Starting phenix.real_space_refine on Wed Mar 4 14:32:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6plp_20371/03_2026/6plp_20371.cif Found real_map, /net/cci-nas-00/data/ceres_data/6plp_20371/03_2026/6plp_20371.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6plp_20371/03_2026/6plp_20371.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6plp_20371/03_2026/6plp_20371.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6plp_20371/03_2026/6plp_20371.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6plp_20371/03_2026/6plp_20371.map" } resolution = 3.3 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= 0.092 sd= 5.309 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 25 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: 2.37, per 1000 atoms: 0.17 Number of scatterers: 14240 At special positions: 0 Unit cell: (105.786, 107.745, 135.824, 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=2.19 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 168 " distance=2.19 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 168 " distance=2.19 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 168 " distance=2.19 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 168 " distance=2.19 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.03 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.03 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied 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: 1.11 Conformation dependent library (CDL) restraints added in 639.7 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: 60 helices and 25 sheets defined 39.3% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 25 through 30 Processing helix chain 'A' and resid 30 through 35 Processing helix chain 'A' and resid 36 through 40 removed outlier: 3.998A pdb=" N GLY A 39 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 3.881A 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: 4.039A 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 256 removed outlier: 4.462A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 260 Processing helix chain 'A' and resid 264 through 285 removed outlier: 3.755A pdb=" N ARG A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY A 270 " --> pdb=" O PRO A 266 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN A 282 " --> pdb=" O THR A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 325 removed outlier: 3.575A pdb=" N MET A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 425 removed outlier: 4.052A pdb=" N PHE A 395 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) Proline residue: A 411 - end of helix removed outlier: 4.233A pdb=" N LEU A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TRP A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR A 425 " --> pdb=" O TYR A 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'B' and resid 36 through 40 removed outlier: 3.999A pdb=" N GLY B 39 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 3.881A 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: 4.039A 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 256 removed outlier: 4.462A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 260 Processing helix chain 'B' and resid 264 through 285 removed outlier: 3.755A pdb=" N ARG B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY B 270 " --> pdb=" O PRO B 266 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR B 280 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN B 282 " --> pdb=" O THR B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 325 removed outlier: 3.575A pdb=" N MET B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 305 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 425 removed outlier: 4.053A pdb=" N PHE B 395 " --> pdb=" O MET B 391 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER B 397 " --> pdb=" O LYS B 393 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 402 " --> pdb=" O ARG B 398 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP B 403 " --> pdb=" O ALA B 399 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) Proline residue: B 411 - end of helix removed outlier: 4.234A pdb=" N LEU B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TRP B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR B 425 " --> pdb=" O TYR B 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 30 through 35 Processing helix chain 'C' and resid 36 through 40 removed outlier: 3.998A pdb=" N GLY C 39 " --> pdb=" O LYS C 36 " (cutoff:3.500A) removed outlier: 3.881A 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: 4.039A 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 256 removed outlier: 4.461A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 260 Processing helix chain 'C' and resid 264 through 285 removed outlier: 3.755A pdb=" N ARG C 268 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY C 270 " --> pdb=" O PRO C 266 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR C 280 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN C 282 " --> pdb=" O THR C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 325 removed outlier: 3.575A pdb=" N MET C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL C 305 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE C 323 " --> pdb=" O ALA C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 425 removed outlier: 4.052A pdb=" N PHE C 395 " --> pdb=" O MET C 391 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER C 397 " --> pdb=" O LYS C 393 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE C 402 " --> pdb=" O ARG C 398 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP C 403 " --> pdb=" O ALA C 399 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) Proline residue: C 411 - end of helix removed outlier: 4.234A pdb=" N LEU C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE C 416 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TRP C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR C 425 " --> pdb=" O TYR C 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 30 Processing helix chain 'D' and resid 30 through 35 Processing helix chain 'D' and resid 36 through 40 removed outlier: 3.998A pdb=" N GLY D 39 " --> pdb=" O LYS D 36 " (cutoff:3.500A) removed outlier: 3.882A 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: 4.039A 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 256 removed outlier: 4.462A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 260 Processing helix chain 'D' and resid 264 through 285 removed outlier: 3.755A pdb=" N ARG D 268 " --> pdb=" O ALA D 264 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY D 270 " --> pdb=" O PRO D 266 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL D 276 " --> pdb=" O GLY D 272 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR D 280 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR D 281 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN D 282 " --> pdb=" O THR D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 325 removed outlier: 3.575A pdb=" N MET D 303 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 305 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 425 removed outlier: 4.053A pdb=" N PHE D 395 " --> pdb=" O MET D 391 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER D 397 " --> pdb=" O LYS D 393 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE D 402 " --> pdb=" O ARG D 398 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP D 403 " --> pdb=" O ALA D 399 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG D 407 " --> pdb=" O ASP D 403 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL D 408 " --> pdb=" O THR D 404 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE D 410 " --> pdb=" O SER D 406 " (cutoff:3.500A) Proline residue: D 411 - end of helix removed outlier: 4.233A pdb=" N LEU D 415 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TRP D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR D 425 " --> pdb=" O TYR D 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 30 Processing helix chain 'E' and resid 30 through 35 Processing helix chain 'E' and resid 36 through 40 removed outlier: 3.999A pdb=" N GLY E 39 " --> pdb=" O LYS E 36 " (cutoff:3.500A) removed outlier: 3.881A 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: 4.040A 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 256 removed outlier: 4.462A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 260 Processing helix chain 'E' and resid 264 through 285 removed outlier: 3.755A pdb=" N ARG E 268 " --> pdb=" O ALA E 264 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY E 270 " --> pdb=" O PRO E 266 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL E 276 " --> pdb=" O GLY E 272 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR E 280 " --> pdb=" O VAL E 276 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR E 281 " --> pdb=" O LEU E 277 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN E 282 " --> pdb=" O THR E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 325 removed outlier: 3.575A pdb=" N MET E 303 " --> pdb=" O ILE E 299 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL E 305 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 425 removed outlier: 4.052A pdb=" N PHE E 395 " --> pdb=" O MET E 391 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER E 397 " --> pdb=" O LYS E 393 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE E 402 " --> pdb=" O ARG E 398 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP E 403 " --> pdb=" O ALA E 399 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG E 407 " --> pdb=" O ASP E 403 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL E 408 " --> pdb=" O THR E 404 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE E 410 " --> pdb=" O SER E 406 " (cutoff:3.500A) Proline residue: E 411 - end of helix removed outlier: 4.233A pdb=" N LEU E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE E 416 " --> pdb=" O LEU E 412 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TRP E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR E 425 " --> pdb=" O TYR E 421 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 99 through 100 removed outlier: 3.566A pdb=" N LEU A 99 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP A 84 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL A 55 " --> pdb=" O GLU A 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 123 removed outlier: 3.721A pdb=" N ASN A 123 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP A 84 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N GLN A 193 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 6.691A 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 removed outlier: 3.795A pdb=" N MET A 170 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A 228 " --> pdb=" O MET A 170 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 227 " --> pdb=" O ARG A 212 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG A 212 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 165 through 167 Processing sheet with id=AA5, first strand: chain 'A' and resid 216 through 217 removed outlier: 3.789A pdb=" N LYS A 216 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE A 223 " --> pdb=" O LYS A 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 99 through 100 removed outlier: 3.566A pdb=" N LEU B 99 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP B 84 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 122 through 123 removed outlier: 3.721A pdb=" N ASN B 123 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP B 84 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N GLN B 193 " --> pdb=" O CYS B 57 " (cutoff:3.500A) removed outlier: 6.691A 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 removed outlier: 3.794A pdb=" N MET B 170 " --> pdb=" O ALA B 228 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA B 228 " --> pdb=" O MET B 170 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B 227 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG B 212 " --> pdb=" O GLU B 227 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 165 through 167 Processing sheet with id=AB1, first strand: chain 'B' and resid 216 through 217 removed outlier: 3.789A pdb=" N LYS B 216 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE B 223 " --> pdb=" O LYS B 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 99 through 100 removed outlier: 3.565A pdb=" N LEU C 99 " --> pdb=" O ILE C 136 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP C 84 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 122 through 123 removed outlier: 3.721A pdb=" N ASN C 123 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP C 84 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N GLN C 193 " --> pdb=" O CYS C 57 " (cutoff:3.500A) removed outlier: 6.691A 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 removed outlier: 3.795A pdb=" N MET C 170 " --> pdb=" O ALA C 228 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 228 " --> pdb=" O MET C 170 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU C 227 " --> pdb=" O ARG C 212 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG C 212 " --> pdb=" O GLU C 227 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 165 through 167 Processing sheet with id=AB6, first strand: chain 'C' and resid 216 through 217 removed outlier: 3.789A pdb=" N LYS C 216 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE C 223 " --> pdb=" O LYS C 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 99 through 100 removed outlier: 3.566A pdb=" N LEU D 99 " --> pdb=" O ILE D 136 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP D 84 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 122 through 123 removed outlier: 3.721A pdb=" N ASN D 123 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP D 84 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N GLN D 193 " --> pdb=" O CYS D 57 " (cutoff:3.500A) removed outlier: 6.691A 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 removed outlier: 3.794A pdb=" N MET D 170 " --> pdb=" O ALA D 228 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA D 228 " --> pdb=" O MET D 170 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU D 227 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG D 212 " --> pdb=" O GLU D 227 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 165 through 167 Processing sheet with id=AC2, first strand: chain 'D' and resid 216 through 217 removed outlier: 3.789A pdb=" N LYS D 216 " --> pdb=" O PHE D 223 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE D 223 " --> pdb=" O LYS D 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 99 through 100 removed outlier: 3.566A pdb=" N LEU E 99 " --> pdb=" O ILE E 136 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP E 84 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL E 55 " --> pdb=" O GLU E 185 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 122 through 123 removed outlier: 3.721A pdb=" N ASN E 123 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP E 84 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N GLN E 193 " --> pdb=" O CYS E 57 " (cutoff:3.500A) removed outlier: 6.691A 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 removed outlier: 3.795A pdb=" N MET E 170 " --> pdb=" O ALA E 228 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA E 228 " --> pdb=" O MET E 170 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU E 227 " --> pdb=" O ARG E 212 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG E 212 " --> pdb=" O GLU E 227 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 165 through 167 Processing sheet with id=AC7, first strand: chain 'E' and resid 216 through 217 removed outlier: 3.790A pdb=" N LYS E 216 " --> pdb=" O PHE E 223 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE E 223 " --> pdb=" O LYS E 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 565 hydrogen bonds defined for protein. 1635 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: 2.31 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4385 1.34 - 1.46: 3523 1.46 - 1.58: 6507 1.58 - 1.70: 0 1.70 - 1.81: 170 Bond restraints: 14585 Sorted by residual: bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.76e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.75e+00 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.75e+00 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.74e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.71e+00 ... (remaining 14580 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 19286 1.34 - 2.67: 354 2.67 - 4.01: 75 4.01 - 5.35: 45 5.35 - 6.69: 15 Bond angle restraints: 19775 Sorted by residual: angle pdb=" CB ABU C 504 " pdb=" CG ABU C 504 " pdb=" CD ABU C 504 " ideal model delta sigma weight residual 116.08 109.39 6.69 3.00e+00 1.11e-01 4.97e+00 angle pdb=" CB ABU B 504 " pdb=" CG ABU B 504 " pdb=" CD ABU B 504 " ideal model delta sigma weight residual 116.08 109.40 6.68 3.00e+00 1.11e-01 4.96e+00 angle pdb=" CB ABU A 504 " pdb=" CG ABU A 504 " pdb=" CD ABU A 504 " ideal model delta sigma weight residual 116.08 109.40 6.68 3.00e+00 1.11e-01 4.95e+00 angle pdb=" CB ABU D 504 " pdb=" CG ABU D 504 " pdb=" CD ABU D 504 " ideal model delta sigma weight residual 116.08 109.43 6.65 3.00e+00 1.11e-01 4.91e+00 angle pdb=" CB ABU E 504 " pdb=" CG ABU E 504 " pdb=" CD ABU E 504 " ideal model delta sigma weight residual 116.08 109.44 6.64 3.00e+00 1.11e-01 4.90e+00 ... (remaining 19770 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.75: 8725 21.75 - 43.50: 150 43.50 - 65.24: 5 65.24 - 86.99: 30 86.99 - 108.74: 20 Dihedral angle restraints: 8930 sinusoidal: 3815 harmonic: 5115 Sorted by residual: dihedral pdb=" CB CYS C 154 " pdb=" SG CYS C 154 " pdb=" SG CYS C 168 " pdb=" CB CYS C 168 " ideal model delta sinusoidal sigma weight residual 93.00 36.38 56.62 1 1.00e+01 1.00e-02 4.32e+01 dihedral pdb=" CB CYS D 154 " pdb=" SG CYS D 154 " pdb=" SG CYS D 168 " pdb=" CB CYS D 168 " ideal model delta sinusoidal sigma weight residual 93.00 36.39 56.61 1 1.00e+01 1.00e-02 4.32e+01 dihedral pdb=" CB CYS E 154 " pdb=" SG CYS E 154 " pdb=" SG CYS E 168 " pdb=" CB CYS E 168 " ideal model delta sinusoidal sigma weight residual 93.00 36.40 56.60 1 1.00e+01 1.00e-02 4.31e+01 ... (remaining 8927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2059 0.078 - 0.156: 196 0.156 - 0.235: 0 0.235 - 0.313: 5 0.313 - 0.391: 5 Chirality restraints: 2265 Sorted by residual: chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-02 2.50e+03 3.82e+02 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-02 2.50e+03 3.80e+02 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-02 2.50e+03 3.80e+02 ... (remaining 2262 not shown) Planarity restraints: 2455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 102 " 0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO D 103 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 410 " 0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO D 411 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO D 411 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 411 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 410 " 0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO C 411 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO C 411 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 411 " 0.016 5.00e-02 4.00e+02 ... (remaining 2452 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4025 2.81 - 3.33: 12257 3.33 - 3.85: 21913 3.85 - 4.38: 27100 4.38 - 4.90: 45477 Nonbonded interactions: 110772 Sorted by model distance: nonbonded pdb=" OG1 THR C 178 " pdb=" OD1 ASN C 180 " model vdw 2.285 3.040 nonbonded pdb=" OG1 THR E 178 " pdb=" OD1 ASN E 180 " model vdw 2.286 3.040 nonbonded pdb=" OG1 THR A 178 " pdb=" OD1 ASN A 180 " model vdw 2.286 3.040 nonbonded pdb=" OG1 THR D 178 " pdb=" OD1 ASN D 180 " model vdw 2.286 3.040 nonbonded pdb=" OG1 THR B 178 " pdb=" OD1 ASN B 180 " model vdw 2.286 3.040 ... (remaining 110767 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: 0.02 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: 3.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.320 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.162 14610 Z= 0.207 Angle : 0.756 24.210 19840 Z= 0.321 Chirality : 0.046 0.391 2265 Planarity : 0.003 0.028 2450 Dihedral : 11.125 108.738 5580 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % 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: -4.40 (0.15), residues: 1710 helix: -4.20 (0.11), residues: 465 sheet: -2.53 (0.24), residues: 335 loop : -2.31 (0.17), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 234 TYR 0.004 0.000 TYR D 74 PHE 0.003 0.001 PHE B 258 TRP 0.002 0.000 TRP A 422 HIS 0.001 0.000 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00210 (14585) covalent geometry : angle 0.52608 (19775) SS BOND : bond 0.11439 ( 10) SS BOND : angle 5.75362 ( 20) hydrogen bonds : bond 0.32624 ( 475) hydrogen bonds : angle 10.39129 ( 1635) link_BETA1-4 : bond 0.06465 ( 10) link_BETA1-4 : angle 13.15746 ( 30) link_NAG-ASN : bond 0.00136 ( 5) link_NAG-ASN : angle 0.71023 ( 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 495 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 495 time to evaluate : 0.526 Fit side-chains REVERT: A 71 THR cc_start: 0.8787 (p) cc_final: 0.8553 (p) REVERT: A 75 ARG cc_start: 0.7329 (ttm-80) cc_final: 0.6824 (ttm110) REVERT: A 86 ASP cc_start: 0.8536 (t0) cc_final: 0.8314 (t70) REVERT: A 92 SER cc_start: 0.8643 (p) cc_final: 0.8373 (t) REVERT: A 96 ASP cc_start: 0.8389 (m-30) cc_final: 0.7837 (m-30) REVERT: A 105 MET cc_start: 0.7872 (mmm) cc_final: 0.7412 (ppp) REVERT: A 113 ASP cc_start: 0.8346 (p0) cc_final: 0.8012 (p0) REVERT: A 138 LYS cc_start: 0.8925 (mtpt) cc_final: 0.8401 (mtpp) REVERT: A 163 MET cc_start: 0.6950 (mpp) cc_final: 0.6316 (mpp) REVERT: A 206 LYS cc_start: 0.7780 (mtpt) cc_final: 0.7558 (mttt) REVERT: A 222 LYS cc_start: 0.6855 (ptmm) cc_final: 0.6487 (pttt) REVERT: A 291 PRO cc_start: 0.9313 (Cg_endo) cc_final: 0.9107 (Cg_exo) REVERT: A 295 TYR cc_start: 0.8200 (p90) cc_final: 0.7526 (p90) REVERT: A 398 ARG cc_start: 0.6573 (ttm170) cc_final: 0.6325 (ttm170) REVERT: B 45 ARG cc_start: 0.8660 (ptt90) cc_final: 0.8351 (ptm-80) REVERT: B 71 THR cc_start: 0.8691 (p) cc_final: 0.8474 (p) REVERT: B 96 ASP cc_start: 0.8398 (m-30) cc_final: 0.7744 (m-30) REVERT: B 105 MET cc_start: 0.7770 (mmm) cc_final: 0.7233 (ppp) REVERT: B 113 ASP cc_start: 0.8388 (p0) cc_final: 0.8068 (p0) REVERT: B 138 LYS cc_start: 0.8978 (mtpt) cc_final: 0.8685 (mtmm) REVERT: B 163 MET cc_start: 0.6889 (mpp) cc_final: 0.6226 (mpp) REVERT: B 206 LYS cc_start: 0.7774 (mtpt) cc_final: 0.7546 (mttt) REVERT: B 207 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8159 (tt0) REVERT: B 222 LYS cc_start: 0.7058 (ptmm) cc_final: 0.6646 (pttt) REVERT: B 295 TYR cc_start: 0.8299 (p90) cc_final: 0.7706 (p90) REVERT: B 398 ARG cc_start: 0.6530 (ttm170) cc_final: 0.6323 (ttm170) REVERT: C 75 ARG cc_start: 0.7283 (ttm-80) cc_final: 0.6816 (ttm110) REVERT: C 86 ASP cc_start: 0.8389 (t0) cc_final: 0.8173 (t70) REVERT: C 92 SER cc_start: 0.8730 (p) cc_final: 0.8441 (t) REVERT: C 96 ASP cc_start: 0.8480 (m-30) cc_final: 0.7854 (m-30) REVERT: C 105 MET cc_start: 0.7885 (mmm) cc_final: 0.7421 (ppp) REVERT: C 113 ASP cc_start: 0.8402 (p0) cc_final: 0.8080 (p0) REVERT: C 138 LYS cc_start: 0.9018 (mtpt) cc_final: 0.8574 (mtpp) REVERT: C 163 MET cc_start: 0.7012 (mpp) cc_final: 0.6425 (mpp) REVERT: C 206 LYS cc_start: 0.7891 (mtpt) cc_final: 0.7655 (mttt) REVERT: C 222 LYS cc_start: 0.7034 (ptmm) cc_final: 0.6638 (pttt) REVERT: C 233 GLU cc_start: 0.6920 (tt0) cc_final: 0.6692 (tt0) REVERT: C 291 PRO cc_start: 0.9322 (Cg_endo) cc_final: 0.9114 (Cg_exo) REVERT: C 295 TYR cc_start: 0.8259 (p90) cc_final: 0.7645 (p90) REVERT: C 398 ARG cc_start: 0.6656 (ttm170) cc_final: 0.6455 (ttm170) REVERT: D 75 ARG cc_start: 0.7322 (ttm-80) cc_final: 0.6857 (ttm110) REVERT: D 86 ASP cc_start: 0.8340 (t0) cc_final: 0.8113 (t70) REVERT: D 96 ASP cc_start: 0.8505 (m-30) cc_final: 0.7940 (m-30) REVERT: D 105 MET cc_start: 0.7785 (mmm) cc_final: 0.7166 (ppp) REVERT: D 138 LYS cc_start: 0.8843 (mtpt) cc_final: 0.8562 (mtmm) REVERT: D 173 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6725 (mt-10) REVERT: D 206 LYS cc_start: 0.7660 (mtpt) cc_final: 0.7327 (mttt) REVERT: D 222 LYS cc_start: 0.7108 (ptmm) cc_final: 0.6461 (pttt) REVERT: D 233 GLU cc_start: 0.6784 (tt0) cc_final: 0.6555 (tt0) REVERT: D 295 TYR cc_start: 0.8356 (p90) cc_final: 0.7916 (p90) REVERT: D 398 ARG cc_start: 0.6617 (ttm170) cc_final: 0.6382 (ttm170) REVERT: E 45 ARG cc_start: 0.8761 (ptt90) cc_final: 0.8508 (ptm-80) REVERT: E 86 ASP cc_start: 0.8521 (t0) cc_final: 0.8291 (t70) REVERT: E 92 SER cc_start: 0.8564 (p) cc_final: 0.8259 (t) REVERT: E 96 ASP cc_start: 0.8477 (m-30) cc_final: 0.7979 (m-30) REVERT: E 105 MET cc_start: 0.7881 (mmm) cc_final: 0.7457 (ppp) REVERT: E 113 ASP cc_start: 0.8395 (p0) cc_final: 0.8067 (p0) REVERT: E 138 LYS cc_start: 0.8864 (mtpt) cc_final: 0.8338 (mtpp) REVERT: E 206 LYS cc_start: 0.7644 (mtpt) cc_final: 0.7398 (mttt) REVERT: E 291 PRO cc_start: 0.9285 (Cg_endo) cc_final: 0.9064 (Cg_exo) REVERT: E 295 TYR cc_start: 0.8289 (p90) cc_final: 0.7570 (p90) outliers start: 0 outliers final: 0 residues processed: 495 average time/residue: 0.1135 time to fit residues: 81.7147 Evaluate side-chains 324 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.0670 chunk 103 optimal weight: 0.0980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 0.5980 overall best weight: 0.2918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 193 GLN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN D 261 ASN E 261 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.179563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.140877 restraints weight = 17644.750| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 3.56 r_work: 0.3369 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.2196 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= 0.138 Angle : 0.682 11.986 19840 Z= 0.328 Chirality : 0.045 0.172 2265 Planarity : 0.004 0.037 2450 Dihedral : 9.850 67.788 2200 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.52 % Allowed : 10.71 % Favored : 86.77 % 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: -3.30 (0.17), residues: 1710 helix: -2.37 (0.18), residues: 530 sheet: -1.63 (0.25), residues: 325 loop : -2.25 (0.18), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 147 TYR 0.014 0.001 TYR E 317 PHE 0.010 0.001 PHE B 177 TRP 0.007 0.001 TRP C 302 HIS 0.002 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00274 (14585) covalent geometry : angle 0.61751 (19775) SS BOND : bond 0.00269 ( 10) SS BOND : angle 0.97727 ( 20) hydrogen bonds : bond 0.05870 ( 475) hydrogen bonds : angle 5.95726 ( 1635) link_BETA1-4 : bond 0.01617 ( 10) link_BETA1-4 : angle 5.08045 ( 30) link_NAG-ASN : bond 0.02242 ( 5) link_NAG-ASN : angle 7.73233 ( 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 407 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 368 time to evaluate : 0.426 Fit side-chains REVERT: A 28 GLU cc_start: 0.7025 (mp0) cc_final: 0.6743 (mp0) REVERT: A 45 ARG cc_start: 0.8696 (ptt90) cc_final: 0.8317 (ptm-80) REVERT: A 77 ASN cc_start: 0.7954 (t0) cc_final: 0.7727 (t0) REVERT: A 86 ASP cc_start: 0.8347 (t0) cc_final: 0.8026 (t70) REVERT: A 92 SER cc_start: 0.8856 (p) cc_final: 0.8504 (t) REVERT: A 96 ASP cc_start: 0.8127 (m-30) cc_final: 0.7664 (m-30) REVERT: A 105 MET cc_start: 0.8192 (mmm) cc_final: 0.7200 (ppp) REVERT: A 113 ASP cc_start: 0.8077 (p0) cc_final: 0.7854 (p0) REVERT: A 138 LYS cc_start: 0.8565 (mtpt) cc_final: 0.8061 (mtpp) REVERT: A 179 MET cc_start: 0.7309 (mmm) cc_final: 0.7030 (mmm) REVERT: A 206 LYS cc_start: 0.7490 (mtpt) cc_final: 0.7280 (mttt) REVERT: A 295 TYR cc_start: 0.8052 (p90) cc_final: 0.7281 (p90) REVERT: A 398 ARG cc_start: 0.6711 (ttm170) cc_final: 0.6351 (ttm170) REVERT: A 418 ASN cc_start: 0.6533 (t0) cc_final: 0.6242 (m110) REVERT: B 45 ARG cc_start: 0.8577 (ptt90) cc_final: 0.8251 (ptm-80) REVERT: B 69 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7345 (mm-30) REVERT: B 72 MET cc_start: 0.8449 (mtt) cc_final: 0.8241 (mtt) REVERT: B 96 ASP cc_start: 0.8126 (m-30) cc_final: 0.7641 (m-30) REVERT: B 105 MET cc_start: 0.8041 (mmm) cc_final: 0.7083 (ppp) REVERT: B 138 LYS cc_start: 0.8577 (mtpt) cc_final: 0.8311 (mtmm) REVERT: B 141 ASN cc_start: 0.8262 (m-40) cc_final: 0.8039 (m-40) REVERT: B 163 MET cc_start: 0.6781 (mpp) cc_final: 0.6237 (mpp) REVERT: B 179 MET cc_start: 0.7395 (mmm) cc_final: 0.7128 (mmm) REVERT: B 295 TYR cc_start: 0.8130 (p90) cc_final: 0.7439 (p90) REVERT: B 398 ARG cc_start: 0.6727 (ttm170) cc_final: 0.6380 (ttm170) REVERT: B 422 TRP cc_start: 0.8239 (m100) cc_final: 0.7889 (m100) REVERT: C 24 MET cc_start: 0.6697 (ptp) cc_final: 0.6477 (ptp) REVERT: C 28 GLU cc_start: 0.6981 (mp0) cc_final: 0.6684 (mp0) REVERT: C 45 ARG cc_start: 0.8593 (ptm-80) cc_final: 0.8357 (ptm160) REVERT: C 72 MET cc_start: 0.8451 (mtt) cc_final: 0.8001 (ttm) REVERT: C 77 ASN cc_start: 0.7918 (t0) cc_final: 0.7672 (t0) REVERT: C 86 ASP cc_start: 0.8242 (t0) cc_final: 0.7953 (t70) REVERT: C 96 ASP cc_start: 0.8214 (m-30) cc_final: 0.7753 (m-30) REVERT: C 105 MET cc_start: 0.8224 (mmm) cc_final: 0.7333 (ppp) REVERT: C 138 LYS cc_start: 0.8619 (mtpt) cc_final: 0.8184 (mtpp) REVERT: C 179 MET cc_start: 0.7595 (mmm) cc_final: 0.7043 (mmm) REVERT: C 206 LYS cc_start: 0.7671 (mtpt) cc_final: 0.7398 (mttt) REVERT: C 250 ILE cc_start: 0.4813 (mm) cc_final: 0.4413 (mm) REVERT: C 295 TYR cc_start: 0.8091 (p90) cc_final: 0.7403 (p90) REVERT: C 398 ARG cc_start: 0.6831 (ttm170) cc_final: 0.6484 (ttm170) REVERT: D 28 GLU cc_start: 0.7162 (mp0) cc_final: 0.6548 (mp0) REVERT: D 45 ARG cc_start: 0.8864 (ptt90) cc_final: 0.8480 (ptm-80) REVERT: D 75 ARG cc_start: 0.7061 (ttm-80) cc_final: 0.6817 (ttm-80) REVERT: D 77 ASN cc_start: 0.7990 (t0) cc_final: 0.7767 (t0) REVERT: D 86 ASP cc_start: 0.8158 (t0) cc_final: 0.7832 (t70) REVERT: D 96 ASP cc_start: 0.8216 (m-30) cc_final: 0.7790 (m-30) REVERT: D 105 MET cc_start: 0.8097 (mmm) cc_final: 0.7105 (ppp) REVERT: D 138 LYS cc_start: 0.8387 (mtpt) cc_final: 0.8147 (mtmm) REVERT: D 206 LYS cc_start: 0.7334 (mtpt) cc_final: 0.6979 (mttm) REVERT: D 295 TYR cc_start: 0.8205 (p90) cc_final: 0.7692 (p90) REVERT: D 398 ARG cc_start: 0.6742 (ttm170) cc_final: 0.6382 (ttm170) REVERT: D 418 ASN cc_start: 0.6424 (t0) cc_final: 0.6140 (m110) REVERT: E 28 GLU cc_start: 0.7065 (mp0) cc_final: 0.6721 (mp0) REVERT: E 41 ASP cc_start: 0.7796 (t70) cc_final: 0.7461 (t0) REVERT: E 45 ARG cc_start: 0.8708 (ptt90) cc_final: 0.8261 (ptm-80) REVERT: E 69 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7656 (mm-30) REVERT: E 72 MET cc_start: 0.8360 (mtt) cc_final: 0.8009 (mmt) REVERT: E 86 ASP cc_start: 0.8311 (t0) cc_final: 0.7763 (t70) REVERT: E 92 SER cc_start: 0.8727 (p) cc_final: 0.8406 (t) REVERT: E 96 ASP cc_start: 0.8240 (m-30) cc_final: 0.7850 (m-30) REVERT: E 102 ASP cc_start: 0.8259 (t0) cc_final: 0.7900 (m-30) REVERT: E 105 MET cc_start: 0.8241 (mmm) cc_final: 0.7358 (ppp) REVERT: E 113 ASP cc_start: 0.8186 (p0) cc_final: 0.7883 (p0) REVERT: E 138 LYS cc_start: 0.8447 (mtpt) cc_final: 0.8227 (mtpp) REVERT: E 141 ASN cc_start: 0.8092 (m-40) cc_final: 0.7855 (m-40) REVERT: E 170 MET cc_start: 0.7882 (ptp) cc_final: 0.7465 (ptp) REVERT: E 295 TYR cc_start: 0.8084 (p90) cc_final: 0.7259 (p90) REVERT: E 418 ASN cc_start: 0.6430 (t0) cc_final: 0.6203 (m110) outliers start: 39 outliers final: 25 residues processed: 392 average time/residue: 0.1099 time to fit residues: 63.3203 Evaluate side-chains 335 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 310 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 275 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 4.9990 chunk 146 optimal weight: 7.9990 chunk 140 optimal weight: 6.9990 chunk 59 optimal weight: 0.0970 chunk 167 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 19 optimal weight: 0.4980 chunk 97 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 ASN D 261 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.174374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.136165 restraints weight = 17491.273| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 3.56 r_work: 0.3305 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14610 Z= 0.122 Angle : 0.641 11.705 19840 Z= 0.298 Chirality : 0.045 0.170 2265 Planarity : 0.003 0.030 2450 Dihedral : 7.035 44.044 2200 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.39 % Allowed : 14.26 % Favored : 83.35 % 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: -2.24 (0.19), residues: 1710 helix: -1.18 (0.21), residues: 525 sheet: -1.17 (0.25), residues: 375 loop : -1.77 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 75 TYR 0.023 0.001 TYR D 317 PHE 0.008 0.001 PHE A 417 TRP 0.011 0.001 TRP D 302 HIS 0.002 0.001 HIS D 125 Details of bonding type rmsd covalent geometry : bond 0.00270 (14585) covalent geometry : angle 0.57374 (19775) SS BOND : bond 0.00443 ( 10) SS BOND : angle 0.60918 ( 20) hydrogen bonds : bond 0.04248 ( 475) hydrogen bonds : angle 4.94837 ( 1635) link_BETA1-4 : bond 0.00759 ( 10) link_BETA1-4 : angle 4.62716 ( 30) link_NAG-ASN : bond 0.01275 ( 5) link_NAG-ASN : angle 8.17812 ( 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 370 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 333 time to evaluate : 0.363 Fit side-chains REVERT: A 28 GLU cc_start: 0.7088 (mp0) cc_final: 0.6887 (mp0) REVERT: A 41 ASP cc_start: 0.8243 (t0) cc_final: 0.7920 (t0) REVERT: A 45 ARG cc_start: 0.8755 (ptt90) cc_final: 0.8383 (ptm-80) REVERT: A 72 MET cc_start: 0.8561 (mtt) cc_final: 0.8151 (mmt) REVERT: A 86 ASP cc_start: 0.8459 (t0) cc_final: 0.8156 (t70) REVERT: A 92 SER cc_start: 0.8838 (p) cc_final: 0.8463 (t) REVERT: A 96 ASP cc_start: 0.8247 (m-30) cc_final: 0.7853 (m-30) REVERT: A 105 MET cc_start: 0.8288 (mmm) cc_final: 0.7116 (ppp) REVERT: A 138 LYS cc_start: 0.8452 (mtpt) cc_final: 0.7945 (mtpp) REVERT: A 141 ASN cc_start: 0.8221 (m-40) cc_final: 0.7999 (m-40) REVERT: A 206 LYS cc_start: 0.7535 (mtpt) cc_final: 0.7244 (mttt) REVERT: A 295 TYR cc_start: 0.8154 (p90) cc_final: 0.7528 (p90) REVERT: A 398 ARG cc_start: 0.6735 (ttm170) cc_final: 0.6330 (ttm170) REVERT: B 41 ASP cc_start: 0.8089 (t0) cc_final: 0.7795 (t0) REVERT: B 45 ARG cc_start: 0.8625 (ptt90) cc_final: 0.8140 (ptm-80) REVERT: B 69 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7755 (mm-30) REVERT: B 72 MET cc_start: 0.8551 (mtt) cc_final: 0.8335 (mtt) REVERT: B 86 ASP cc_start: 0.8218 (t0) cc_final: 0.7840 (t70) REVERT: B 96 ASP cc_start: 0.8224 (m-30) cc_final: 0.7803 (m-30) REVERT: B 105 MET cc_start: 0.8162 (mmm) cc_final: 0.7126 (ppp) REVERT: B 138 LYS cc_start: 0.8625 (mtpt) cc_final: 0.8346 (mtmm) REVERT: B 163 MET cc_start: 0.6958 (mpp) cc_final: 0.6460 (mpp) REVERT: B 177 PHE cc_start: 0.7874 (m-80) cc_final: 0.7672 (m-10) REVERT: B 295 TYR cc_start: 0.8181 (p90) cc_final: 0.7470 (p90) REVERT: B 398 ARG cc_start: 0.6797 (ttm170) cc_final: 0.6390 (ttm170) REVERT: C 24 MET cc_start: 0.6770 (ptp) cc_final: 0.6506 (ptp) REVERT: C 41 ASP cc_start: 0.8004 (t0) cc_final: 0.7744 (t0) REVERT: C 86 ASP cc_start: 0.8400 (t0) cc_final: 0.8099 (t70) REVERT: C 96 ASP cc_start: 0.8288 (m-30) cc_final: 0.7847 (m-30) REVERT: C 105 MET cc_start: 0.8273 (mmm) cc_final: 0.7274 (ppp) REVERT: C 138 LYS cc_start: 0.8510 (mtpt) cc_final: 0.8053 (mtpp) REVERT: C 163 MET cc_start: 0.7035 (mpp) cc_final: 0.6801 (mpp) REVERT: C 179 MET cc_start: 0.7677 (mmm) cc_final: 0.7060 (mmm) REVERT: C 206 LYS cc_start: 0.7682 (mtpt) cc_final: 0.7423 (mttt) REVERT: C 250 ILE cc_start: 0.4784 (mm) cc_final: 0.4437 (mm) REVERT: C 295 TYR cc_start: 0.8183 (p90) cc_final: 0.7516 (p90) REVERT: C 398 ARG cc_start: 0.6869 (ttm170) cc_final: 0.6476 (ttm170) REVERT: D 28 GLU cc_start: 0.7200 (mp0) cc_final: 0.6589 (mp0) REVERT: D 45 ARG cc_start: 0.8903 (ptt90) cc_final: 0.8500 (ptm-80) REVERT: D 72 MET cc_start: 0.8616 (mtt) cc_final: 0.8226 (mmm) REVERT: D 96 ASP cc_start: 0.8311 (m-30) cc_final: 0.7865 (m-30) REVERT: D 105 MET cc_start: 0.8206 (mmm) cc_final: 0.7219 (ppp) REVERT: D 138 LYS cc_start: 0.8192 (mtpt) cc_final: 0.7672 (mtpp) REVERT: D 139 ASN cc_start: 0.8980 (p0) cc_final: 0.8593 (p0) REVERT: D 141 ASN cc_start: 0.7966 (m-40) cc_final: 0.7693 (m-40) REVERT: D 156 MET cc_start: 0.8312 (mmt) cc_final: 0.8044 (mmt) REVERT: D 206 LYS cc_start: 0.7396 (mtpt) cc_final: 0.7025 (mttm) REVERT: D 295 TYR cc_start: 0.8214 (p90) cc_final: 0.7868 (p90) REVERT: D 398 ARG cc_start: 0.6711 (ttm170) cc_final: 0.6321 (ttm170) REVERT: E 28 GLU cc_start: 0.6953 (mp0) cc_final: 0.6624 (mp0) REVERT: E 72 MET cc_start: 0.8545 (mtt) cc_final: 0.8291 (mmt) REVERT: E 92 SER cc_start: 0.8707 (p) cc_final: 0.8367 (t) REVERT: E 96 ASP cc_start: 0.8320 (m-30) cc_final: 0.7909 (m-30) REVERT: E 102 ASP cc_start: 0.8268 (t0) cc_final: 0.7830 (m-30) REVERT: E 105 MET cc_start: 0.8334 (mmm) cc_final: 0.7321 (ppp) REVERT: E 138 LYS cc_start: 0.8421 (mtpt) cc_final: 0.8015 (mtpp) REVERT: E 170 MET cc_start: 0.7987 (ptp) cc_final: 0.7684 (ptp) REVERT: E 295 TYR cc_start: 0.8168 (p90) cc_final: 0.7347 (p90) REVERT: E 418 ASN cc_start: 0.6416 (t0) cc_final: 0.6101 (m110) outliers start: 37 outliers final: 26 residues processed: 362 average time/residue: 0.0999 time to fit residues: 54.8643 Evaluate side-chains 353 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 327 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 275 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 3 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 151 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 261 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.164141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.122541 restraints weight = 17957.530| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 3.68 r_work: 0.3138 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 14610 Z= 0.196 Angle : 0.677 9.997 19840 Z= 0.326 Chirality : 0.047 0.205 2265 Planarity : 0.004 0.038 2450 Dihedral : 5.427 38.620 2200 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.94 % Allowed : 14.90 % Favored : 81.16 % 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: -1.68 (0.20), residues: 1710 helix: -0.79 (0.22), residues: 525 sheet: -0.88 (0.25), residues: 385 loop : -1.36 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 229 TYR 0.017 0.002 TYR E 144 PHE 0.018 0.002 PHE A 309 TRP 0.011 0.001 TRP C 186 HIS 0.005 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00454 (14585) covalent geometry : angle 0.62781 (19775) SS BOND : bond 0.00465 ( 10) SS BOND : angle 0.86245 ( 20) hydrogen bonds : bond 0.03906 ( 475) hydrogen bonds : angle 4.76957 ( 1635) link_BETA1-4 : bond 0.00907 ( 10) link_BETA1-4 : angle 4.40837 ( 30) link_NAG-ASN : bond 0.00938 ( 5) link_NAG-ASN : angle 6.79368 ( 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 411 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 350 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8191 (t0) cc_final: 0.7817 (t0) REVERT: A 45 ARG cc_start: 0.8829 (ptt90) cc_final: 0.8398 (ptm-80) REVERT: A 86 ASP cc_start: 0.8749 (t0) cc_final: 0.8468 (t0) REVERT: A 96 ASP cc_start: 0.8332 (m-30) cc_final: 0.7905 (m-30) REVERT: A 105 MET cc_start: 0.8273 (mmm) cc_final: 0.7222 (ptm) REVERT: A 138 LYS cc_start: 0.8523 (mtpt) cc_final: 0.8222 (mtmm) REVERT: A 139 ASN cc_start: 0.8844 (p0) cc_final: 0.8195 (p0) REVERT: A 141 ASN cc_start: 0.8173 (m-40) cc_final: 0.7763 (m-40) REVERT: A 179 MET cc_start: 0.7639 (mmm) cc_final: 0.7211 (mmm) REVERT: A 188 GLU cc_start: 0.8886 (mp0) cc_final: 0.8524 (mp0) REVERT: A 206 LYS cc_start: 0.7602 (mtpt) cc_final: 0.7278 (mttt) REVERT: A 254 SER cc_start: 0.8972 (m) cc_final: 0.8528 (p) REVERT: A 295 TYR cc_start: 0.8170 (p90) cc_final: 0.7888 (p90) REVERT: A 398 ARG cc_start: 0.6772 (ttm170) cc_final: 0.6308 (ttm170) REVERT: B 41 ASP cc_start: 0.8211 (t0) cc_final: 0.7782 (t0) REVERT: B 96 ASP cc_start: 0.8317 (m-30) cc_final: 0.7864 (m-30) REVERT: B 105 MET cc_start: 0.8221 (mmm) cc_final: 0.7182 (ppp) REVERT: B 130 ASP cc_start: 0.8322 (m-30) cc_final: 0.8050 (m-30) REVERT: B 138 LYS cc_start: 0.8424 (mtpt) cc_final: 0.8145 (mtmm) REVERT: B 163 MET cc_start: 0.7560 (mpp) cc_final: 0.7054 (mpp) REVERT: B 179 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7427 (mmm) REVERT: B 188 GLU cc_start: 0.8862 (mp0) cc_final: 0.8501 (mp0) REVERT: B 295 TYR cc_start: 0.8201 (p90) cc_final: 0.7730 (p90) REVERT: B 398 ARG cc_start: 0.6879 (ttm170) cc_final: 0.6416 (ttm170) REVERT: C 41 ASP cc_start: 0.8102 (t0) cc_final: 0.7725 (t0) REVERT: C 96 ASP cc_start: 0.8296 (m-30) cc_final: 0.7884 (m-30) REVERT: C 105 MET cc_start: 0.8474 (mmm) cc_final: 0.7199 (ppp) REVERT: C 130 ASP cc_start: 0.8435 (m-30) cc_final: 0.8101 (m-30) REVERT: C 138 LYS cc_start: 0.8347 (mtpt) cc_final: 0.7938 (mtpp) REVERT: C 179 MET cc_start: 0.7979 (mmm) cc_final: 0.7623 (mmm) REVERT: C 188 GLU cc_start: 0.8941 (mp0) cc_final: 0.8620 (mp0) REVERT: C 206 LYS cc_start: 0.7737 (mtpt) cc_final: 0.7460 (mttt) REVERT: C 222 LYS cc_start: 0.6380 (ptmm) cc_final: 0.6153 (ptmt) REVERT: C 295 TYR cc_start: 0.8207 (p90) cc_final: 0.7748 (p90) REVERT: C 398 ARG cc_start: 0.6927 (ttm170) cc_final: 0.6493 (ttm170) REVERT: D 28 GLU cc_start: 0.7207 (mp0) cc_final: 0.6661 (mp0) REVERT: D 41 ASP cc_start: 0.8327 (t0) cc_final: 0.7897 (t0) REVERT: D 86 ASP cc_start: 0.8915 (t0) cc_final: 0.8107 (t70) REVERT: D 96 ASP cc_start: 0.8423 (m-30) cc_final: 0.7979 (m-30) REVERT: D 105 MET cc_start: 0.8305 (mmm) cc_final: 0.7152 (ptm) REVERT: D 130 ASP cc_start: 0.8283 (m-30) cc_final: 0.7942 (m-30) REVERT: D 138 LYS cc_start: 0.8241 (mtpt) cc_final: 0.7888 (mtmm) REVERT: D 139 ASN cc_start: 0.8896 (p0) cc_final: 0.8451 (p0) REVERT: D 141 ASN cc_start: 0.7908 (m-40) cc_final: 0.7412 (m-40) REVERT: D 188 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8512 (mp0) REVERT: D 206 LYS cc_start: 0.7460 (mtpt) cc_final: 0.7072 (mttm) REVERT: D 254 SER cc_start: 0.8842 (m) cc_final: 0.8468 (p) REVERT: D 398 ARG cc_start: 0.6740 (ttm170) cc_final: 0.6314 (ttm170) REVERT: E 28 GLU cc_start: 0.6995 (mp0) cc_final: 0.6771 (mp0) REVERT: E 41 ASP cc_start: 0.8342 (t0) cc_final: 0.7843 (t0) REVERT: E 70 THR cc_start: 0.8410 (m) cc_final: 0.8183 (p) REVERT: E 96 ASP cc_start: 0.8291 (m-30) cc_final: 0.7862 (m-30) REVERT: E 105 MET cc_start: 0.8377 (mmm) cc_final: 0.7373 (ptm) REVERT: E 130 ASP cc_start: 0.8377 (m-30) cc_final: 0.8098 (m-30) REVERT: E 138 LYS cc_start: 0.8233 (mtpt) cc_final: 0.7900 (mtpp) REVERT: E 188 GLU cc_start: 0.8841 (mp0) cc_final: 0.8617 (mp0) REVERT: E 254 SER cc_start: 0.8933 (m) cc_final: 0.8500 (p) REVERT: E 295 TYR cc_start: 0.8111 (p90) cc_final: 0.7421 (p90) outliers start: 61 outliers final: 41 residues processed: 397 average time/residue: 0.1075 time to fit residues: 62.8544 Evaluate side-chains 356 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 313 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 419 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 95 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 153 optimal weight: 0.0270 chunk 9 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 163 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 ASN D 261 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.166120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.125754 restraints weight = 17963.003| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 3.65 r_work: 0.3183 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14610 Z= 0.112 Angle : 0.611 9.659 19840 Z= 0.286 Chirality : 0.045 0.187 2265 Planarity : 0.003 0.028 2450 Dihedral : 4.858 27.260 2200 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.10 % Allowed : 16.90 % Favored : 80.00 % 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: -1.36 (0.20), residues: 1710 helix: -0.39 (0.23), residues: 525 sheet: -0.50 (0.27), residues: 365 loop : -1.38 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 229 TYR 0.016 0.001 TYR E 317 PHE 0.010 0.001 PHE D 417 TRP 0.006 0.001 TRP C 302 HIS 0.002 0.001 HIS D 125 Details of bonding type rmsd covalent geometry : bond 0.00249 (14585) covalent geometry : angle 0.56183 (19775) SS BOND : bond 0.00183 ( 10) SS BOND : angle 0.54353 ( 20) hydrogen bonds : bond 0.03368 ( 475) hydrogen bonds : angle 4.42601 ( 1635) link_BETA1-4 : bond 0.00801 ( 10) link_BETA1-4 : angle 4.12087 ( 30) link_NAG-ASN : bond 0.00717 ( 5) link_NAG-ASN : angle 6.63403 ( 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 348 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 300 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8081 (t0) cc_final: 0.7735 (t0) REVERT: A 45 ARG cc_start: 0.8701 (ptt90) cc_final: 0.8369 (ptm-80) REVERT: A 86 ASP cc_start: 0.8632 (t0) cc_final: 0.8408 (t70) REVERT: A 96 ASP cc_start: 0.8319 (m-30) cc_final: 0.7919 (m-30) REVERT: A 105 MET cc_start: 0.8271 (mmm) cc_final: 0.7207 (ptm) REVERT: A 138 LYS cc_start: 0.8502 (mtpt) cc_final: 0.8258 (mtmm) REVERT: A 139 ASN cc_start: 0.8825 (p0) cc_final: 0.8080 (p0) REVERT: A 141 ASN cc_start: 0.8223 (m-40) cc_final: 0.7792 (m-40) REVERT: A 179 MET cc_start: 0.7459 (mmm) cc_final: 0.7014 (mmm) REVERT: A 206 LYS cc_start: 0.7635 (mtpt) cc_final: 0.7359 (mttt) REVERT: A 254 SER cc_start: 0.8994 (m) cc_final: 0.8591 (p) REVERT: A 295 TYR cc_start: 0.8082 (p90) cc_final: 0.7685 (p90) REVERT: A 398 ARG cc_start: 0.6775 (ttm170) cc_final: 0.6289 (ttm170) REVERT: B 72 MET cc_start: 0.8661 (mtt) cc_final: 0.8393 (mmt) REVERT: B 96 ASP cc_start: 0.8300 (m-30) cc_final: 0.7904 (m-30) REVERT: B 105 MET cc_start: 0.8266 (mmm) cc_final: 0.7193 (ppp) REVERT: B 130 ASP cc_start: 0.8276 (m-30) cc_final: 0.7993 (m-30) REVERT: B 138 LYS cc_start: 0.8430 (mtpt) cc_final: 0.8127 (mtmm) REVERT: B 163 MET cc_start: 0.7212 (mpp) cc_final: 0.6927 (mtm) REVERT: B 188 GLU cc_start: 0.8792 (mp0) cc_final: 0.8426 (pm20) REVERT: B 295 TYR cc_start: 0.8168 (p90) cc_final: 0.7662 (p90) REVERT: B 398 ARG cc_start: 0.6859 (ttm170) cc_final: 0.6382 (ttm170) REVERT: C 41 ASP cc_start: 0.7945 (t0) cc_final: 0.7564 (t0) REVERT: C 72 MET cc_start: 0.8190 (tpp) cc_final: 0.7850 (tpp) REVERT: C 96 ASP cc_start: 0.8311 (m-30) cc_final: 0.7845 (m-30) REVERT: C 105 MET cc_start: 0.8444 (mmm) cc_final: 0.7201 (ppp) REVERT: C 130 ASP cc_start: 0.8359 (m-30) cc_final: 0.8010 (m-30) REVERT: C 138 LYS cc_start: 0.8306 (mtpt) cc_final: 0.7881 (mtpp) REVERT: C 156 MET cc_start: 0.8005 (mtp) cc_final: 0.7753 (mtm) REVERT: C 179 MET cc_start: 0.7931 (mmm) cc_final: 0.7570 (mmm) REVERT: C 206 LYS cc_start: 0.7674 (mtpt) cc_final: 0.7298 (mttt) REVERT: C 216 LYS cc_start: 0.6713 (OUTLIER) cc_final: 0.6354 (ptpt) REVERT: C 295 TYR cc_start: 0.8135 (p90) cc_final: 0.7653 (p90) REVERT: C 398 ARG cc_start: 0.6905 (ttm170) cc_final: 0.6445 (ttm170) REVERT: D 28 GLU cc_start: 0.7382 (mp0) cc_final: 0.6735 (mp0) REVERT: D 41 ASP cc_start: 0.8245 (t0) cc_final: 0.8030 (t0) REVERT: D 72 MET cc_start: 0.8739 (mtt) cc_final: 0.8417 (mmm) REVERT: D 86 ASP cc_start: 0.8918 (t0) cc_final: 0.8141 (t70) REVERT: D 96 ASP cc_start: 0.8370 (m-30) cc_final: 0.7933 (m-30) REVERT: D 105 MET cc_start: 0.8297 (mmm) cc_final: 0.7150 (ptm) REVERT: D 130 ASP cc_start: 0.8245 (m-30) cc_final: 0.7910 (m-30) REVERT: D 138 LYS cc_start: 0.8145 (mtpt) cc_final: 0.7799 (mtmm) REVERT: D 139 ASN cc_start: 0.8847 (p0) cc_final: 0.8318 (p0) REVERT: D 141 ASN cc_start: 0.7908 (m-40) cc_final: 0.7429 (m-40) REVERT: D 206 LYS cc_start: 0.7437 (mtpt) cc_final: 0.6907 (mttm) REVERT: D 254 SER cc_start: 0.8912 (m) cc_final: 0.8474 (p) REVERT: D 391 MET cc_start: 0.1594 (mmm) cc_final: 0.1265 (mmm) REVERT: D 398 ARG cc_start: 0.6749 (ttm170) cc_final: 0.6313 (ttm170) REVERT: E 28 GLU cc_start: 0.7165 (mp0) cc_final: 0.6800 (mp0) REVERT: E 41 ASP cc_start: 0.8257 (t0) cc_final: 0.7901 (t0) REVERT: E 70 THR cc_start: 0.8391 (m) cc_final: 0.8162 (p) REVERT: E 72 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8282 (mmt) REVERT: E 96 ASP cc_start: 0.8282 (m-30) cc_final: 0.7863 (m-30) REVERT: E 105 MET cc_start: 0.8329 (mmm) cc_final: 0.7232 (ppp) REVERT: E 130 ASP cc_start: 0.8313 (m-30) cc_final: 0.7994 (m-30) REVERT: E 138 LYS cc_start: 0.8281 (mtpt) cc_final: 0.7978 (mtpp) REVERT: E 295 TYR cc_start: 0.8062 (p90) cc_final: 0.7356 (p90) outliers start: 48 outliers final: 37 residues processed: 334 average time/residue: 0.1008 time to fit residues: 50.7555 Evaluate side-chains 336 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 297 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 419 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 17 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 35 optimal weight: 3.9990 chunk 160 optimal weight: 8.9990 chunk 167 optimal weight: 0.9980 chunk 75 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 ASN C 261 ASN D 261 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.184356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.144457 restraints weight = 17971.406| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 3.52 r_work: 0.3166 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14610 Z= 0.148 Angle : 0.609 9.482 19840 Z= 0.285 Chirality : 0.045 0.179 2265 Planarity : 0.003 0.037 2450 Dihedral : 4.678 21.771 2200 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.55 % Allowed : 17.87 % Favored : 78.58 % 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: -1.20 (0.20), residues: 1710 helix: -0.28 (0.23), residues: 525 sheet: -0.47 (0.27), residues: 370 loop : -1.23 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 229 TYR 0.015 0.001 TYR B 317 PHE 0.012 0.001 PHE A 417 TRP 0.008 0.001 TRP E 186 HIS 0.003 0.001 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00347 (14585) covalent geometry : angle 0.56225 (19775) SS BOND : bond 0.00247 ( 10) SS BOND : angle 0.77531 ( 20) hydrogen bonds : bond 0.03287 ( 475) hydrogen bonds : angle 4.41049 ( 1635) link_BETA1-4 : bond 0.00760 ( 10) link_BETA1-4 : angle 3.90530 ( 30) link_NAG-ASN : bond 0.00614 ( 5) link_NAG-ASN : angle 6.50207 ( 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 370 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 315 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8285 (t0) cc_final: 0.8028 (t0) REVERT: A 72 MET cc_start: 0.8609 (mmt) cc_final: 0.8236 (tpp) REVERT: A 86 ASP cc_start: 0.8831 (t0) cc_final: 0.8584 (t70) REVERT: A 89 LEU cc_start: 0.8089 (mp) cc_final: 0.7744 (mt) REVERT: A 96 ASP cc_start: 0.8412 (m-30) cc_final: 0.8035 (m-30) REVERT: A 105 MET cc_start: 0.8349 (mmm) cc_final: 0.7186 (ppp) REVERT: A 138 LYS cc_start: 0.8761 (mtpt) cc_final: 0.8471 (mtmm) REVERT: A 139 ASN cc_start: 0.8932 (p0) cc_final: 0.8106 (p0) REVERT: A 141 ASN cc_start: 0.8463 (m-40) cc_final: 0.7951 (m-40) REVERT: A 179 MET cc_start: 0.7856 (mmm) cc_final: 0.7387 (mmm) REVERT: A 206 LYS cc_start: 0.7847 (mtpt) cc_final: 0.7568 (mttt) REVERT: A 254 SER cc_start: 0.8955 (m) cc_final: 0.8528 (p) REVERT: A 279 MET cc_start: 0.5982 (OUTLIER) cc_final: 0.4754 (ttm) REVERT: A 295 TYR cc_start: 0.8305 (p90) cc_final: 0.7941 (p90) REVERT: A 398 ARG cc_start: 0.6804 (ttm170) cc_final: 0.6306 (ttm170) REVERT: B 41 ASP cc_start: 0.8202 (t0) cc_final: 0.7925 (t0) REVERT: B 72 MET cc_start: 0.8752 (mtt) cc_final: 0.8520 (mmt) REVERT: B 86 ASP cc_start: 0.8944 (t0) cc_final: 0.8452 (t0) REVERT: B 96 ASP cc_start: 0.8416 (m-30) cc_final: 0.8195 (m-30) REVERT: B 105 MET cc_start: 0.8272 (mmm) cc_final: 0.7308 (ppp) REVERT: B 130 ASP cc_start: 0.8438 (m-30) cc_final: 0.8174 (m-30) REVERT: B 138 LYS cc_start: 0.8611 (mtpt) cc_final: 0.8279 (mtmm) REVERT: B 163 MET cc_start: 0.7423 (mpp) cc_final: 0.7114 (mtm) REVERT: B 179 MET cc_start: 0.8122 (mmm) cc_final: 0.7432 (mmm) REVERT: B 188 GLU cc_start: 0.8776 (mp0) cc_final: 0.8339 (pm20) REVERT: B 295 TYR cc_start: 0.8342 (p90) cc_final: 0.7888 (p90) REVERT: B 398 ARG cc_start: 0.6868 (ttm170) cc_final: 0.6396 (ttm170) REVERT: C 41 ASP cc_start: 0.8134 (t0) cc_final: 0.7756 (t0) REVERT: C 86 ASP cc_start: 0.9078 (t0) cc_final: 0.8488 (t70) REVERT: C 96 ASP cc_start: 0.8437 (m-30) cc_final: 0.8072 (m-30) REVERT: C 105 MET cc_start: 0.8516 (mmm) cc_final: 0.7294 (ppp) REVERT: C 130 ASP cc_start: 0.8487 (m-30) cc_final: 0.8156 (m-30) REVERT: C 138 LYS cc_start: 0.8530 (mtpt) cc_final: 0.8295 (mtpp) REVERT: C 179 MET cc_start: 0.8093 (mmm) cc_final: 0.7728 (mmm) REVERT: C 295 TYR cc_start: 0.8397 (p90) cc_final: 0.7966 (p90) REVERT: C 398 ARG cc_start: 0.6953 (ttm170) cc_final: 0.6495 (ttm170) REVERT: D 28 GLU cc_start: 0.7566 (mp0) cc_final: 0.6845 (mp0) REVERT: D 41 ASP cc_start: 0.8336 (t0) cc_final: 0.8069 (t0) REVERT: D 72 MET cc_start: 0.8746 (mtt) cc_final: 0.8438 (mmm) REVERT: D 96 ASP cc_start: 0.8443 (m-30) cc_final: 0.8036 (m-30) REVERT: D 105 MET cc_start: 0.8391 (mmm) cc_final: 0.7158 (ppp) REVERT: D 130 ASP cc_start: 0.8394 (m-30) cc_final: 0.8051 (m-30) REVERT: D 138 LYS cc_start: 0.8452 (mtpt) cc_final: 0.8058 (mtmm) REVERT: D 139 ASN cc_start: 0.8843 (p0) cc_final: 0.8484 (p0) REVERT: D 141 ASN cc_start: 0.8199 (m-40) cc_final: 0.7987 (m-40) REVERT: D 254 SER cc_start: 0.8928 (m) cc_final: 0.8448 (p) REVERT: D 279 MET cc_start: 0.5953 (OUTLIER) cc_final: 0.5128 (ttm) REVERT: D 398 ARG cc_start: 0.6782 (ttm170) cc_final: 0.6342 (ttm170) REVERT: E 28 GLU cc_start: 0.7371 (mp0) cc_final: 0.6910 (mp0) REVERT: E 41 ASP cc_start: 0.8343 (t0) cc_final: 0.7969 (t0) REVERT: E 70 THR cc_start: 0.8547 (m) cc_final: 0.8307 (p) REVERT: E 72 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8271 (tpp) REVERT: E 96 ASP cc_start: 0.8392 (m-30) cc_final: 0.8003 (m-30) REVERT: E 105 MET cc_start: 0.8358 (mmm) cc_final: 0.7393 (ptm) REVERT: E 130 ASP cc_start: 0.8516 (m-30) cc_final: 0.8202 (m-30) REVERT: E 138 LYS cc_start: 0.8506 (mtpt) cc_final: 0.8256 (mtpp) REVERT: E 156 MET cc_start: 0.8372 (mmt) cc_final: 0.8050 (mmt) REVERT: E 229 ARG cc_start: 0.7492 (mmt90) cc_final: 0.7218 (mmt90) REVERT: E 257 SER cc_start: 0.8286 (p) cc_final: 0.7991 (t) REVERT: E 295 TYR cc_start: 0.8293 (p90) cc_final: 0.7613 (p90) outliers start: 55 outliers final: 44 residues processed: 355 average time/residue: 0.1023 time to fit residues: 54.4160 Evaluate side-chains 350 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 303 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 279 MET Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 419 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 19 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 41 optimal weight: 0.0870 chunk 120 optimal weight: 8.9990 chunk 159 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 ASN C 261 ASN D 261 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.181354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.141403 restraints weight = 17974.691| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 3.51 r_work: 0.3119 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14610 Z= 0.181 Angle : 0.634 9.145 19840 Z= 0.300 Chirality : 0.045 0.173 2265 Planarity : 0.004 0.035 2450 Dihedral : 4.703 22.203 2200 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.61 % Allowed : 17.81 % Favored : 78.58 % 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: -1.15 (0.20), residues: 1710 helix: -0.27 (0.23), residues: 525 sheet: -0.46 (0.27), residues: 380 loop : -1.16 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 229 TYR 0.016 0.001 TYR B 317 PHE 0.012 0.002 PHE D 417 TRP 0.009 0.001 TRP E 186 HIS 0.003 0.001 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00430 (14585) covalent geometry : angle 0.59197 (19775) SS BOND : bond 0.00311 ( 10) SS BOND : angle 0.94581 ( 20) hydrogen bonds : bond 0.03383 ( 475) hydrogen bonds : angle 4.45738 ( 1635) link_BETA1-4 : bond 0.00812 ( 10) link_BETA1-4 : angle 3.79357 ( 30) link_NAG-ASN : bond 0.00558 ( 5) link_NAG-ASN : angle 6.31941 ( 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 376 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 320 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8295 (t0) cc_final: 0.7990 (t0) REVERT: A 72 MET cc_start: 0.8638 (mmt) cc_final: 0.8213 (tpp) REVERT: A 89 LEU cc_start: 0.8115 (mp) cc_final: 0.7908 (mt) REVERT: A 96 ASP cc_start: 0.8423 (m-30) cc_final: 0.8218 (m-30) REVERT: A 105 MET cc_start: 0.8281 (mmm) cc_final: 0.7164 (ppp) REVERT: A 138 LYS cc_start: 0.8720 (mtpt) cc_final: 0.8410 (mtmm) REVERT: A 139 ASN cc_start: 0.8899 (p0) cc_final: 0.8181 (p0) REVERT: A 141 ASN cc_start: 0.8423 (m-40) cc_final: 0.7877 (m-40) REVERT: A 179 MET cc_start: 0.7872 (mmm) cc_final: 0.7349 (mmm) REVERT: A 254 SER cc_start: 0.8935 (m) cc_final: 0.8445 (p) REVERT: A 292 LYS cc_start: 0.8110 (mttt) cc_final: 0.7791 (mttm) REVERT: A 295 TYR cc_start: 0.8335 (p90) cc_final: 0.7975 (p90) REVERT: A 398 ARG cc_start: 0.6771 (ttm170) cc_final: 0.6237 (ttm170) REVERT: B 41 ASP cc_start: 0.8226 (t0) cc_final: 0.7908 (t0) REVERT: B 72 MET cc_start: 0.8777 (mtt) cc_final: 0.8553 (mmt) REVERT: B 86 ASP cc_start: 0.8963 (t0) cc_final: 0.8497 (t70) REVERT: B 96 ASP cc_start: 0.8562 (m-30) cc_final: 0.8216 (m-30) REVERT: B 105 MET cc_start: 0.8222 (mmm) cc_final: 0.7162 (ppp) REVERT: B 130 ASP cc_start: 0.8432 (m-30) cc_final: 0.8145 (m-30) REVERT: B 138 LYS cc_start: 0.8653 (mtpt) cc_final: 0.8318 (mtmm) REVERT: B 163 MET cc_start: 0.7583 (mpp) cc_final: 0.7366 (mtm) REVERT: B 179 MET cc_start: 0.8143 (mmm) cc_final: 0.7751 (mmm) REVERT: B 188 GLU cc_start: 0.8799 (mp0) cc_final: 0.8551 (pm20) REVERT: B 254 SER cc_start: 0.8965 (m) cc_final: 0.8513 (p) REVERT: B 295 TYR cc_start: 0.8296 (p90) cc_final: 0.7824 (p90) REVERT: B 398 ARG cc_start: 0.6889 (ttm170) cc_final: 0.6411 (ttm170) REVERT: C 41 ASP cc_start: 0.8146 (t0) cc_final: 0.7767 (t0) REVERT: C 86 ASP cc_start: 0.9089 (t0) cc_final: 0.8412 (t0) REVERT: C 105 MET cc_start: 0.8570 (mmm) cc_final: 0.7251 (ppp) REVERT: C 130 ASP cc_start: 0.8479 (m-30) cc_final: 0.8120 (m-30) REVERT: C 138 LYS cc_start: 0.8476 (mtpt) cc_final: 0.8221 (mtpp) REVERT: C 179 MET cc_start: 0.8049 (mmm) cc_final: 0.7613 (mmm) REVERT: C 188 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8461 (pm20) REVERT: C 295 TYR cc_start: 0.8380 (p90) cc_final: 0.8030 (p90) REVERT: C 398 ARG cc_start: 0.6959 (ttm170) cc_final: 0.6506 (ttm170) REVERT: D 28 GLU cc_start: 0.7542 (mp0) cc_final: 0.6817 (mp0) REVERT: D 41 ASP cc_start: 0.8331 (t0) cc_final: 0.8049 (t0) REVERT: D 72 MET cc_start: 0.8742 (mtt) cc_final: 0.8302 (ttm) REVERT: D 96 ASP cc_start: 0.8423 (m-30) cc_final: 0.8022 (m-30) REVERT: D 105 MET cc_start: 0.8392 (mmm) cc_final: 0.7121 (ppp) REVERT: D 130 ASP cc_start: 0.8463 (m-30) cc_final: 0.8081 (m-30) REVERT: D 138 LYS cc_start: 0.8501 (mtpt) cc_final: 0.8108 (mtmm) REVERT: D 139 ASN cc_start: 0.8762 (p0) cc_final: 0.8435 (p0) REVERT: D 181 ASP cc_start: 0.7887 (m-30) cc_final: 0.7599 (t0) REVERT: D 254 SER cc_start: 0.8900 (m) cc_final: 0.8415 (p) REVERT: D 391 MET cc_start: 0.1630 (mmm) cc_final: 0.1166 (mmm) REVERT: D 398 ARG cc_start: 0.6795 (ttm170) cc_final: 0.6324 (ttm170) REVERT: E 28 GLU cc_start: 0.7356 (mp0) cc_final: 0.6914 (mp0) REVERT: E 41 ASP cc_start: 0.8304 (t0) cc_final: 0.7865 (t0) REVERT: E 70 THR cc_start: 0.8554 (m) cc_final: 0.8315 (p) REVERT: E 72 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8251 (tpp) REVERT: E 96 ASP cc_start: 0.8404 (m-30) cc_final: 0.8005 (m-30) REVERT: E 105 MET cc_start: 0.8374 (mmm) cc_final: 0.7367 (ptm) REVERT: E 130 ASP cc_start: 0.8499 (m-30) cc_final: 0.8162 (m-30) REVERT: E 138 LYS cc_start: 0.8516 (mtpt) cc_final: 0.8262 (mtpp) REVERT: E 156 MET cc_start: 0.8456 (mmt) cc_final: 0.8113 (mmt) REVERT: E 170 MET cc_start: 0.8551 (ptp) cc_final: 0.8197 (ptp) REVERT: E 229 ARG cc_start: 0.7587 (mmt90) cc_final: 0.7174 (mmt90) REVERT: E 257 SER cc_start: 0.8313 (p) cc_final: 0.8019 (t) REVERT: E 292 LYS cc_start: 0.8097 (mttt) cc_final: 0.7596 (mttp) REVERT: E 295 TYR cc_start: 0.8265 (p90) cc_final: 0.7590 (p90) outliers start: 56 outliers final: 46 residues processed: 362 average time/residue: 0.1060 time to fit residues: 57.4558 Evaluate side-chains 363 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 315 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 419 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 60 optimal weight: 8.9990 chunk 143 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 142 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 113 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 261 ASN D 261 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.181887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.142126 restraints weight = 18172.037| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 3.50 r_work: 0.3135 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14610 Z= 0.149 Angle : 0.626 9.245 19840 Z= 0.294 Chirality : 0.045 0.165 2265 Planarity : 0.004 0.049 2450 Dihedral : 4.633 21.875 2200 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.00 % Allowed : 18.26 % Favored : 77.74 % 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: -1.02 (0.21), residues: 1710 helix: -0.11 (0.23), residues: 530 sheet: -0.43 (0.27), residues: 370 loop : -1.09 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 229 TYR 0.016 0.001 TYR E 317 PHE 0.012 0.001 PHE D 417 TRP 0.009 0.001 TRP E 186 HIS 0.002 0.001 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00352 (14585) covalent geometry : angle 0.58705 (19775) SS BOND : bond 0.00286 ( 10) SS BOND : angle 0.87955 ( 20) hydrogen bonds : bond 0.03269 ( 475) hydrogen bonds : angle 4.37332 ( 1635) link_BETA1-4 : bond 0.00771 ( 10) link_BETA1-4 : angle 3.67588 ( 30) link_NAG-ASN : bond 0.00492 ( 5) link_NAG-ASN : angle 5.97910 ( 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 383 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 321 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8253 (t0) cc_final: 0.7934 (t0) REVERT: A 72 MET cc_start: 0.8659 (mmt) cc_final: 0.8282 (tpp) REVERT: A 96 ASP cc_start: 0.8547 (m-30) cc_final: 0.8148 (m-30) REVERT: A 105 MET cc_start: 0.8269 (mmm) cc_final: 0.7110 (ppp) REVERT: A 138 LYS cc_start: 0.8714 (mtpt) cc_final: 0.8398 (mtmm) REVERT: A 139 ASN cc_start: 0.8878 (p0) cc_final: 0.8091 (p0) REVERT: A 141 ASN cc_start: 0.8409 (m-40) cc_final: 0.7858 (m-40) REVERT: A 179 MET cc_start: 0.7866 (mmm) cc_final: 0.7321 (mmm) REVERT: A 254 SER cc_start: 0.8927 (m) cc_final: 0.8378 (p) REVERT: A 279 MET cc_start: 0.5892 (OUTLIER) cc_final: 0.4745 (ttm) REVERT: A 292 LYS cc_start: 0.8078 (mttt) cc_final: 0.7704 (mttm) REVERT: A 295 TYR cc_start: 0.8349 (p90) cc_final: 0.7896 (p90) REVERT: A 398 ARG cc_start: 0.6794 (ttm170) cc_final: 0.6237 (ttm170) REVERT: B 41 ASP cc_start: 0.8171 (t0) cc_final: 0.7818 (t0) REVERT: B 45 ARG cc_start: 0.9007 (ptt90) cc_final: 0.8597 (ptm-80) REVERT: B 72 MET cc_start: 0.8777 (mtt) cc_final: 0.8550 (mmt) REVERT: B 86 ASP cc_start: 0.8982 (t0) cc_final: 0.8487 (t70) REVERT: B 96 ASP cc_start: 0.8499 (m-30) cc_final: 0.8189 (m-30) REVERT: B 105 MET cc_start: 0.8227 (mmm) cc_final: 0.7146 (ppp) REVERT: B 130 ASP cc_start: 0.8439 (m-30) cc_final: 0.8128 (m-30) REVERT: B 138 LYS cc_start: 0.8612 (mtpt) cc_final: 0.8285 (mtmm) REVERT: B 179 MET cc_start: 0.8123 (mmm) cc_final: 0.7766 (mmm) REVERT: B 188 GLU cc_start: 0.8819 (mp0) cc_final: 0.8570 (pm20) REVERT: B 254 SER cc_start: 0.8932 (m) cc_final: 0.8467 (p) REVERT: B 279 MET cc_start: 0.5917 (OUTLIER) cc_final: 0.5493 (ttm) REVERT: B 295 TYR cc_start: 0.8250 (p90) cc_final: 0.7766 (p90) REVERT: B 398 ARG cc_start: 0.6885 (ttm170) cc_final: 0.6397 (ttm170) REVERT: C 86 ASP cc_start: 0.9098 (t0) cc_final: 0.8414 (t0) REVERT: C 105 MET cc_start: 0.8468 (mmm) cc_final: 0.7263 (ppp) REVERT: C 130 ASP cc_start: 0.8427 (m-30) cc_final: 0.8050 (m-30) REVERT: C 179 MET cc_start: 0.8016 (mmm) cc_final: 0.7579 (mmm) REVERT: C 188 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8436 (pm20) REVERT: C 295 TYR cc_start: 0.8369 (p90) cc_final: 0.7929 (p90) REVERT: C 398 ARG cc_start: 0.6973 (ttm170) cc_final: 0.6510 (ttm170) REVERT: D 28 GLU cc_start: 0.7542 (mp0) cc_final: 0.7338 (mp0) REVERT: D 41 ASP cc_start: 0.8261 (t0) cc_final: 0.7982 (t0) REVERT: D 72 MET cc_start: 0.8743 (mtt) cc_final: 0.8308 (ttm) REVERT: D 96 ASP cc_start: 0.8411 (m-30) cc_final: 0.8011 (m-30) REVERT: D 105 MET cc_start: 0.8327 (mmm) cc_final: 0.7125 (ppp) REVERT: D 130 ASP cc_start: 0.8417 (m-30) cc_final: 0.8017 (m-30) REVERT: D 138 LYS cc_start: 0.8429 (mtpt) cc_final: 0.8039 (mtmm) REVERT: D 139 ASN cc_start: 0.8803 (p0) cc_final: 0.8363 (p0) REVERT: D 141 ASN cc_start: 0.8207 (m-40) cc_final: 0.7733 (m-40) REVERT: D 181 ASP cc_start: 0.7837 (m-30) cc_final: 0.7569 (t0) REVERT: D 193 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.6685 (mt0) REVERT: D 254 SER cc_start: 0.8876 (m) cc_final: 0.8388 (p) REVERT: D 279 MET cc_start: 0.5875 (OUTLIER) cc_final: 0.5185 (ttm) REVERT: D 398 ARG cc_start: 0.6826 (ttm170) cc_final: 0.6340 (ttm170) REVERT: E 28 GLU cc_start: 0.7327 (mp0) cc_final: 0.6878 (mp0) REVERT: E 70 THR cc_start: 0.8536 (m) cc_final: 0.8307 (p) REVERT: E 72 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8233 (tpp) REVERT: E 96 ASP cc_start: 0.8392 (m-30) cc_final: 0.8003 (m-30) REVERT: E 105 MET cc_start: 0.8368 (mmm) cc_final: 0.7339 (ptm) REVERT: E 130 ASP cc_start: 0.8467 (m-30) cc_final: 0.8126 (m-30) REVERT: E 138 LYS cc_start: 0.8484 (mtpt) cc_final: 0.8217 (mtpp) REVERT: E 139 ASN cc_start: 0.8787 (p0) cc_final: 0.8463 (p0) REVERT: E 156 MET cc_start: 0.8444 (mmt) cc_final: 0.8092 (mmt) REVERT: E 170 MET cc_start: 0.8498 (ptp) cc_final: 0.8114 (ptp) REVERT: E 257 SER cc_start: 0.8308 (p) cc_final: 0.8019 (t) REVERT: E 295 TYR cc_start: 0.8257 (p90) cc_final: 0.7573 (p90) outliers start: 62 outliers final: 43 residues processed: 362 average time/residue: 0.1034 time to fit residues: 56.3213 Evaluate side-chains 360 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 311 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 279 MET Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain E residue 424 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 75 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 130 optimal weight: 0.0570 chunk 114 optimal weight: 0.6980 chunk 147 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 7 optimal weight: 0.0270 chunk 29 optimal weight: 0.9990 chunk 152 optimal weight: 6.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 ASN C 261 ASN D 261 ASN E 141 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.184060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.145232 restraints weight = 18261.426| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 3.56 r_work: 0.3394 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14610 Z= 0.102 Angle : 0.597 9.660 19840 Z= 0.281 Chirality : 0.043 0.154 2265 Planarity : 0.003 0.031 2450 Dihedral : 4.389 19.925 2200 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.77 % Allowed : 19.55 % Favored : 77.68 % 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: -0.85 (0.21), residues: 1710 helix: 0.13 (0.24), residues: 525 sheet: -0.38 (0.27), residues: 370 loop : -1.04 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 229 TYR 0.014 0.001 TYR D 317 PHE 0.011 0.001 PHE A 417 TRP 0.007 0.001 TRP E 186 HIS 0.002 0.001 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00233 (14585) covalent geometry : angle 0.56338 (19775) SS BOND : bond 0.00241 ( 10) SS BOND : angle 0.79031 ( 20) hydrogen bonds : bond 0.03065 ( 475) hydrogen bonds : angle 4.16506 ( 1635) link_BETA1-4 : bond 0.00733 ( 10) link_BETA1-4 : angle 3.45059 ( 30) link_NAG-ASN : bond 0.00472 ( 5) link_NAG-ASN : angle 5.29688 ( 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 355 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 312 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8410 (t0) cc_final: 0.8182 (t0) REVERT: A 72 MET cc_start: 0.8650 (mmt) cc_final: 0.8408 (tpp) REVERT: A 86 ASP cc_start: 0.9107 (t0) cc_final: 0.8736 (t70) REVERT: A 96 ASP cc_start: 0.8453 (m-30) cc_final: 0.8211 (m-30) REVERT: A 105 MET cc_start: 0.8269 (mmm) cc_final: 0.7320 (ppp) REVERT: A 138 LYS cc_start: 0.9004 (mtpt) cc_final: 0.8672 (mtmm) REVERT: A 139 ASN cc_start: 0.8995 (p0) cc_final: 0.8147 (p0) REVERT: A 141 ASN cc_start: 0.8710 (m-40) cc_final: 0.8223 (m-40) REVERT: A 179 MET cc_start: 0.8184 (mmm) cc_final: 0.7714 (mmm) REVERT: A 279 MET cc_start: 0.6609 (OUTLIER) cc_final: 0.5243 (ttm) REVERT: A 295 TYR cc_start: 0.8558 (p90) cc_final: 0.8111 (p90) REVERT: A 398 ARG cc_start: 0.6861 (ttm170) cc_final: 0.6330 (ttm170) REVERT: A 416 ILE cc_start: 0.8314 (mt) cc_final: 0.8087 (tp) REVERT: B 41 ASP cc_start: 0.8321 (t0) cc_final: 0.8074 (t0) REVERT: B 45 ARG cc_start: 0.9234 (ptt90) cc_final: 0.8877 (ptm-80) REVERT: B 72 MET cc_start: 0.8791 (mtt) cc_final: 0.8525 (mmm) REVERT: B 86 ASP cc_start: 0.8999 (t0) cc_final: 0.8579 (t70) REVERT: B 96 ASP cc_start: 0.8501 (m-30) cc_final: 0.8255 (m-30) REVERT: B 105 MET cc_start: 0.8218 (mmm) cc_final: 0.7337 (ppp) REVERT: B 130 ASP cc_start: 0.8541 (m-30) cc_final: 0.8303 (m-30) REVERT: B 138 LYS cc_start: 0.8957 (mtpt) cc_final: 0.8505 (mtmm) REVERT: B 179 MET cc_start: 0.8328 (mmm) cc_final: 0.7717 (mmm) REVERT: B 279 MET cc_start: 0.6575 (OUTLIER) cc_final: 0.6008 (ttm) REVERT: B 295 TYR cc_start: 0.8470 (p90) cc_final: 0.8016 (p90) REVERT: B 398 ARG cc_start: 0.6930 (ttm170) cc_final: 0.6482 (ttm170) REVERT: C 86 ASP cc_start: 0.9180 (t0) cc_final: 0.8619 (t70) REVERT: C 105 MET cc_start: 0.8448 (mmm) cc_final: 0.7488 (ppp) REVERT: C 130 ASP cc_start: 0.8577 (m-30) cc_final: 0.8287 (m-30) REVERT: C 179 MET cc_start: 0.8273 (mmm) cc_final: 0.7948 (mmm) REVERT: C 188 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8351 (pm20) REVERT: C 279 MET cc_start: 0.6500 (ttm) cc_final: 0.6151 (ttm) REVERT: C 295 TYR cc_start: 0.8609 (p90) cc_final: 0.8273 (p90) REVERT: C 398 ARG cc_start: 0.6984 (ttm170) cc_final: 0.6541 (ttm170) REVERT: C 416 ILE cc_start: 0.8355 (mt) cc_final: 0.8085 (tp) REVERT: D 28 GLU cc_start: 0.7707 (mp0) cc_final: 0.7505 (mp0) REVERT: D 72 MET cc_start: 0.8754 (mtt) cc_final: 0.8455 (mmm) REVERT: D 96 ASP cc_start: 0.8418 (m-30) cc_final: 0.8112 (m-30) REVERT: D 105 MET cc_start: 0.8377 (mmm) cc_final: 0.7322 (ppp) REVERT: D 130 ASP cc_start: 0.8589 (m-30) cc_final: 0.8293 (m-30) REVERT: D 139 ASN cc_start: 0.8886 (p0) cc_final: 0.8538 (p0) REVERT: D 181 ASP cc_start: 0.8026 (m-30) cc_final: 0.7769 (t0) REVERT: D 193 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7160 (mt0) REVERT: D 216 LYS cc_start: 0.7377 (mttm) cc_final: 0.7177 (mttm) REVERT: D 254 SER cc_start: 0.8878 (m) cc_final: 0.8321 (p) REVERT: D 279 MET cc_start: 0.6435 (OUTLIER) cc_final: 0.6011 (ttm) REVERT: D 398 ARG cc_start: 0.6889 (ttm170) cc_final: 0.6425 (ttm170) REVERT: D 416 ILE cc_start: 0.8320 (mt) cc_final: 0.8041 (tp) REVERT: E 28 GLU cc_start: 0.7506 (mp0) cc_final: 0.7078 (mp0) REVERT: E 70 THR cc_start: 0.8706 (m) cc_final: 0.8463 (p) REVERT: E 96 ASP cc_start: 0.8402 (m-30) cc_final: 0.8075 (m-30) REVERT: E 105 MET cc_start: 0.8371 (mmm) cc_final: 0.7426 (ppp) REVERT: E 107 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.8088 (t0) REVERT: E 130 ASP cc_start: 0.8630 (m-30) cc_final: 0.8381 (m-30) REVERT: E 138 LYS cc_start: 0.8679 (mtpt) cc_final: 0.8394 (mtpp) REVERT: E 156 MET cc_start: 0.8547 (mmt) cc_final: 0.8175 (mmt) REVERT: E 170 MET cc_start: 0.8949 (ptp) cc_final: 0.8604 (ptp) REVERT: E 257 SER cc_start: 0.8419 (p) cc_final: 0.8099 (t) REVERT: E 279 MET cc_start: 0.6893 (ttm) cc_final: 0.6521 (ttm) REVERT: E 287 ARG cc_start: 0.7471 (ptp-170) cc_final: 0.7254 (ptp-170) REVERT: E 295 TYR cc_start: 0.8487 (p90) cc_final: 0.7908 (p90) outliers start: 43 outliers final: 32 residues processed: 341 average time/residue: 0.1039 time to fit residues: 53.1865 Evaluate side-chains 342 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 304 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 279 MET Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 419 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 139 optimal weight: 1.9990 chunk 61 optimal weight: 0.0050 chunk 141 optimal weight: 0.9990 chunk 148 optimal weight: 0.6980 chunk 7 optimal weight: 0.0570 chunk 65 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 99 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 overall best weight: 0.5114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 261 ASN E 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.184538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.146017 restraints weight = 18083.302| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 3.52 r_work: 0.3403 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14610 Z= 0.103 Angle : 0.604 10.484 19840 Z= 0.283 Chirality : 0.043 0.144 2265 Planarity : 0.003 0.030 2450 Dihedral : 4.316 20.597 2200 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.06 % Allowed : 20.97 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.21), residues: 1710 helix: 0.30 (0.24), residues: 530 sheet: -0.33 (0.27), residues: 370 loop : -1.03 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 229 TYR 0.014 0.001 TYR B 317 PHE 0.011 0.001 PHE A 417 TRP 0.006 0.001 TRP E 186 HIS 0.002 0.001 HIS D 125 Details of bonding type rmsd covalent geometry : bond 0.00237 (14585) covalent geometry : angle 0.57479 (19775) SS BOND : bond 0.00256 ( 10) SS BOND : angle 0.81153 ( 20) hydrogen bonds : bond 0.02970 ( 475) hydrogen bonds : angle 4.08363 ( 1635) link_BETA1-4 : bond 0.00758 ( 10) link_BETA1-4 : angle 3.28142 ( 30) link_NAG-ASN : bond 0.00474 ( 5) link_NAG-ASN : angle 5.01381 ( 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 348 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 316 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.8630 (mmt) cc_final: 0.8411 (tpp) REVERT: A 86 ASP cc_start: 0.9105 (t0) cc_final: 0.8698 (t70) REVERT: A 96 ASP cc_start: 0.8441 (m-30) cc_final: 0.8200 (m-30) REVERT: A 105 MET cc_start: 0.8231 (mmm) cc_final: 0.7328 (ppp) REVERT: A 138 LYS cc_start: 0.9034 (mtpt) cc_final: 0.8696 (mtmm) REVERT: A 139 ASN cc_start: 0.8998 (p0) cc_final: 0.8090 (p0) REVERT: A 141 ASN cc_start: 0.8675 (m-40) cc_final: 0.8121 (m-40) REVERT: A 179 MET cc_start: 0.8165 (mmm) cc_final: 0.7695 (mmm) REVERT: A 279 MET cc_start: 0.6606 (OUTLIER) cc_final: 0.5249 (ttm) REVERT: A 295 TYR cc_start: 0.8573 (p90) cc_final: 0.8156 (p90) REVERT: A 398 ARG cc_start: 0.6867 (ttm170) cc_final: 0.6339 (ttm170) REVERT: A 416 ILE cc_start: 0.8306 (mt) cc_final: 0.8099 (tp) REVERT: B 41 ASP cc_start: 0.8301 (t0) cc_final: 0.8062 (t0) REVERT: B 45 ARG cc_start: 0.9228 (ptt90) cc_final: 0.8871 (ptm-80) REVERT: B 72 MET cc_start: 0.8765 (mtt) cc_final: 0.8508 (mmm) REVERT: B 86 ASP cc_start: 0.8991 (t0) cc_final: 0.8554 (t70) REVERT: B 96 ASP cc_start: 0.8484 (m-30) cc_final: 0.8271 (m-30) REVERT: B 105 MET cc_start: 0.8177 (mmm) cc_final: 0.7336 (ppp) REVERT: B 130 ASP cc_start: 0.8540 (m-30) cc_final: 0.8302 (m-30) REVERT: B 138 LYS cc_start: 0.8915 (mtpt) cc_final: 0.8470 (mtmm) REVERT: B 179 MET cc_start: 0.8360 (mmm) cc_final: 0.8109 (mmm) REVERT: B 279 MET cc_start: 0.6561 (OUTLIER) cc_final: 0.6046 (ttm) REVERT: B 295 TYR cc_start: 0.8507 (p90) cc_final: 0.7993 (p90) REVERT: B 398 ARG cc_start: 0.6929 (ttm170) cc_final: 0.6474 (ttm170) REVERT: C 105 MET cc_start: 0.8469 (mmm) cc_final: 0.7456 (ppp) REVERT: C 130 ASP cc_start: 0.8552 (m-30) cc_final: 0.8263 (m-30) REVERT: C 179 MET cc_start: 0.8251 (mmm) cc_final: 0.7921 (mmm) REVERT: C 188 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8285 (pm20) REVERT: C 279 MET cc_start: 0.6538 (ttm) cc_final: 0.6180 (ttm) REVERT: C 295 TYR cc_start: 0.8626 (p90) cc_final: 0.8238 (p90) REVERT: C 398 ARG cc_start: 0.6976 (ttm170) cc_final: 0.6524 (ttm170) REVERT: C 416 ILE cc_start: 0.8370 (mt) cc_final: 0.8112 (tp) REVERT: D 72 MET cc_start: 0.8738 (mtt) cc_final: 0.8493 (ttm) REVERT: D 96 ASP cc_start: 0.8414 (m-30) cc_final: 0.8088 (m-30) REVERT: D 105 MET cc_start: 0.8364 (mmm) cc_final: 0.7312 (ppp) REVERT: D 130 ASP cc_start: 0.8548 (m-30) cc_final: 0.8261 (m-30) REVERT: D 139 ASN cc_start: 0.8916 (p0) cc_final: 0.8628 (p0) REVERT: D 141 ASN cc_start: 0.8550 (m-40) cc_final: 0.8277 (m-40) REVERT: D 181 ASP cc_start: 0.8035 (m-30) cc_final: 0.7773 (t0) REVERT: D 193 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7172 (mt0) REVERT: D 254 SER cc_start: 0.8892 (m) cc_final: 0.8349 (p) REVERT: D 279 MET cc_start: 0.6479 (OUTLIER) cc_final: 0.6142 (ttm) REVERT: D 398 ARG cc_start: 0.6873 (ttm170) cc_final: 0.6405 (ttm170) REVERT: D 416 ILE cc_start: 0.8337 (mt) cc_final: 0.8073 (tp) REVERT: E 70 THR cc_start: 0.8680 (m) cc_final: 0.8423 (p) REVERT: E 96 ASP cc_start: 0.8386 (m-30) cc_final: 0.8037 (m-30) REVERT: E 105 MET cc_start: 0.8373 (mmm) cc_final: 0.7421 (ppp) REVERT: E 130 ASP cc_start: 0.8612 (m-30) cc_final: 0.8370 (m-30) REVERT: E 138 LYS cc_start: 0.8683 (mtpt) cc_final: 0.8428 (mtpp) REVERT: E 156 MET cc_start: 0.8463 (mmt) cc_final: 0.8089 (mmt) REVERT: E 170 MET cc_start: 0.8979 (ptp) cc_final: 0.8677 (ptp) REVERT: E 193 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7404 (mt0) REVERT: E 279 MET cc_start: 0.6904 (OUTLIER) cc_final: 0.6513 (ttm) REVERT: E 292 LYS cc_start: 0.8489 (mttt) cc_final: 0.8029 (mttp) REVERT: E 295 TYR cc_start: 0.8520 (p90) cc_final: 0.7878 (p90) outliers start: 32 outliers final: 25 residues processed: 340 average time/residue: 0.1006 time to fit residues: 51.8195 Evaluate side-chains 342 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 310 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 279 MET Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 279 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 154 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 ASN E 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.183674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.145234 restraints weight = 18159.822| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 3.51 r_work: 0.3393 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 14610 Z= 0.193 Angle : 0.813 59.142 19840 Z= 0.443 Chirality : 0.045 0.151 2265 Planarity : 0.003 0.056 2450 Dihedral : 4.321 21.072 2200 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.26 % Allowed : 20.71 % Favored : 77.03 % 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: -0.75 (0.21), residues: 1710 helix: 0.29 (0.24), residues: 530 sheet: -0.34 (0.27), residues: 370 loop : -1.04 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG E 287 TYR 0.012 0.001 TYR B 317 PHE 0.011 0.001 PHE A 417 TRP 0.007 0.001 TRP E 186 HIS 0.002 0.001 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00433 (14585) covalent geometry : angle 0.79169 (19775) SS BOND : bond 0.00288 ( 10) SS BOND : angle 0.93967 ( 20) hydrogen bonds : bond 0.03058 ( 475) hydrogen bonds : angle 4.08730 ( 1635) link_BETA1-4 : bond 0.01050 ( 10) link_BETA1-4 : angle 3.28744 ( 30) link_NAG-ASN : bond 0.00388 ( 5) link_NAG-ASN : angle 5.04209 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3001.27 seconds wall clock time: 52 minutes 10.39 seconds (3130.39 seconds total)