 TYR E 144 PHE 0.023 0.003 PHE B 258 TRP 0.017 0.003 TRP C 302 HIS 0.003 0.002 HIS D 231 Details of bonding type rmsd covalent geometry : bond 0.01052 (14585) covalent geometry : angle 1.13447 (19775) SS BOND : bond 0.01012 ( 10) SS BOND : angle 3.69271 ( 20) hydrogen bonds : bond 0.26068 ( 550) hydrogen bonds : angle 10.55163 ( 2010) link_BETA1-4 : bond 0.00566 ( 10) link_BETA1-4 : angle 5.67722 ( 30) link_NAG-ASN : bond 0.00164 ( 5) link_NAG-ASN : angle 1.09070 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 469 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8376 (ptt) cc_final: 0.7773 (ptm) REVERT: A 102 ASP cc_start: 0.8147 (t0) cc_final: 0.7921 (t0) REVERT: A 104 SER cc_start: 0.9212 (t) cc_final: 0.8978 (p) REVERT: A 126 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7570 (pm20) REVERT: A 130 ASP cc_start: 0.8072 (m-30) cc_final: 0.7712 (m-30) REVERT: A 227 GLU cc_start: 0.8578 (pt0) cc_final: 0.8315 (pt0) REVERT: A 233 GLU cc_start: 0.7814 (tt0) cc_final: 0.7211 (mt-10) REVERT: A 316 GLU cc_start: 0.7248 (tm-30) cc_final: 0.6569 (tm-30) REVERT: A 391 MET cc_start: 0.7013 (mmm) cc_final: 0.6790 (mmm) REVERT: A 398 ARG cc_start: 0.7801 (ttm170) cc_final: 0.7081 (tpp-160) REVERT: B 24 MET cc_start: 0.8215 (ptt) cc_final: 0.7351 (ptm) REVERT: B 157 ASP cc_start: 0.8535 (t0) cc_final: 0.8320 (t70) REVERT: B 181 ASP cc_start: 0.8211 (m-30) cc_final: 0.7906 (m-30) REVERT: B 311 PHE cc_start: 0.7333 (t80) cc_final: 0.7126 (t80) REVERT: B 316 GLU cc_start: 0.7142 (tm-30) cc_final: 0.6557 (tm-30) REVERT: B 391 MET cc_start: 0.6833 (mmm) cc_final: 0.6607 (mmm) REVERT: B 398 ARG cc_start: 0.7892 (ttm170) cc_final: 0.7319 (tpp-160) REVERT: C 24 MET cc_start: 0.8287 (ptt) cc_final: 0.7417 (ptm) REVERT: C 96 ASP cc_start: 0.8465 (m-30) cc_final: 0.8153 (m-30) REVERT: C 138 LYS cc_start: 0.8822 (mtpt) cc_final: 0.8429 (mttt) REVERT: C 233 GLU cc_start: 0.7786 (tt0) cc_final: 0.7571 (tt0) REVERT: C 311 PHE cc_start: 0.7324 (t80) cc_final: 0.7082 (t80) REVERT: C 316 GLU cc_start: 0.7333 (tm-30) cc_final: 0.6980 (tm-30) REVERT: C 398 ARG cc_start: 0.7868 (ttm170) cc_final: 0.7237 (tpp-160) REVERT: D 24 MET cc_start: 0.8410 (ptt) cc_final: 0.7613 (ptt) REVERT: D 157 ASP cc_start: 0.8537 (t0) cc_final: 0.8286 (t70) REVERT: D 311 PHE cc_start: 0.7408 (t80) cc_final: 0.7053 (t80) REVERT: D 316 GLU cc_start: 0.7091 (tm-30) cc_final: 0.6740 (tm-30) REVERT: D 398 ARG cc_start: 0.7887 (ttm170) cc_final: 0.7259 (tpp-160) REVERT: E 24 MET cc_start: 0.8424 (ptt) cc_final: 0.7916 (ptt) REVERT: E 72 MET cc_start: 0.8890 (mtm) cc_final: 0.8588 (mtm) REVERT: E 181 ASP cc_start: 0.8267 (m-30) cc_final: 0.8009 (m-30) REVERT: E 208 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7887 (pp20) REVERT: E 233 GLU cc_start: 0.7751 (tt0) cc_final: 0.7118 (mt-10) REVERT: E 311 PHE cc_start: 0.7275 (t80) cc_final: 0.7033 (t80) REVERT: E 316 GLU cc_start: 0.7359 (tm-30) cc_final: 0.6862 (tm-30) REVERT: E 398 ARG cc_start: 0.7794 (ttm170) cc_final: 0.7101 (tpp-160) outliers start: 0 outliers final: 1 residues processed: 469 average time/residue: 0.5095 time to fit residues: 264.0677 Evaluate side-chains 288 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 287 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 219 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.0270 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 141 ASN A 231 HIS B 62 ASN B 82 GLN B 131 ASN B 141 ASN B 180 ASN B 231 HIS C 62 ASN C 82 GLN C 131 ASN C 141 ASN C 231 HIS D 62 ASN D 82 GLN D 131 ASN D 141 ASN D 180 ASN D 231 HIS E 62 ASN E 82 GLN E 141 ASN E 180 ASN E 231 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.147838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.108987 restraints weight = 16931.597| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 3.65 r_work: 0.3093 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14610 Z= 0.146 Angle : 0.745 8.935 19840 Z= 0.371 Chirality : 0.048 0.168 2265 Planarity : 0.005 0.047 2450 Dihedral : 9.657 58.884 2202 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.68 % Allowed : 13.81 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.72 (0.16), residues: 1710 helix: -3.21 (0.15), residues: 590 sheet: -1.52 (0.27), residues: 340 loop : -2.17 (0.18), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 229 TYR 0.008 0.001 TYR E 218 PHE 0.014 0.001 PHE E 414 TRP 0.013 0.001 TRP D 84 HIS 0.003 0.001 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00329 (14585) covalent geometry : angle 0.72535 (19775) SS BOND : bond 0.00580 ( 10) SS BOND : angle 1.86682 ( 20) hydrogen bonds : bond 0.04497 ( 550) hydrogen bonds : angle 5.99118 ( 2010) link_BETA1-4 : bond 0.00445 ( 10) link_BETA1-4 : angle 4.23019 ( 30) link_NAG-ASN : bond 0.00173 ( 5) link_NAG-ASN : angle 0.49660 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 314 time to evaluate : 0.473 Fit side-chains REVERT: A 104 SER cc_start: 0.9132 (t) cc_final: 0.8891 (p) REVERT: A 126 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7339 (pm20) REVERT: A 208 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8251 (tp30) REVERT: A 233 GLU cc_start: 0.7384 (tt0) cc_final: 0.6834 (mt-10) REVERT: A 243 MET cc_start: 0.8260 (mtm) cc_final: 0.7911 (ptp) REVERT: A 316 GLU cc_start: 0.6900 (tm-30) cc_final: 0.6336 (tm-30) REVERT: A 398 ARG cc_start: 0.7571 (ttm170) cc_final: 0.6913 (tpp-160) REVERT: A 419 ILE cc_start: 0.7947 (mm) cc_final: 0.7724 (mt) REVERT: B 24 MET cc_start: 0.7309 (ptt) cc_final: 0.6901 (ptt) REVERT: B 62 ASN cc_start: 0.8737 (m-40) cc_final: 0.8513 (m110) REVERT: B 126 GLU cc_start: 0.7615 (pm20) cc_final: 0.6791 (mt-10) REVERT: B 138 LYS cc_start: 0.8443 (mtpt) cc_final: 0.8220 (mttm) REVERT: B 157 ASP cc_start: 0.8417 (t0) cc_final: 0.8144 (t0) REVERT: B 208 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8303 (tp30) REVERT: B 233 GLU cc_start: 0.7186 (tt0) cc_final: 0.6595 (mt-10) REVERT: B 243 MET cc_start: 0.8078 (ptp) cc_final: 0.7785 (ptp) REVERT: B 316 GLU cc_start: 0.6786 (tm-30) cc_final: 0.6337 (tm-30) REVERT: B 398 ARG cc_start: 0.7671 (ttm170) cc_final: 0.7090 (tpp-160) REVERT: C 24 MET cc_start: 0.7422 (ptt) cc_final: 0.6963 (ptm) REVERT: C 62 ASN cc_start: 0.8706 (m-40) cc_final: 0.8452 (m110) REVERT: C 126 GLU cc_start: 0.7676 (pm20) cc_final: 0.6944 (mt-10) REVERT: C 130 ASP cc_start: 0.8205 (m-30) cc_final: 0.7960 (m-30) REVERT: C 138 LYS cc_start: 0.8406 (mtpt) cc_final: 0.8184 (ttmm) REVERT: C 227 GLU cc_start: 0.8769 (pt0) cc_final: 0.8442 (pt0) REVERT: C 233 GLU cc_start: 0.7564 (tt0) cc_final: 0.7018 (mt-10) REVERT: C 243 MET cc_start: 0.8069 (ptp) cc_final: 0.7824 (ptp) REVERT: C 316 GLU cc_start: 0.7041 (tm-30) cc_final: 0.6715 (tm-30) REVERT: C 398 ARG cc_start: 0.7731 (ttm170) cc_final: 0.7124 (tpp-160) REVERT: D 24 MET cc_start: 0.7485 (ptt) cc_final: 0.7068 (ptt) REVERT: D 157 ASP cc_start: 0.8538 (t0) cc_final: 0.8228 (t70) REVERT: D 179 MET cc_start: 0.8504 (tpt) cc_final: 0.8191 (tpt) REVERT: D 207 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8597 (tt0) REVERT: D 235 GLN cc_start: 0.8235 (mm-40) cc_final: 0.7979 (mm-40) REVERT: D 398 ARG cc_start: 0.7707 (ttm170) cc_final: 0.7032 (tpp-160) REVERT: E 24 MET cc_start: 0.7567 (ptt) cc_final: 0.7310 (ptt) REVERT: E 72 MET cc_start: 0.8839 (mtm) cc_final: 0.8469 (mtm) REVERT: E 102 ASP cc_start: 0.7956 (t0) cc_final: 0.7575 (t70) REVERT: E 173 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7978 (mt-10) REVERT: E 208 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8281 (tp30) REVERT: E 227 GLU cc_start: 0.8498 (pt0) cc_final: 0.8269 (pt0) REVERT: E 233 GLU cc_start: 0.7442 (tt0) cc_final: 0.6854 (mt-10) REVERT: E 316 GLU cc_start: 0.6989 (tm-30) cc_final: 0.6593 (tm-30) REVERT: E 398 ARG cc_start: 0.7585 (ttm170) cc_final: 0.6991 (tpp-160) outliers start: 57 outliers final: 25 residues processed: 343 average time/residue: 0.4934 time to fit residues: 187.5739 Evaluate side-chains 310 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 285 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 420 PHE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 420 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 140 optimal weight: 0.2980 chunk 59 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 44 optimal weight: 0.0470 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN D 62 ASN E 58 ASN E 62 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.145843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.108064 restraints weight = 16966.312| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 3.57 r_work: 0.3079 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14610 Z= 0.141 Angle : 0.676 7.093 19840 Z= 0.334 Chirality : 0.047 0.166 2265 Planarity : 0.004 0.039 2450 Dihedral : 6.909 34.227 2200 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.48 % Allowed : 17.03 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.18), residues: 1710 helix: -2.21 (0.19), residues: 590 sheet: -0.68 (0.30), residues: 320 loop : -1.92 (0.19), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 229 TYR 0.021 0.002 TYR C 238 PHE 0.020 0.001 PHE D 322 TRP 0.010 0.001 TRP A 84 HIS 0.001 0.000 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00332 (14585) covalent geometry : angle 0.65372 (19775) SS BOND : bond 0.00606 ( 10) SS BOND : angle 1.91119 ( 20) hydrogen bonds : bond 0.03825 ( 550) hydrogen bonds : angle 5.20706 ( 2010) link_BETA1-4 : bond 0.00318 ( 10) link_BETA1-4 : angle 4.26723 ( 30) link_NAG-ASN : bond 0.00102 ( 5) link_NAG-ASN : angle 0.43296 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 310 time to evaluate : 0.513 Fit side-chains REVERT: A 24 MET cc_start: 0.6793 (ptm) cc_final: 0.6470 (ptm) REVERT: A 102 ASP cc_start: 0.8215 (t0) cc_final: 0.7891 (t70) REVERT: A 126 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7363 (pm20) REVERT: A 207 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8504 (tt0) REVERT: A 233 GLU cc_start: 0.7286 (tt0) cc_final: 0.6745 (mt-10) REVERT: A 235 GLN cc_start: 0.8135 (mm110) cc_final: 0.7685 (mm-40) REVERT: A 261 ASN cc_start: 0.6919 (p0) cc_final: 0.6597 (t0) REVERT: A 312 SER cc_start: 0.8260 (m) cc_final: 0.7792 (p) REVERT: A 316 GLU cc_start: 0.6931 (tm-30) cc_final: 0.6468 (tm-30) REVERT: A 398 ARG cc_start: 0.7539 (ttm170) cc_final: 0.6868 (tpp-160) REVERT: B 24 MET cc_start: 0.7275 (ptt) cc_final: 0.7035 (ptt) REVERT: B 126 GLU cc_start: 0.7615 (pm20) cc_final: 0.6778 (mt-10) REVERT: B 208 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8290 (tp30) REVERT: B 233 GLU cc_start: 0.7154 (tt0) cc_final: 0.6554 (mt-10) REVERT: B 243 MET cc_start: 0.7995 (ptp) cc_final: 0.7698 (ptp) REVERT: B 316 GLU cc_start: 0.6962 (tm-30) cc_final: 0.6401 (tm-30) REVERT: B 398 ARG cc_start: 0.7637 (ttm170) cc_final: 0.7056 (tpp-160) REVERT: C 24 MET cc_start: 0.7390 (ptt) cc_final: 0.7010 (ptm) REVERT: C 62 ASN cc_start: 0.8617 (m-40) cc_final: 0.8402 (m110) REVERT: C 126 GLU cc_start: 0.7582 (pm20) cc_final: 0.6688 (mt-10) REVERT: C 130 ASP cc_start: 0.8129 (m-30) cc_final: 0.7880 (m-30) REVERT: C 138 LYS cc_start: 0.8451 (mtpt) cc_final: 0.8200 (ttmm) REVERT: C 207 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8583 (tt0) REVERT: C 233 GLU cc_start: 0.7487 (tt0) cc_final: 0.7002 (mt-10) REVERT: C 243 MET cc_start: 0.7995 (ptp) cc_final: 0.7003 (ptp) REVERT: C 312 SER cc_start: 0.8193 (m) cc_final: 0.7842 (p) REVERT: C 316 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6693 (tm-30) REVERT: C 325 ARG cc_start: 0.6846 (ptm-80) cc_final: 0.6616 (ptm-80) REVERT: C 398 ARG cc_start: 0.7749 (ttm170) cc_final: 0.7080 (tpp-160) REVERT: D 24 MET cc_start: 0.7231 (ptt) cc_final: 0.6951 (ptt) REVERT: D 34 MET cc_start: 0.8683 (mtt) cc_final: 0.8379 (mtp) REVERT: D 102 ASP cc_start: 0.8217 (t0) cc_final: 0.7706 (t70) REVERT: D 126 GLU cc_start: 0.7611 (pm20) cc_final: 0.6674 (mt-10) REVERT: D 179 MET cc_start: 0.8462 (tpt) cc_final: 0.8074 (tpt) REVERT: D 207 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8563 (tt0) REVERT: D 235 GLN cc_start: 0.8267 (mm-40) cc_final: 0.7970 (mm-40) REVERT: D 312 SER cc_start: 0.8299 (m) cc_final: 0.7918 (p) REVERT: D 398 ARG cc_start: 0.7744 (ttm170) cc_final: 0.7001 (tpp-160) REVERT: E 24 MET cc_start: 0.7487 (ptt) cc_final: 0.7254 (ptt) REVERT: E 72 MET cc_start: 0.8839 (mtm) cc_final: 0.8465 (mtm) REVERT: E 207 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8119 (tm-30) REVERT: E 233 GLU cc_start: 0.7463 (tt0) cc_final: 0.6852 (mt-10) REVERT: E 235 GLN cc_start: 0.8176 (mm110) cc_final: 0.7792 (mm-40) REVERT: E 261 ASN cc_start: 0.7151 (p0) cc_final: 0.6806 (p0) REVERT: E 316 GLU cc_start: 0.7093 (tm-30) cc_final: 0.6500 (tm-30) REVERT: E 398 ARG cc_start: 0.7548 (ttm170) cc_final: 0.6940 (tpp-160) outliers start: 54 outliers final: 24 residues processed: 336 average time/residue: 0.4488 time to fit residues: 169.2990 Evaluate side-chains 317 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 293 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 420 PHE Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 420 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 42 optimal weight: 0.1980 chunk 165 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 chunk 108 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 0.0270 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 62 ASN B 62 ASN D 62 ASN E 62 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.146210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.108340 restraints weight = 17063.636| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.55 r_work: 0.3109 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14610 Z= 0.116 Angle : 0.630 7.179 19840 Z= 0.311 Chirality : 0.045 0.161 2265 Planarity : 0.003 0.037 2450 Dihedral : 5.581 28.118 2200 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.23 % Allowed : 18.90 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.19), residues: 1710 helix: -1.53 (0.20), residues: 590 sheet: -0.05 (0.31), residues: 310 loop : -1.84 (0.19), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 229 TYR 0.014 0.001 TYR C 238 PHE 0.012 0.001 PHE D 322 TRP 0.009 0.001 TRP A 84 HIS 0.001 0.000 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00272 (14585) covalent geometry : angle 0.60939 (19775) SS BOND : bond 0.00492 ( 10) SS BOND : angle 1.66640 ( 20) hydrogen bonds : bond 0.03244 ( 550) hydrogen bonds : angle 4.73502 ( 2010) link_BETA1-4 : bond 0.00366 ( 10) link_BETA1-4 : angle 3.98070 ( 30) link_NAG-ASN : bond 0.00190 ( 5) link_NAG-ASN : angle 0.31261 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 295 time to evaluate : 0.499 Fit side-chains REVERT: A 24 MET cc_start: 0.6953 (ptm) cc_final: 0.6747 (ptm) REVERT: A 102 ASP cc_start: 0.8181 (t0) cc_final: 0.7856 (t70) REVERT: A 126 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7766 (mt-10) REVERT: A 207 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8529 (tt0) REVERT: A 233 GLU cc_start: 0.7269 (tt0) cc_final: 0.6765 (mt-10) REVERT: A 235 GLN cc_start: 0.8190 (mm110) cc_final: 0.7716 (mm-40) REVERT: A 312 SER cc_start: 0.8290 (m) cc_final: 0.7819 (p) REVERT: A 316 GLU cc_start: 0.6926 (tm-30) cc_final: 0.6287 (tm-30) REVERT: A 398 ARG cc_start: 0.7535 (ttm170) cc_final: 0.6823 (tpp-160) REVERT: B 24 MET cc_start: 0.7297 (ptt) cc_final: 0.7095 (ptm) REVERT: B 233 GLU cc_start: 0.7159 (tt0) cc_final: 0.6635 (mt-10) REVERT: B 312 SER cc_start: 0.8280 (m) cc_final: 0.7879 (p) REVERT: B 316 GLU cc_start: 0.6996 (tm-30) cc_final: 0.6450 (tm-30) REVERT: B 398 ARG cc_start: 0.7602 (ttm170) cc_final: 0.7070 (tpp-160) REVERT: C 138 LYS cc_start: 0.8494 (mtpt) cc_final: 0.8266 (ttmm) REVERT: C 207 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8576 (tt0) REVERT: C 233 GLU cc_start: 0.7477 (tt0) cc_final: 0.7034 (mt-10) REVERT: C 243 MET cc_start: 0.8094 (ptp) cc_final: 0.7092 (ptp) REVERT: C 258 PHE cc_start: 0.9007 (m-80) cc_final: 0.8747 (m-80) REVERT: C 312 SER cc_start: 0.8263 (m) cc_final: 0.7894 (p) REVERT: C 316 GLU cc_start: 0.7132 (tm-30) cc_final: 0.6664 (tm-30) REVERT: C 398 ARG cc_start: 0.7790 (ttm170) cc_final: 0.7084 (tpp-160) REVERT: D 24 MET cc_start: 0.7198 (ptt) cc_final: 0.6882 (ptp) REVERT: D 34 MET cc_start: 0.8723 (mtt) cc_final: 0.8462 (mtp) REVERT: D 102 ASP cc_start: 0.8270 (t0) cc_final: 0.7692 (t70) REVERT: D 179 MET cc_start: 0.8477 (tpt) cc_final: 0.8082 (tpt) REVERT: D 207 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8566 (tt0) REVERT: D 235 GLN cc_start: 0.8398 (mm-40) cc_final: 0.8122 (mm-40) REVERT: D 312 SER cc_start: 0.8314 (m) cc_final: 0.7925 (p) REVERT: D 398 ARG cc_start: 0.7725 (ttm170) cc_final: 0.6945 (tpp-160) REVERT: E 72 MET cc_start: 0.8837 (mtm) cc_final: 0.8467 (mtm) REVERT: E 102 ASP cc_start: 0.8149 (t0) cc_final: 0.7907 (t70) REVERT: E 163 MET cc_start: 0.7881 (mpp) cc_final: 0.7471 (mtp) REVERT: E 207 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8229 (tm-30) REVERT: E 233 GLU cc_start: 0.7468 (tt0) cc_final: 0.6903 (mt-10) REVERT: E 235 GLN cc_start: 0.8194 (mm110) cc_final: 0.7841 (mm-40) REVERT: E 295 TYR cc_start: 0.8662 (p90) cc_final: 0.8318 (p90) REVERT: E 312 SER cc_start: 0.8087 (m) cc_final: 0.7670 (p) REVERT: E 316 GLU cc_start: 0.7078 (tm-30) cc_final: 0.6583 (tm-30) REVERT: E 398 ARG cc_start: 0.7515 (ttm170) cc_final: 0.6857 (tpp-160) outliers start: 50 outliers final: 26 residues processed: 309 average time/residue: 0.4650 time to fit residues: 160.5557 Evaluate side-chains 311 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 285 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 420 PHE Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 424 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 95 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 ASN C 62 ASN D 62 ASN E 62 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.141287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.103699 restraints weight = 17120.826| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.49 r_work: 0.2989 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14610 Z= 0.207 Angle : 0.673 7.336 19840 Z= 0.336 Chirality : 0.047 0.164 2265 Planarity : 0.004 0.039 2450 Dihedral : 5.399 22.926 2200 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.77 % Allowed : 19.48 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.19), residues: 1710 helix: -1.26 (0.21), residues: 590 sheet: -0.05 (0.31), residues: 320 loop : -1.76 (0.19), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 229 TYR 0.013 0.002 TYR C 238 PHE 0.023 0.002 PHE E 322 TRP 0.011 0.001 TRP D 302 HIS 0.002 0.000 HIS E 125 Details of bonding type rmsd covalent geometry : bond 0.00503 (14585) covalent geometry : angle 0.65315 (19775) SS BOND : bond 0.00661 ( 10) SS BOND : angle 1.97134 ( 20) hydrogen bonds : bond 0.03458 ( 550) hydrogen bonds : angle 4.79620 ( 2010) link_BETA1-4 : bond 0.00412 ( 10) link_BETA1-4 : angle 3.92498 ( 30) link_NAG-ASN : bond 0.00113 ( 5) link_NAG-ASN : angle 0.53427 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 287 time to evaluate : 0.441 Fit side-chains REVERT: A 24 MET cc_start: 0.7150 (ptm) cc_final: 0.6932 (ptm) REVERT: A 102 ASP cc_start: 0.8331 (t70) cc_final: 0.8056 (t70) REVERT: A 126 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7340 (pm20) REVERT: A 156 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.7183 (mmt) REVERT: A 207 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8169 (tm-30) REVERT: A 233 GLU cc_start: 0.7287 (tt0) cc_final: 0.6806 (mt-10) REVERT: A 235 GLN cc_start: 0.8231 (mm110) cc_final: 0.7771 (mm-40) REVERT: A 312 SER cc_start: 0.8292 (m) cc_final: 0.7819 (p) REVERT: A 316 GLU cc_start: 0.7095 (tm-30) cc_final: 0.6259 (tm-30) REVERT: A 398 ARG cc_start: 0.7545 (ttm170) cc_final: 0.6805 (tpp-160) REVERT: B 24 MET cc_start: 0.7289 (ptt) cc_final: 0.7015 (ptm) REVERT: B 207 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8547 (tt0) REVERT: B 312 SER cc_start: 0.8253 (m) cc_final: 0.7841 (p) REVERT: B 316 GLU cc_start: 0.7021 (tm-30) cc_final: 0.6409 (tm-30) REVERT: B 398 ARG cc_start: 0.7663 (ttm170) cc_final: 0.7079 (tpp-160) REVERT: C 24 MET cc_start: 0.7002 (ptm) cc_final: 0.6777 (ptm) REVERT: C 138 LYS cc_start: 0.8479 (mtpt) cc_final: 0.8240 (ttmm) REVERT: C 156 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.7323 (mmt) REVERT: C 207 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8559 (tt0) REVERT: C 233 GLU cc_start: 0.7505 (tt0) cc_final: 0.7008 (mt-10) REVERT: C 243 MET cc_start: 0.8115 (ptp) cc_final: 0.7112 (ptp) REVERT: C 258 PHE cc_start: 0.9059 (m-80) cc_final: 0.8809 (m-80) REVERT: C 312 SER cc_start: 0.8258 (m) cc_final: 0.7888 (p) REVERT: C 316 GLU cc_start: 0.7233 (tm-30) cc_final: 0.6735 (tm-30) REVERT: C 398 ARG cc_start: 0.7765 (ttm170) cc_final: 0.7009 (tpp-160) REVERT: D 24 MET cc_start: 0.7251 (ptt) cc_final: 0.6969 (ptp) REVERT: D 102 ASP cc_start: 0.8276 (t0) cc_final: 0.7678 (t70) REVERT: D 207 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8556 (tt0) REVERT: D 235 GLN cc_start: 0.8389 (mm-40) cc_final: 0.8140 (mm-40) REVERT: D 312 SER cc_start: 0.8347 (m) cc_final: 0.7924 (p) REVERT: D 398 ARG cc_start: 0.7715 (ttm170) cc_final: 0.6913 (tpp-160) REVERT: E 24 MET cc_start: 0.7215 (ptt) cc_final: 0.6990 (ptp) REVERT: E 72 MET cc_start: 0.8908 (mtm) cc_final: 0.8554 (mtm) REVERT: E 207 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8190 (tm-30) REVERT: E 233 GLU cc_start: 0.7557 (tt0) cc_final: 0.6942 (mt-10) REVERT: E 235 GLN cc_start: 0.8257 (mm110) cc_final: 0.7934 (mm-40) REVERT: E 312 SER cc_start: 0.8062 (m) cc_final: 0.7634 (p) REVERT: E 316 GLU cc_start: 0.7113 (tm-30) cc_final: 0.6516 (tm-30) REVERT: E 398 ARG cc_start: 0.7525 (ttm170) cc_final: 0.6818 (tpp-160) outliers start: 74 outliers final: 45 residues processed: 327 average time/residue: 0.4161 time to fit residues: 153.9076 Evaluate side-chains 315 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 268 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 420 PHE Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 424 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 17 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 75 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN B 62 ASN B 82 GLN C 62 ASN C 180 ASN D 62 ASN E 62 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.142442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.104446 restraints weight = 16975.654| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 3.52 r_work: 0.2999 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14610 Z= 0.167 Angle : 0.647 8.208 19840 Z= 0.323 Chirality : 0.046 0.160 2265 Planarity : 0.003 0.040 2450 Dihedral : 5.271 20.367 2200 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.87 % Allowed : 21.87 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.19), residues: 1710 helix: -1.05 (0.22), residues: 590 sheet: 0.05 (0.31), residues: 320 loop : -1.70 (0.19), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 234 TYR 0.012 0.002 TYR C 144 PHE 0.015 0.001 PHE E 322 TRP 0.009 0.001 TRP A 186 HIS 0.001 0.000 HIS E 125 Details of bonding type rmsd covalent geometry : bond 0.00405 (14585) covalent geometry : angle 0.62808 (19775) SS BOND : bond 0.00571 ( 10) SS BOND : angle 1.85610 ( 20) hydrogen bonds : bond 0.03259 ( 550) hydrogen bonds : angle 4.66764 ( 2010) link_BETA1-4 : bond 0.00431 ( 10) link_BETA1-4 : angle 3.74887 ( 30) link_NAG-ASN : bond 0.00161 ( 5) link_NAG-ASN : angle 0.40872 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 265 time to evaluate : 0.466 Fit side-chains REVERT: A 102 ASP cc_start: 0.8320 (t70) cc_final: 0.7825 (t70) REVERT: A 126 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7319 (pm20) REVERT: A 207 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8494 (tt0) REVERT: A 233 GLU cc_start: 0.7221 (tt0) cc_final: 0.6715 (mt-10) REVERT: A 235 GLN cc_start: 0.8240 (mm110) cc_final: 0.7766 (mm-40) REVERT: A 312 SER cc_start: 0.8318 (m) cc_final: 0.7828 (p) REVERT: A 316 GLU cc_start: 0.7015 (tm-30) cc_final: 0.6234 (tm-30) REVERT: A 398 ARG cc_start: 0.7550 (ttm170) cc_final: 0.6806 (tpp-160) REVERT: B 24 MET cc_start: 0.7237 (ptt) cc_final: 0.7036 (ptm) REVERT: B 126 GLU cc_start: 0.7506 (pm20) cc_final: 0.6615 (mt-10) REVERT: B 207 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8522 (tt0) REVERT: B 312 SER cc_start: 0.8246 (m) cc_final: 0.7834 (p) REVERT: B 316 GLU cc_start: 0.7038 (tm-30) cc_final: 0.6403 (tm-30) REVERT: B 398 ARG cc_start: 0.7592 (ttm170) cc_final: 0.7017 (tpp-160) REVERT: C 24 MET cc_start: 0.7027 (ptm) cc_final: 0.6544 (ptm) REVERT: C 101 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7803 (tt) REVERT: C 102 ASP cc_start: 0.8434 (t70) cc_final: 0.7779 (t70) REVERT: C 138 LYS cc_start: 0.8461 (mtpt) cc_final: 0.8213 (ttmm) REVERT: C 207 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8558 (tt0) REVERT: C 233 GLU cc_start: 0.7444 (tt0) cc_final: 0.6947 (mt-10) REVERT: C 243 MET cc_start: 0.8084 (ptp) cc_final: 0.7080 (ptp) REVERT: C 279 MET cc_start: 0.7215 (tpt) cc_final: 0.6755 (tpt) REVERT: C 312 SER cc_start: 0.8251 (m) cc_final: 0.7876 (p) REVERT: C 316 GLU cc_start: 0.7213 (tm-30) cc_final: 0.6583 (tm-30) REVERT: C 398 ARG cc_start: 0.7744 (ttm170) cc_final: 0.6961 (tpp-160) REVERT: D 24 MET cc_start: 0.7219 (ptt) cc_final: 0.6961 (ptp) REVERT: D 102 ASP cc_start: 0.8265 (t0) cc_final: 0.7508 (t70) REVERT: D 207 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8590 (tt0) REVERT: D 235 GLN cc_start: 0.8402 (mm-40) cc_final: 0.8115 (mm-40) REVERT: D 312 SER cc_start: 0.8338 (m) cc_final: 0.7941 (p) REVERT: D 398 ARG cc_start: 0.7691 (ttm170) cc_final: 0.6872 (tpp-160) REVERT: E 72 MET cc_start: 0.8903 (mtm) cc_final: 0.8538 (mtm) REVERT: E 102 ASP cc_start: 0.8210 (t0) cc_final: 0.7723 (t70) REVERT: E 207 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8209 (tm-30) REVERT: E 233 GLU cc_start: 0.7538 (tt0) cc_final: 0.6918 (mt-10) REVERT: E 235 GLN cc_start: 0.8270 (mm110) cc_final: 0.7955 (mm-40) REVERT: E 247 SER cc_start: 0.8526 (OUTLIER) cc_final: 0.8247 (t) REVERT: E 290 LEU cc_start: 0.9109 (mm) cc_final: 0.8845 (mt) REVERT: E 312 SER cc_start: 0.8071 (m) cc_final: 0.7642 (p) REVERT: E 316 GLU cc_start: 0.7093 (tm-30) cc_final: 0.6522 (tm-30) REVERT: E 398 ARG cc_start: 0.7514 (ttm170) cc_final: 0.6767 (tpp-160) outliers start: 60 outliers final: 36 residues processed: 295 average time/residue: 0.4388 time to fit residues: 145.6834 Evaluate side-chains 304 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 266 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 420 PHE Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 424 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 19 optimal weight: 0.4980 chunk 75 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN B 62 ASN B 82 GLN C 62 ASN D 62 ASN E 62 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.142413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.105988 restraints weight = 16923.052| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 3.32 r_work: 0.3076 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14610 Z= 0.122 Angle : 0.618 8.863 19840 Z= 0.307 Chirality : 0.045 0.157 2265 Planarity : 0.003 0.039 2450 Dihedral : 5.045 20.799 2200 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.55 % Allowed : 22.19 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.20), residues: 1710 helix: -0.82 (0.22), residues: 605 sheet: 0.23 (0.30), residues: 315 loop : -1.62 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 229 TYR 0.012 0.001 TYR A 144 PHE 0.013 0.001 PHE E 322 TRP 0.009 0.001 TRP C 422 HIS 0.001 0.000 HIS D 125 Details of bonding type rmsd covalent geometry : bond 0.00291 (14585) covalent geometry : angle 0.60107 (19775) SS BOND : bond 0.00482 ( 10) SS BOND : angle 1.72191 ( 20) hydrogen bonds : bond 0.03001 ( 550) hydrogen bonds : angle 4.42280 ( 2010) link_BETA1-4 : bond 0.00425 ( 10) link_BETA1-4 : angle 3.54994 ( 30) link_NAG-ASN : bond 0.00184 ( 5) link_NAG-ASN : angle 0.31665 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 276 time to evaluate : 0.624 Fit side-chains REVERT: A 102 ASP cc_start: 0.8470 (t70) cc_final: 0.7928 (t70) REVERT: A 207 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8506 (tt0) REVERT: A 233 GLU cc_start: 0.7305 (tt0) cc_final: 0.6839 (mt-10) REVERT: A 235 GLN cc_start: 0.8352 (mm110) cc_final: 0.7870 (mm-40) REVERT: A 243 MET cc_start: 0.8444 (mtm) cc_final: 0.8144 (ptp) REVERT: A 312 SER cc_start: 0.8364 (m) cc_final: 0.7864 (p) REVERT: A 316 GLU cc_start: 0.7070 (tm-30) cc_final: 0.6241 (tm-30) REVERT: A 398 ARG cc_start: 0.7535 (ttm170) cc_final: 0.6811 (tpp-160) REVERT: A 419 ILE cc_start: 0.8010 (mm) cc_final: 0.7799 (mt) REVERT: B 179 MET cc_start: 0.8611 (tpt) cc_final: 0.8142 (tpt) REVERT: B 207 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8547 (tt0) REVERT: B 312 SER cc_start: 0.8359 (m) cc_final: 0.7943 (p) REVERT: B 316 GLU cc_start: 0.7088 (tm-30) cc_final: 0.6439 (tm-30) REVERT: B 398 ARG cc_start: 0.7582 (ttm170) cc_final: 0.7005 (tpp-160) REVERT: C 24 MET cc_start: 0.7205 (ptm) cc_final: 0.6847 (ptm) REVERT: C 101 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7959 (tp) REVERT: C 138 LYS cc_start: 0.8595 (mtpt) cc_final: 0.8337 (ttmm) REVERT: C 207 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8608 (tt0) REVERT: C 233 GLU cc_start: 0.7530 (tt0) cc_final: 0.7082 (mt-10) REVERT: C 312 SER cc_start: 0.8308 (m) cc_final: 0.7946 (p) REVERT: C 316 GLU cc_start: 0.7283 (tm-30) cc_final: 0.6770 (tm-30) REVERT: C 398 ARG cc_start: 0.7753 (ttm170) cc_final: 0.7001 (tpp-160) REVERT: D 102 ASP cc_start: 0.8342 (t0) cc_final: 0.7532 (t70) REVERT: D 207 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8597 (tt0) REVERT: D 235 GLN cc_start: 0.8514 (mm-40) cc_final: 0.8185 (mm-40) REVERT: D 312 SER cc_start: 0.8343 (m) cc_final: 0.7954 (p) REVERT: D 398 ARG cc_start: 0.7647 (ttm170) cc_final: 0.6884 (tpp-160) REVERT: E 72 MET cc_start: 0.8965 (mtm) cc_final: 0.8588 (mtm) REVERT: E 102 ASP cc_start: 0.8283 (t0) cc_final: 0.7828 (t70) REVERT: E 207 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8228 (tm-30) REVERT: E 233 GLU cc_start: 0.7576 (tt0) cc_final: 0.7000 (mt-10) REVERT: E 235 GLN cc_start: 0.8386 (mm110) cc_final: 0.8037 (mm-40) REVERT: E 290 LEU cc_start: 0.9125 (mm) cc_final: 0.8919 (mt) REVERT: E 312 SER cc_start: 0.8134 (m) cc_final: 0.7695 (p) REVERT: E 316 GLU cc_start: 0.7242 (tm-30) cc_final: 0.6647 (tm-30) REVERT: E 398 ARG cc_start: 0.7503 (ttm170) cc_final: 0.6766 (tpp-160) outliers start: 55 outliers final: 32 residues processed: 306 average time/residue: 0.4199 time to fit residues: 144.5987 Evaluate side-chains 288 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 255 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 420 PHE Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 281 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 60 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN B 62 ASN B 82 GLN B 131 ASN C 62 ASN C 131 ASN D 62 ASN E 62 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.140980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.104440 restraints weight = 17062.895| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 3.36 r_work: 0.3064 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 14610 Z= 0.161 Angle : 0.662 10.915 19840 Z= 0.329 Chirality : 0.046 0.163 2265 Planarity : 0.003 0.036 2450 Dihedral : 5.142 28.662 2200 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.90 % Allowed : 23.23 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.20), residues: 1710 helix: -0.75 (0.22), residues: 605 sheet: 0.05 (0.28), residues: 365 loop : -1.53 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 229 TYR 0.013 0.002 TYR A 213 PHE 0.011 0.001 PHE C 115 TRP 0.009 0.001 TRP A 186 HIS 0.002 0.000 HIS A 217 Details of bonding type rmsd covalent geometry : bond 0.00391 (14585) covalent geometry : angle 0.64134 (19775) SS BOND : bond 0.00597 ( 10) SS BOND : angle 2.85579 ( 20) hydrogen bonds : bond 0.03081 ( 550) hydrogen bonds : angle 4.50511 ( 2010) link_BETA1-4 : bond 0.00456 ( 10) link_BETA1-4 : angle 3.57166 ( 30) link_NAG-ASN : bond 0.00160 ( 5) link_NAG-ASN : angle 0.45874 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 262 time to evaluate : 0.517 Fit side-chains REVERT: A 102 ASP cc_start: 0.8400 (t70) cc_final: 0.7859 (t70) REVERT: A 207 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8523 (tt0) REVERT: A 233 GLU cc_start: 0.7401 (tt0) cc_final: 0.6913 (mt-10) REVERT: A 235 GLN cc_start: 0.8407 (mm110) cc_final: 0.7956 (mm110) REVERT: A 312 SER cc_start: 0.8406 (m) cc_final: 0.7903 (p) REVERT: A 316 GLU cc_start: 0.7134 (tm-30) cc_final: 0.6282 (tm-30) REVERT: A 398 ARG cc_start: 0.7545 (ttm170) cc_final: 0.6804 (tpp-160) REVERT: A 419 ILE cc_start: 0.8021 (mm) cc_final: 0.7805 (mt) REVERT: B 24 MET cc_start: 0.6854 (ptm) cc_final: 0.6424 (ptm) REVERT: B 207 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8562 (tt0) REVERT: B 312 SER cc_start: 0.8368 (m) cc_final: 0.7950 (p) REVERT: B 316 GLU cc_start: 0.7189 (tm-30) cc_final: 0.6563 (tm-30) REVERT: B 398 ARG cc_start: 0.7643 (ttm170) cc_final: 0.6993 (tpp-160) REVERT: C 24 MET cc_start: 0.7153 (ptm) cc_final: 0.6924 (ptm) REVERT: C 101 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.8038 (tp) REVERT: C 138 LYS cc_start: 0.8613 (mtpt) cc_final: 0.8351 (ttmm) REVERT: C 207 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8624 (tt0) REVERT: C 233 GLU cc_start: 0.7608 (tt0) cc_final: 0.7152 (mt-10) REVERT: C 312 SER cc_start: 0.8329 (m) cc_final: 0.7959 (p) REVERT: C 316 GLU cc_start: 0.7340 (tm-30) cc_final: 0.6697 (tm-30) REVERT: C 398 ARG cc_start: 0.7744 (ttm170) cc_final: 0.6973 (tpp-160) REVERT: D 102 ASP cc_start: 0.8315 (t0) cc_final: 0.7780 (t70) REVERT: D 207 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8648 (tt0) REVERT: D 235 GLN cc_start: 0.8558 (mm-40) cc_final: 0.8271 (mm-40) REVERT: D 312 SER cc_start: 0.8383 (m) cc_final: 0.7995 (p) REVERT: D 398 ARG cc_start: 0.7673 (ttm170) cc_final: 0.6887 (tpp-160) REVERT: E 24 MET cc_start: 0.7177 (ptm) cc_final: 0.6975 (ptm) REVERT: E 72 MET cc_start: 0.8939 (mtm) cc_final: 0.8579 (mtm) REVERT: E 101 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7883 (tp) REVERT: E 102 ASP cc_start: 0.8323 (t0) cc_final: 0.7848 (t70) REVERT: E 207 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8269 (tm-30) REVERT: E 233 GLU cc_start: 0.7665 (tt0) cc_final: 0.7074 (mt-10) REVERT: E 235 GLN cc_start: 0.8421 (mm110) cc_final: 0.8075 (mm-40) REVERT: E 247 SER cc_start: 0.8666 (OUTLIER) cc_final: 0.8381 (t) REVERT: E 290 LEU cc_start: 0.9144 (mm) cc_final: 0.8898 (mt) REVERT: E 312 SER cc_start: 0.8138 (m) cc_final: 0.7692 (p) REVERT: E 316 GLU cc_start: 0.7337 (tm-30) cc_final: 0.6722 (tm-30) REVERT: E 398 ARG cc_start: 0.7513 (ttm170) cc_final: 0.6755 (tpp-160) outliers start: 45 outliers final: 31 residues processed: 287 average time/residue: 0.4022 time to fit residues: 130.7579 Evaluate side-chains 297 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 263 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 420 PHE Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 281 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 75 optimal weight: 0.6980 chunk 113 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 7 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 171 GLN B 62 ASN B 82 GLN C 62 ASN D 62 ASN E 62 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.147168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.109349 restraints weight = 16679.511| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 3.52 r_work: 0.3086 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 14610 Z= 0.134 Angle : 0.658 14.204 19840 Z= 0.327 Chirality : 0.045 0.184 2265 Planarity : 0.003 0.038 2450 Dihedral : 5.154 37.142 2200 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.71 % Allowed : 23.42 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.20), residues: 1710 helix: -0.64 (0.22), residues: 605 sheet: 0.08 (0.28), residues: 365 loop : -1.48 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 229 TYR 0.011 0.001 TYR C 144 PHE 0.031 0.001 PHE A 322 TRP 0.009 0.001 TRP A 186 HIS 0.003 0.000 HIS C 217 Details of bonding type rmsd covalent geometry : bond 0.00325 (14585) covalent geometry : angle 0.63588 (19775) SS BOND : bond 0.00506 ( 10) SS BOND : angle 3.31819 ( 20) hydrogen bonds : bond 0.03015 ( 550) hydrogen bonds : angle 4.42219 ( 2010) link_BETA1-4 : bond 0.00459 ( 10) link_BETA1-4 : angle 3.46748 ( 30) link_NAG-ASN : bond 0.00182 ( 5) link_NAG-ASN : angle 0.38353 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 261 time to evaluate : 0.585 Fit side-chains REVERT: A 72 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8503 (tpt) REVERT: A 102 ASP cc_start: 0.8225 (t70) cc_final: 0.7672 (t70) REVERT: A 207 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8486 (tt0) REVERT: A 233 GLU cc_start: 0.7200 (tt0) cc_final: 0.6709 (mt-10) REVERT: A 235 GLN cc_start: 0.8313 (mm110) cc_final: 0.7823 (mm-40) REVERT: A 312 SER cc_start: 0.8269 (m) cc_final: 0.7799 (p) REVERT: A 316 GLU cc_start: 0.6929 (tm-30) cc_final: 0.6127 (tm-30) REVERT: A 398 ARG cc_start: 0.7485 (ttm170) cc_final: 0.6738 (tpp-160) REVERT: B 24 MET cc_start: 0.6612 (ptm) cc_final: 0.6258 (ptm) REVERT: B 207 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8467 (tt0) REVERT: B 312 SER cc_start: 0.8263 (m) cc_final: 0.7859 (p) REVERT: B 316 GLU cc_start: 0.6994 (tm-30) cc_final: 0.6375 (tm-30) REVERT: B 398 ARG cc_start: 0.7603 (ttm170) cc_final: 0.6937 (tpp-160) REVERT: C 24 MET cc_start: 0.6940 (ptm) cc_final: 0.6575 (ptm) REVERT: C 101 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7822 (tp) REVERT: C 105 MET cc_start: 0.8490 (mmp) cc_final: 0.8288 (mmt) REVERT: C 138 LYS cc_start: 0.8423 (mtpt) cc_final: 0.8175 (ttmm) REVERT: C 171 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.8038 (mt0) REVERT: C 207 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8592 (tt0) REVERT: C 233 GLU cc_start: 0.7375 (tt0) cc_final: 0.6920 (mt-10) REVERT: C 312 SER cc_start: 0.8208 (m) cc_final: 0.7844 (p) REVERT: C 316 GLU cc_start: 0.7094 (tm-30) cc_final: 0.6473 (tm-30) REVERT: C 398 ARG cc_start: 0.7642 (ttm170) cc_final: 0.6870 (tpp-160) REVERT: D 207 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8594 (tt0) REVERT: D 235 GLN cc_start: 0.8444 (mm-40) cc_final: 0.8104 (mm-40) REVERT: D 312 SER cc_start: 0.8238 (m) cc_final: 0.7859 (p) REVERT: D 398 ARG cc_start: 0.7633 (ttm170) cc_final: 0.6822 (tpp-160) REVERT: E 72 MET cc_start: 0.8833 (mtm) cc_final: 0.8488 (mtm) REVERT: E 102 ASP cc_start: 0.8204 (t0) cc_final: 0.7592 (t70) REVERT: E 207 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8198 (tm-30) REVERT: E 233 GLU cc_start: 0.7458 (tt0) cc_final: 0.6864 (mt-10) REVERT: E 235 GLN cc_start: 0.8313 (mm110) cc_final: 0.8019 (mm-40) REVERT: E 247 SER cc_start: 0.8505 (OUTLIER) cc_final: 0.8213 (t) REVERT: E 312 SER cc_start: 0.8013 (m) cc_final: 0.7585 (p) REVERT: E 316 GLU cc_start: 0.7050 (tm-30) cc_final: 0.6357 (tm-30) REVERT: E 398 ARG cc_start: 0.7469 (ttm170) cc_final: 0.6672 (tpp-160) outliers start: 42 outliers final: 29 residues processed: 284 average time/residue: 0.4303 time to fit residues: 137.8973 Evaluate side-chains 284 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 251 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 420 PHE Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 281 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 139 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 chunk 148 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 126 optimal weight: 0.1980 chunk 88 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN B 62 ASN B 82 GLN C 62 ASN D 62 ASN E 62 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.148034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.109951 restraints weight = 16586.618| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.53 r_work: 0.3091 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14610 Z= 0.134 Angle : 0.658 9.529 19840 Z= 0.326 Chirality : 0.046 0.205 2265 Planarity : 0.003 0.034 2450 Dihedral : 5.164 44.848 2200 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.94 % Allowed : 24.65 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.20), residues: 1710 helix: -0.57 (0.22), residues: 605 sheet: 0.12 (0.29), residues: 365 loop : -1.49 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 229 TYR 0.011 0.001 TYR E 144 PHE 0.028 0.001 PHE A 322 TRP 0.009 0.001 TRP A 186 HIS 0.001 0.000 HIS E 125 Details of bonding type rmsd covalent geometry : bond 0.00324 (14585) covalent geometry : angle 0.63813 (19775) SS BOND : bond 0.00479 ( 10) SS BOND : angle 3.03298 ( 20) hydrogen bonds : bond 0.03022 ( 550) hydrogen bonds : angle 4.36889 ( 2010) link_BETA1-4 : bond 0.00486 ( 10) link_BETA1-4 : angle 3.41714 ( 30) link_NAG-ASN : bond 0.00181 ( 5) link_NAG-ASN : angle 0.40923 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 256 time to evaluate : 0.434 Fit side-chains REVERT: A 102 ASP cc_start: 0.8202 (t70) cc_final: 0.7666 (t70) REVERT: A 207 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8496 (tt0) REVERT: A 233 GLU cc_start: 0.7185 (tt0) cc_final: 0.6705 (mt-10) REVERT: A 243 MET cc_start: 0.8477 (mtm) cc_final: 0.8179 (ptp) REVERT: A 312 SER cc_start: 0.8268 (m) cc_final: 0.7819 (p) REVERT: A 316 GLU cc_start: 0.6915 (tm-30) cc_final: 0.6119 (tm-30) REVERT: A 398 ARG cc_start: 0.7463 (ttm170) cc_final: 0.6710 (tpp-160) REVERT: B 24 MET cc_start: 0.6565 (ptm) cc_final: 0.6206 (ptm) REVERT: B 207 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8451 (tt0) REVERT: B 312 SER cc_start: 0.8220 (m) cc_final: 0.7821 (p) REVERT: B 316 GLU cc_start: 0.6931 (tm-30) cc_final: 0.6348 (tm-30) REVERT: B 398 ARG cc_start: 0.7589 (ttm170) cc_final: 0.6927 (tpp-160) REVERT: C 24 MET cc_start: 0.6941 (ptm) cc_final: 0.6648 (ptm) REVERT: C 101 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7725 (tp) REVERT: C 138 LYS cc_start: 0.8400 (mtpt) cc_final: 0.8032 (mtpm) REVERT: C 207 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8564 (tt0) REVERT: C 233 GLU cc_start: 0.7303 (tt0) cc_final: 0.6876 (mt-10) REVERT: C 312 SER cc_start: 0.8191 (m) cc_final: 0.7834 (p) REVERT: C 316 GLU cc_start: 0.7009 (tm-30) cc_final: 0.6451 (tm-30) REVERT: C 398 ARG cc_start: 0.7614 (ttm170) cc_final: 0.6814 (tpp-160) REVERT: D 102 ASP cc_start: 0.8151 (t70) cc_final: 0.7507 (t70) REVERT: D 207 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8589 (tt0) REVERT: D 229 ARG cc_start: 0.8294 (mtt-85) cc_final: 0.7953 (mtt-85) REVERT: D 235 GLN cc_start: 0.8428 (mm-40) cc_final: 0.8086 (mm-40) REVERT: D 312 SER cc_start: 0.8228 (m) cc_final: 0.7843 (p) REVERT: D 398 ARG cc_start: 0.7577 (ttm170) cc_final: 0.6776 (tpp-160) REVERT: E 24 MET cc_start: 0.6847 (ptm) cc_final: 0.6583 (ptm) REVERT: E 72 MET cc_start: 0.8789 (mtm) cc_final: 0.8431 (mtm) REVERT: E 102 ASP cc_start: 0.8153 (t0) cc_final: 0.7716 (t70) REVERT: E 207 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8194 (tm-30) REVERT: E 233 GLU cc_start: 0.7486 (tt0) cc_final: 0.6902 (mt-10) REVERT: E 247 SER cc_start: 0.8480 (OUTLIER) cc_final: 0.8178 (t) REVERT: E 312 SER cc_start: 0.7995 (m) cc_final: 0.7569 (p) REVERT: E 316 GLU cc_start: 0.7089 (tm-30) cc_final: 0.6418 (tm-30) REVERT: E 398 ARG cc_start: 0.7424 (ttm170) cc_final: 0.6634 (tpp-160) outliers start: 30 outliers final: 25 residues processed: 270 average time/residue: 0.4236 time to fit residues: 128.9926 Evaluate side-chains 281 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 254 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 281 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 154 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 30 optimal weight: 0.0030 chunk 105 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 82 GLN B 62 ASN C 62 ASN C 82 GLN D 62 ASN E 62 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.145586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.107505 restraints weight = 16664.003| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 3.51 r_work: 0.3008 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14610 Z= 0.180 Angle : 0.682 9.073 19840 Z= 0.339 Chirality : 0.047 0.191 2265 Planarity : 0.003 0.033 2450 Dihedral : 5.238 44.401 2200 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.45 % Allowed : 24.19 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.20), residues: 1710 helix: -0.56 (0.22), residues: 605 sheet: 0.10 (0.29), residues: 365 loop : -1.48 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 229 TYR 0.013 0.002 TYR E 421 PHE 0.028 0.001 PHE A 322 TRP 0.010 0.001 TRP D 422 HIS 0.001 0.000 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00440 (14585) covalent geometry : angle 0.66264 (19775) SS BOND : bond 0.00586 ( 10) SS BOND : angle 3.06204 ( 20) hydrogen bonds : bond 0.03183 ( 550) hydrogen bonds : angle 4.52057 ( 2010) link_BETA1-4 : bond 0.00475 ( 10) link_BETA1-4 : angle 3.48717 ( 30) link_NAG-ASN : bond 0.00115 ( 5) link_NAG-ASN : angle 0.55607 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4373.65 seconds wall clock time: 75 minutes 10.56 seconds (4510.56 seconds total)