Starting phenix.real_space_refine on Sat Sep 12 06:51:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pm1_20383/09_2026/6pm1_20383.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pm1_20383/09_2026/6pm1_20383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6pm1_20383/09_2026/6pm1_20383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pm1_20383/09_2026/6pm1_20383.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6pm1_20383/09_2026/6pm1_20383.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pm1_20383/09_2026/6pm1_20383.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pm1_20383/09_2026/6pm1_20383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pm1_20383/09_2026/6pm1_20383.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.045 sd= 4.739 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 9215 2.51 5 N 2285 2.21 5 O 2555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14160 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2786 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 15 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 chiralities: 3 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'TAU': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E, G, H, I, J Time building chain proxies: 2.72, per 1000 atoms: 0.19 Number of scatterers: 14160 At special positions: 0 Unit cell: (106.167, 107.813, 135.795, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 2555 8.00 N 2285 7.00 C 9215 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=2.05 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.02 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 168 " distance=2.05 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 168 " distance=2.05 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 168 " distance=2.05 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 168 " distance=2.05 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.02 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.02 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.02 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " distance=2.02 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: 1.19 Conformation dependent library (CDL) restraints added in 614.0 milliseconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 25 sheets defined 39.9% alpha, 39.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 25 through 34 removed outlier: 3.591A pdb=" N ASP A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 40 removed outlier: 3.971A pdb=" N GLY A 39 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 4.176A 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 removed outlier: 3.561A pdb=" N ALA A 90 " --> pdb=" O PRO A 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 87 through 90' Processing helix chain 'A' and resid 102 through 109 removed outlier: 3.730A pdb=" N LEU A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASP A 107 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE A 109 " --> pdb=" O LEU A 106 " (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 243 through 256 removed outlier: 3.528A pdb=" N ILE A 250 " --> pdb=" O PRO A 246 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 285 removed outlier: 3.914A pdb=" N THR A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 299 through 322 removed outlier: 4.035A pdb=" N VAL A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 406 removed outlier: 4.352A pdb=" N ILE A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA A 399 " --> pdb=" O PHE A 395 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS A 400 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR A 404 " --> pdb=" O LYS A 400 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 423 removed outlier: 4.285A pdb=" N LEU A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TRP A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 428 removed outlier: 3.928A pdb=" N ILE A 428 " --> pdb=" O THR A 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 34 removed outlier: 3.591A pdb=" N ASP B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 removed outlier: 3.970A pdb=" N GLY B 39 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 4.176A 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 removed outlier: 3.561A pdb=" N ALA B 90 " --> pdb=" O PRO B 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 87 through 90' Processing helix chain 'B' and resid 102 through 109 removed outlier: 3.731A pdb=" N LEU B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASP B 107 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE B 109 " --> pdb=" O LEU B 106 " (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 243 through 256 removed outlier: 3.528A pdb=" N ILE B 250 " --> pdb=" O PRO B 246 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 252 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 285 removed outlier: 3.914A pdb=" N THR B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR B 280 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 299 through 322 removed outlier: 4.035A pdb=" N VAL B 305 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 406 removed outlier: 4.351A pdb=" N ILE B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER B 397 " --> pdb=" O LYS B 393 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA B 399 " --> pdb=" O PHE B 395 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS B 400 " --> pdb=" O ILE B 396 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR B 404 " --> pdb=" O LYS B 400 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 423 removed outlier: 4.284A pdb=" N LEU B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TRP B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 428 removed outlier: 3.929A pdb=" N ILE B 428 " --> pdb=" O THR B 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 34 removed outlier: 3.590A pdb=" N ASP C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 40 removed outlier: 3.971A pdb=" N GLY C 39 " --> pdb=" O LYS C 36 " (cutoff:3.500A) removed outlier: 4.177A 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 removed outlier: 3.562A pdb=" N ALA C 90 " --> pdb=" O PRO C 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 87 through 90' Processing helix chain 'C' and resid 102 through 109 removed outlier: 3.731A pdb=" N LEU C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASP C 107 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE C 109 " --> pdb=" O LEU C 106 " (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 243 through 256 removed outlier: 3.529A pdb=" N ILE C 250 " --> pdb=" O PRO C 246 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 285 removed outlier: 3.914A pdb=" N THR C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR C 280 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 299 through 322 removed outlier: 4.035A pdb=" N VAL C 305 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 406 removed outlier: 4.351A pdb=" N ILE C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER C 397 " --> pdb=" O LYS C 393 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA C 399 " --> pdb=" O PHE C 395 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS C 400 " --> pdb=" O ILE C 396 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR C 404 " --> pdb=" O LYS C 400 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 423 removed outlier: 4.284A pdb=" N LEU C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TRP C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 428 removed outlier: 3.929A pdb=" N ILE C 428 " --> pdb=" O THR C 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 34 removed outlier: 3.591A pdb=" N ASP D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 40 removed outlier: 3.970A pdb=" N GLY D 39 " --> pdb=" O LYS D 36 " (cutoff:3.500A) removed outlier: 4.177A 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 removed outlier: 3.560A pdb=" N ALA D 90 " --> pdb=" O PRO D 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 87 through 90' Processing helix chain 'D' and resid 102 through 109 removed outlier: 3.729A pdb=" N LEU D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASP D 107 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE D 109 " --> pdb=" O LEU D 106 " (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 243 through 256 removed outlier: 3.529A pdb=" N ILE D 250 " --> pdb=" O PRO D 246 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 285 removed outlier: 3.915A pdb=" N THR D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL D 276 " --> pdb=" O GLY D 272 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR D 280 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR D 281 " --> pdb=" O LEU D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 299 through 322 removed outlier: 4.035A pdb=" N VAL D 305 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR D 317 " --> pdb=" O ALA D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 406 removed outlier: 4.350A pdb=" N ILE D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER D 397 " --> pdb=" O LYS D 393 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA D 399 " --> pdb=" O PHE D 395 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS D 400 " --> pdb=" O ILE D 396 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR D 404 " --> pdb=" O LYS D 400 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER D 406 " --> pdb=" O ILE D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 423 removed outlier: 4.283A pdb=" N LEU D 415 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TRP D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 428 removed outlier: 3.928A pdb=" N ILE D 428 " --> pdb=" O THR D 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 34 removed outlier: 3.590A pdb=" N ASP E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 40 removed outlier: 3.971A pdb=" N GLY E 39 " --> pdb=" O LYS E 36 " (cutoff:3.500A) removed outlier: 4.176A 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 removed outlier: 3.561A pdb=" N ALA E 90 " --> pdb=" O PRO E 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 90' Processing helix chain 'E' and resid 102 through 109 removed outlier: 3.730A pdb=" N LEU E 106 " --> pdb=" O PRO E 103 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASP E 107 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE E 109 " --> pdb=" O LEU E 106 " (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 243 through 256 removed outlier: 3.528A pdb=" N ILE E 250 " --> pdb=" O PRO E 246 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE E 252 " --> pdb=" O LEU E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 285 removed outlier: 3.915A pdb=" N THR E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL E 276 " --> pdb=" O GLY E 272 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR E 280 " --> pdb=" O VAL E 276 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR E 281 " --> pdb=" O LEU E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 299 through 322 removed outlier: 4.036A pdb=" N VAL E 305 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR E 317 " --> pdb=" O ALA E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 406 removed outlier: 4.351A pdb=" N ILE E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER E 397 " --> pdb=" O LYS E 393 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA E 399 " --> pdb=" O PHE E 395 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS E 400 " --> pdb=" O ILE E 396 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR E 404 " --> pdb=" O LYS E 400 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER E 406 " --> pdb=" O ILE E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 423 removed outlier: 4.283A pdb=" N LEU E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TRP E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 428 removed outlier: 3.929A pdb=" N ILE E 428 " --> pdb=" O THR E 424 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.627A pdb=" N ASN A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.511A 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: 6.327A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N GLN A 193 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE A 59 " --> pdb=" O GLN A 193 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 116 Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 116 Processing sheet with id=AA5, first strand: chain 'A' and resid 216 through 217 Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.627A pdb=" N ASN B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.511A 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: 6.327A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N GLN B 193 " --> pdb=" O CYS B 57 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE B 59 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 114 through 116 Processing sheet with id=AA9, first strand: chain 'B' and resid 114 through 116 Processing sheet with id=AB1, first strand: chain 'B' and resid 216 through 217 Processing sheet with id=AB2, first strand: chain 'C' and resid 98 through 100 removed outlier: 4.627A pdb=" N ASN C 141 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.512A 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: 6.327A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N GLN C 193 " --> pdb=" O CYS C 57 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE C 59 " --> pdb=" O GLN C 193 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 114 through 116 Processing sheet with id=AB5, first strand: chain 'C' and resid 114 through 116 Processing sheet with id=AB6, first strand: chain 'C' and resid 216 through 217 Processing sheet with id=AB7, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.626A pdb=" N ASN D 141 " --> pdb=" O SER D 137 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.512A 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: 6.327A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N GLN D 193 " --> pdb=" O CYS D 57 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE D 59 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 114 through 116 Processing sheet with id=AC1, first strand: chain 'D' and resid 114 through 116 Processing sheet with id=AC2, first strand: chain 'D' and resid 216 through 217 Processing sheet with id=AC3, first strand: chain 'E' and resid 98 through 100 removed outlier: 4.626A pdb=" N ASN E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.511A 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: 6.327A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N GLN E 193 " --> pdb=" O CYS E 57 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE E 59 " --> pdb=" O GLN E 193 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 114 through 116 Processing sheet with id=AC6, first strand: chain 'E' and resid 114 through 116 Processing sheet with id=AC7, first strand: chain 'E' and resid 216 through 217 685 hydrogen bonds defined for protein. 1995 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: 2.52 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4190 1.34 - 1.46: 3705 1.46 - 1.59: 6435 1.59 - 1.71: 0 1.71 - 1.83: 175 Bond restraints: 14505 Sorted by residual: bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.28e+00 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.16e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.14e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.07e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.01e+00 ... (remaining 14500 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 18980 2.37 - 4.74: 535 4.74 - 7.11: 140 7.11 - 9.49: 20 9.49 - 11.86: 10 Bond angle restraints: 19685 Sorted by residual: angle pdb=" C VAL B 127 " pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta sigma weight residual 126.45 134.51 -8.06 1.77e+00 3.19e-01 2.07e+01 angle pdb=" C VAL D 127 " pdb=" N THR D 128 " pdb=" CA THR D 128 " ideal model delta sigma weight residual 126.45 134.51 -8.06 1.77e+00 3.19e-01 2.07e+01 angle pdb=" C VAL C 127 " pdb=" N THR C 128 " pdb=" CA THR C 128 " ideal model delta sigma weight residual 126.45 134.50 -8.05 1.77e+00 3.19e-01 2.07e+01 angle pdb=" C VAL E 127 " pdb=" N THR E 128 " pdb=" CA THR E 128 " ideal model delta sigma weight residual 126.45 134.49 -8.04 1.77e+00 3.19e-01 2.06e+01 angle pdb=" C VAL A 127 " pdb=" N THR A 128 " pdb=" CA THR A 128 " ideal model delta sigma weight residual 126.45 134.45 -8.00 1.77e+00 3.19e-01 2.04e+01 ... (remaining 19680 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.55: 8050 15.55 - 31.09: 425 31.09 - 46.64: 80 46.64 - 62.18: 0 62.18 - 77.73: 5 Dihedral angle restraints: 8560 sinusoidal: 3445 harmonic: 5115 Sorted by residual: dihedral pdb=" CA ASN C 160 " pdb=" C ASN C 160 " pdb=" N PHE C 161 " pdb=" CA PHE C 161 " ideal model delta harmonic sigma weight residual 180.00 -150.06 -29.94 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA ASN A 160 " pdb=" C ASN A 160 " pdb=" N PHE A 161 " pdb=" CA PHE A 161 " ideal model delta harmonic sigma weight residual -180.00 -150.11 -29.89 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA ASN B 160 " pdb=" C ASN B 160 " pdb=" N PHE B 161 " pdb=" CA PHE B 161 " ideal model delta harmonic sigma weight residual -180.00 -150.14 -29.86 0 5.00e+00 4.00e-02 3.57e+01 ... (remaining 8557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1588 0.057 - 0.115: 532 0.115 - 0.172: 105 0.172 - 0.229: 23 0.229 - 0.287: 12 Chirality restraints: 2260 Sorted by residual: chirality pdb=" C5 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C6 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 2257 not shown) Planarity restraints: 2435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE E 410 " 0.045 5.00e-02 4.00e+02 6.71e-02 7.20e+00 pdb=" N PRO E 411 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO E 411 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 411 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 410 " 0.045 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO A 411 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 411 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 411 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 410 " -0.045 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO C 411 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 411 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 411 " -0.037 5.00e-02 4.00e+02 ... (remaining 2432 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 4592 2.84 - 3.36: 11858 3.36 - 3.87: 22721 3.87 - 4.39: 27242 4.39 - 4.90: 45892 Nonbonded interactions: 112305 Sorted by model distance: nonbonded pdb=" OG1 THR C 178 " pdb=" OD1 ASN C 180 " model vdw 2.325 3.040 nonbonded pdb=" OG1 THR A 178 " pdb=" OD1 ASN A 180 " model vdw 2.325 3.040 nonbonded pdb=" OG1 THR D 178 " pdb=" OD1 ASN D 180 " model vdw 2.326 3.040 nonbonded pdb=" OG1 THR E 178 " pdb=" OD1 ASN E 180 " model vdw 2.326 3.040 nonbonded pdb=" OG1 THR B 178 " pdb=" OD1 ASN B 180 " model vdw 2.326 3.040 ... (remaining 112300 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.550 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 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 : 0.008 0.062 14530 Z= 0.322 Angle : 1.068 11.856 19750 Z= 0.528 Chirality : 0.061 0.287 2260 Planarity : 0.008 0.067 2430 Dihedral : 9.613 77.730 5210 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % 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: -4.95 (0.15), residues: 1710 helix: -4.96 (0.06), residues: 585 sheet: -2.09 (0.23), residues: 380 loop : -2.25 (0.18), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 135 TYR 0.022 0.003 TYR B 144 PHE 0.023 0.003 PHE E 115 TRP 0.022 0.002 TRP E 110 HIS 0.005 0.001 HIS C 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00779 / 0.32 (14505) covalent geometry : angle 1.04076 / 0.52 (19685) SS BOND : bond 0.01480 / 0.82 ( 10) SS BOND : angle 3.61627 / 2.54 ( 20) hydrogen bonds : bond 0.27827 / 18.18 ( 540) hydrogen bonds : angle 10.19785 / 7.02 ( 1995) link_BETA1-4 : bond 0.00339 / 0.20 ( 10) link_BETA1-4 : angle 5.38573 / 3.94 ( 30) link_NAG-ASN : bond 0.00153 / 0.09 ( 5) link_NAG-ASN : angle 1.92842 / 1.17 ( 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 463 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 463 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8371 (ptt) cc_final: 0.7694 (ptt) REVERT: A 126 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7178 (mt-10) REVERT: A 210 ASP cc_start: 0.7724 (m-30) cc_final: 0.7470 (m-30) REVERT: A 233 GLU cc_start: 0.6866 (tt0) cc_final: 0.6486 (mt-10) REVERT: A 303 MET cc_start: 0.8805 (mmt) cc_final: 0.8342 (mmt) REVERT: A 415 LEU cc_start: 0.7607 (tt) cc_final: 0.7382 (tm) REVERT: A 420 PHE cc_start: 0.7178 (m-10) cc_final: 0.6909 (t80) REVERT: B 24 MET cc_start: 0.8379 (ptt) cc_final: 0.7623 (ptt) REVERT: B 41 ASP cc_start: 0.8978 (t0) cc_final: 0.8734 (t0) REVERT: B 206 LYS cc_start: 0.8309 (mtpt) cc_final: 0.7432 (mttp) REVERT: B 247 SER cc_start: 0.8492 (t) cc_final: 0.8165 (m) REVERT: B 261 ASN cc_start: 0.7630 (p0) cc_final: 0.7098 (t0) REVERT: B 303 MET cc_start: 0.8944 (mmt) cc_final: 0.8685 (mmt) REVERT: B 415 LEU cc_start: 0.7469 (tt) cc_final: 0.7200 (tm) REVERT: B 420 PHE cc_start: 0.7374 (m-10) cc_final: 0.7077 (t80) REVERT: C 24 MET cc_start: 0.8330 (ptt) cc_final: 0.7100 (ptt) REVERT: C 41 ASP cc_start: 0.8943 (t0) cc_final: 0.8636 (t0) REVERT: C 85 ASN cc_start: 0.8953 (t0) cc_final: 0.8751 (t0) REVERT: C 126 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7381 (mt-10) REVERT: C 210 ASP cc_start: 0.7866 (m-30) cc_final: 0.7607 (m-30) REVERT: C 227 GLU cc_start: 0.8624 (pt0) cc_final: 0.8407 (pt0) REVERT: C 233 GLU cc_start: 0.6819 (tt0) cc_final: 0.6342 (mt-10) REVERT: C 261 ASN cc_start: 0.7555 (p0) cc_final: 0.7107 (t0) REVERT: C 316 GLU cc_start: 0.6713 (tm-30) cc_final: 0.6448 (tm-30) REVERT: C 415 LEU cc_start: 0.7517 (tt) cc_final: 0.7293 (tm) REVERT: C 420 PHE cc_start: 0.7428 (m-10) cc_final: 0.7188 (t80) REVERT: D 24 MET cc_start: 0.8396 (ptt) cc_final: 0.7806 (ptt) REVERT: D 45 ARG cc_start: 0.8998 (ptt90) cc_final: 0.8704 (ptt-90) REVERT: D 72 MET cc_start: 0.8662 (mtm) cc_final: 0.8422 (mtt) REVERT: D 85 ASN cc_start: 0.8993 (t0) cc_final: 0.8718 (t0) REVERT: D 206 LYS cc_start: 0.8279 (mtpt) cc_final: 0.7687 (mttp) REVERT: D 210 ASP cc_start: 0.7807 (m-30) cc_final: 0.7576 (m-30) REVERT: D 227 GLU cc_start: 0.8635 (pt0) cc_final: 0.8429 (pt0) REVERT: D 261 ASN cc_start: 0.7497 (p0) cc_final: 0.7002 (t0) REVERT: D 415 LEU cc_start: 0.7496 (tt) cc_final: 0.7270 (tm) REVERT: E 24 MET cc_start: 0.8228 (ptt) cc_final: 0.6813 (ptt) REVERT: E 102 ASP cc_start: 0.8212 (t0) cc_final: 0.7966 (t70) REVERT: E 104 SER cc_start: 0.8910 (t) cc_final: 0.8658 (p) REVERT: E 206 LYS cc_start: 0.8314 (mtpt) cc_final: 0.7687 (mttp) REVERT: E 261 ASN cc_start: 0.7537 (p0) cc_final: 0.7170 (t0) REVERT: E 420 PHE cc_start: 0.7374 (m-10) cc_final: 0.7076 (t80) outliers start: 0 outliers final: 1 residues processed: 463 average time/residue: 0.5650 time to fit residues: 288.0709 Evaluate side-chains 260 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 259 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 219 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.0980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 ASN B 62 ASN B 82 GLN B 231 HIS C 62 ASN C 123 ASN C 418 ASN D 62 ASN D 418 ASN E 62 ASN E 123 ASN E 418 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.132761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.095318 restraints weight = 17151.153| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.69 r_work: 0.2851 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14530 Z= 0.142 Angle : 0.684 8.190 19750 Z= 0.348 Chirality : 0.046 0.172 2260 Planarity : 0.005 0.044 2430 Dihedral : 5.587 24.998 1892 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.15 % Allowed : 13.97 % Favored : 82.89 % 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: -3.64 (0.16), residues: 1710 helix: -3.36 (0.14), residues: 630 sheet: -0.94 (0.26), residues: 340 loop : -2.09 (0.19), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 229 TYR 0.010 0.001 TYR D 317 PHE 0.018 0.001 PHE D 322 TRP 0.010 0.001 TRP B 110 HIS 0.002 0.000 HIS B 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (14505) covalent geometry : angle 0.66947 / 0.34 (19685) SS BOND : bond 0.00456 / 0.24 ( 10) SS BOND : angle 1.55053 / 0.99 ( 20) hydrogen bonds : bond 0.04641 / 3.04 ( 540) hydrogen bonds : angle 5.40752 / 3.76 ( 1995) link_BETA1-4 : bond 0.00374 / 0.22 ( 10) link_BETA1-4 : angle 3.53674 / 2.55 ( 30) link_NAG-ASN : bond 0.00291 / 0.17 ( 5) link_NAG-ASN : angle 0.60261 / 0.33 ( 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 372 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 324 time to evaluate : 0.351 Fit side-chains REVERT: A 102 ASP cc_start: 0.8087 (t70) cc_final: 0.7707 (t70) REVERT: A 126 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7252 (mt-10) REVERT: A 173 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7504 (tt0) REVERT: A 206 LYS cc_start: 0.7980 (mtpt) cc_final: 0.7375 (mttp) REVERT: A 210 ASP cc_start: 0.7612 (m-30) cc_final: 0.7309 (m-30) REVERT: A 235 GLN cc_start: 0.7818 (mm-40) cc_final: 0.7119 (mm-40) REVERT: B 24 MET cc_start: 0.8118 (ptt) cc_final: 0.7885 (ptt) REVERT: B 28 GLU cc_start: 0.7565 (tm-30) cc_final: 0.6920 (mm-30) REVERT: B 102 ASP cc_start: 0.8010 (t70) cc_final: 0.7640 (t70) REVERT: B 107 ASP cc_start: 0.8540 (m-30) cc_final: 0.8327 (m-30) REVERT: B 130 ASP cc_start: 0.7899 (m-30) cc_final: 0.7553 (t0) REVERT: B 206 LYS cc_start: 0.7814 (mtpt) cc_final: 0.6935 (mttp) REVERT: B 210 ASP cc_start: 0.7804 (m-30) cc_final: 0.7313 (m-30) REVERT: C 24 MET cc_start: 0.7750 (ptt) cc_final: 0.7379 (ptt) REVERT: C 28 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7068 (mm-30) REVERT: C 36 LYS cc_start: 0.7919 (tppt) cc_final: 0.7506 (tptm) REVERT: C 102 ASP cc_start: 0.8056 (t70) cc_final: 0.7657 (t70) REVERT: C 126 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7431 (mt-10) REVERT: C 206 LYS cc_start: 0.7847 (mtpt) cc_final: 0.6927 (mttp) REVERT: C 210 ASP cc_start: 0.7810 (m-30) cc_final: 0.7497 (m-30) REVERT: C 235 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7240 (mt0) REVERT: C 303 MET cc_start: 0.8558 (mmt) cc_final: 0.8337 (mmt) REVERT: C 316 GLU cc_start: 0.6065 (tm-30) cc_final: 0.5847 (tm-30) REVERT: D 72 MET cc_start: 0.8218 (mtm) cc_final: 0.7937 (mtt) REVERT: D 102 ASP cc_start: 0.7975 (t70) cc_final: 0.7522 (t70) REVERT: D 164 ASP cc_start: 0.8886 (p0) cc_final: 0.8561 (p0) REVERT: D 173 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7317 (tt0) REVERT: D 206 LYS cc_start: 0.7822 (mtpt) cc_final: 0.7201 (mttp) REVERT: D 210 ASP cc_start: 0.7816 (m-30) cc_final: 0.7551 (m-30) REVERT: D 235 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7504 (mt0) REVERT: E 24 MET cc_start: 0.7526 (ptt) cc_final: 0.7045 (ptt) REVERT: E 28 GLU cc_start: 0.7649 (tm-30) cc_final: 0.6949 (mm-30) REVERT: E 31 ASP cc_start: 0.7993 (m-30) cc_final: 0.7783 (m-30) REVERT: E 94 TYR cc_start: 0.7716 (t80) cc_final: 0.7284 (t80) REVERT: E 107 ASP cc_start: 0.8490 (m-30) cc_final: 0.8288 (OUTLIER) REVERT: E 130 ASP cc_start: 0.7886 (m-30) cc_final: 0.7559 (t0) REVERT: E 164 ASP cc_start: 0.9067 (p0) cc_final: 0.8727 (p0) REVERT: E 173 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7392 (tt0) REVERT: E 206 LYS cc_start: 0.7860 (mtpt) cc_final: 0.7216 (mttp) REVERT: E 235 GLN cc_start: 0.7859 (mm110) cc_final: 0.7273 (mt0) REVERT: E 243 MET cc_start: 0.6187 (mtm) cc_final: 0.5978 (mtp) REVERT: E 303 MET cc_start: 0.8687 (mmt) cc_final: 0.8158 (mmt) outliers start: 48 outliers final: 10 residues processed: 344 average time/residue: 0.4860 time to fit residues: 186.3641 Evaluate side-chains 292 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 283 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 129 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 40 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 136 optimal weight: 0.0870 chunk 61 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 ASN A 82 GLN A 321 ASN B 58 ASN B 418 ASN C 321 ASN D 321 ASN E 321 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.132597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.095273 restraints weight = 17306.407| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.71 r_work: 0.2846 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14530 Z= 0.127 Angle : 0.618 6.218 19750 Z= 0.309 Chirality : 0.044 0.173 2260 Planarity : 0.004 0.036 2430 Dihedral : 5.063 21.777 1890 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.34 % Allowed : 16.72 % Favored : 79.93 % 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: -2.57 (0.18), residues: 1710 helix: -2.21 (0.18), residues: 630 sheet: -0.41 (0.27), residues: 340 loop : -1.73 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 268 TYR 0.013 0.001 TYR D 144 PHE 0.019 0.001 PHE D 322 TRP 0.009 0.001 TRP D 84 HIS 0.001 0.000 HIS B 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (14505) covalent geometry : angle 0.60195 / 0.31 (19685) SS BOND : bond 0.00454 / 0.24 ( 10) SS BOND : angle 1.46410 / 0.94 ( 20) hydrogen bonds : bond 0.03786 / 2.47 ( 540) hydrogen bonds : angle 4.63207 / 3.22 ( 1995) link_BETA1-4 : bond 0.00499 / 0.27 ( 10) link_BETA1-4 : angle 3.43062 / 2.50 ( 30) link_NAG-ASN : bond 0.00203 / 0.12 ( 5) link_NAG-ASN : angle 0.44951 / 0.26 ( 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 371 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 320 time to evaluate : 0.532 Fit side-chains REVERT: A 102 ASP cc_start: 0.8048 (t70) cc_final: 0.7653 (t70) REVERT: A 126 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7318 (mt-10) REVERT: A 173 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7527 (tt0) REVERT: A 206 LYS cc_start: 0.7962 (mtpt) cc_final: 0.7362 (mttp) REVERT: A 210 ASP cc_start: 0.7624 (m-30) cc_final: 0.7301 (m-30) REVERT: A 235 GLN cc_start: 0.7936 (mm-40) cc_final: 0.7212 (mm-40) REVERT: A 420 PHE cc_start: 0.7926 (m-10) cc_final: 0.6859 (t80) REVERT: B 24 MET cc_start: 0.7783 (ptt) cc_final: 0.7580 (ptt) REVERT: B 41 ASP cc_start: 0.8811 (t0) cc_final: 0.8501 (t0) REVERT: B 62 ASN cc_start: 0.8451 (m-40) cc_final: 0.8000 (m110) REVERT: B 102 ASP cc_start: 0.7954 (t70) cc_final: 0.7551 (t70) REVERT: B 130 ASP cc_start: 0.7889 (m-30) cc_final: 0.7636 (t0) REVERT: B 164 ASP cc_start: 0.8893 (p0) cc_final: 0.8542 (p0) REVERT: B 206 LYS cc_start: 0.7794 (mtpt) cc_final: 0.7013 (mttp) REVERT: B 210 ASP cc_start: 0.7831 (m-30) cc_final: 0.7315 (m-30) REVERT: B 235 GLN cc_start: 0.7851 (mm-40) cc_final: 0.7375 (mm-40) REVERT: B 420 PHE cc_start: 0.8024 (m-10) cc_final: 0.6979 (t80) REVERT: C 24 MET cc_start: 0.7592 (ptt) cc_final: 0.7381 (ptt) REVERT: C 28 GLU cc_start: 0.7546 (tm-30) cc_final: 0.6928 (mm-30) REVERT: C 36 LYS cc_start: 0.7959 (tppt) cc_final: 0.7564 (tptm) REVERT: C 102 ASP cc_start: 0.8038 (t70) cc_final: 0.7640 (t70) REVERT: C 126 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7435 (mt-10) REVERT: C 164 ASP cc_start: 0.8972 (p0) cc_final: 0.8743 (p0) REVERT: C 206 LYS cc_start: 0.7819 (mtpt) cc_final: 0.6922 (mttp) REVERT: C 210 ASP cc_start: 0.7787 (m-30) cc_final: 0.7453 (m-30) REVERT: C 235 GLN cc_start: 0.7995 (mm110) cc_final: 0.7241 (mt0) REVERT: C 303 MET cc_start: 0.8571 (mmt) cc_final: 0.8205 (mmt) REVERT: C 420 PHE cc_start: 0.8101 (m-10) cc_final: 0.7113 (t80) REVERT: D 69 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.6859 (mt-10) REVERT: D 72 MET cc_start: 0.8222 (mtm) cc_final: 0.7954 (mtt) REVERT: D 102 ASP cc_start: 0.7912 (t70) cc_final: 0.7466 (t70) REVERT: D 173 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7387 (tt0) REVERT: D 206 LYS cc_start: 0.7785 (mtpt) cc_final: 0.7170 (mttp) REVERT: D 210 ASP cc_start: 0.7805 (m-30) cc_final: 0.7544 (m-30) REVERT: D 235 GLN cc_start: 0.7886 (mm-40) cc_final: 0.7504 (mt0) REVERT: E 24 MET cc_start: 0.7432 (ptt) cc_final: 0.6987 (ptt) REVERT: E 28 GLU cc_start: 0.7685 (tm-30) cc_final: 0.6954 (mm-30) REVERT: E 62 ASN cc_start: 0.8428 (m-40) cc_final: 0.8169 (m110) REVERT: E 94 TYR cc_start: 0.7821 (t80) cc_final: 0.7463 (t80) REVERT: E 102 ASP cc_start: 0.7916 (t70) cc_final: 0.7325 (t70) REVERT: E 107 ASP cc_start: 0.8517 (m-30) cc_final: 0.8306 (m-30) REVERT: E 130 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7481 (t0) REVERT: E 206 LYS cc_start: 0.7803 (mtpt) cc_final: 0.7136 (mttp) REVERT: E 235 GLN cc_start: 0.7818 (mm110) cc_final: 0.7192 (mt0) REVERT: E 420 PHE cc_start: 0.8029 (m-10) cc_final: 0.6935 (t80) outliers start: 51 outliers final: 20 residues processed: 339 average time/residue: 0.4864 time to fit residues: 184.6180 Evaluate side-chains 310 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 288 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 74 optimal weight: 0.0000 chunk 28 optimal weight: 1.9990 chunk 155 optimal weight: 0.5980 chunk 65 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 153 optimal weight: 0.0570 chunk 53 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 128 optimal weight: 0.9990 overall best weight: 0.5104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 ASN A 321 ASN A 418 ASN C 62 ASN C 82 GLN C 321 ASN D 62 ASN D 82 GLN E 82 GLN E 321 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.133308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.096612 restraints weight = 17208.524| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.68 r_work: 0.2859 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14530 Z= 0.109 Angle : 0.593 7.148 19750 Z= 0.293 Chirality : 0.044 0.156 2260 Planarity : 0.003 0.028 2430 Dihedral : 4.780 21.534 1890 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.26 % Allowed : 17.44 % Favored : 78.30 % 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: -1.89 (0.19), residues: 1710 helix: -1.46 (0.20), residues: 620 sheet: -0.02 (0.29), residues: 340 loop : -1.54 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 45 TYR 0.012 0.001 TYR B 317 PHE 0.022 0.001 PHE A 322 TRP 0.009 0.001 TRP E 84 HIS 0.001 0.000 HIS B 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (14505) covalent geometry : angle 0.57782 / 0.29 (19685) SS BOND : bond 0.00393 / 0.20 ( 10) SS BOND : angle 1.36539 / 0.87 ( 20) hydrogen bonds : bond 0.03212 / 2.09 ( 540) hydrogen bonds : angle 4.10197 / 2.82 ( 1995) link_BETA1-4 : bond 0.00476 / 0.25 ( 10) link_BETA1-4 : angle 3.30912 / 2.40 ( 30) link_NAG-ASN : bond 0.00208 / 0.12 ( 5) link_NAG-ASN : angle 0.36521 / 0.21 ( 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 378 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 313 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.7321 (tttt) cc_final: 0.6890 (ttpt) REVERT: A 102 ASP cc_start: 0.8067 (t70) cc_final: 0.7742 (t70) REVERT: A 126 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7311 (mt-10) REVERT: A 171 GLN cc_start: 0.8343 (pt0) cc_final: 0.7929 (mt0) REVERT: A 206 LYS cc_start: 0.7868 (mtpt) cc_final: 0.7250 (mttp) REVERT: A 210 ASP cc_start: 0.7572 (m-30) cc_final: 0.7263 (m-30) REVERT: A 222 LYS cc_start: 0.7527 (ptmm) cc_final: 0.7260 (ttpt) REVERT: A 235 GLN cc_start: 0.7930 (mm-40) cc_final: 0.7211 (mm-40) REVERT: B 62 ASN cc_start: 0.8386 (m-40) cc_final: 0.7885 (m110) REVERT: B 102 ASP cc_start: 0.7953 (t70) cc_final: 0.7441 (t70) REVERT: B 130 ASP cc_start: 0.7781 (m-30) cc_final: 0.7567 (t0) REVERT: B 206 LYS cc_start: 0.7780 (mtpt) cc_final: 0.6934 (mttp) REVERT: B 210 ASP cc_start: 0.7792 (m-30) cc_final: 0.7242 (m-30) REVERT: B 235 GLN cc_start: 0.7818 (mm-40) cc_final: 0.7348 (mm-40) REVERT: C 28 GLU cc_start: 0.7515 (tm-30) cc_final: 0.6896 (mm-30) REVERT: C 36 LYS cc_start: 0.7979 (tppt) cc_final: 0.7595 (tptm) REVERT: C 69 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.6272 (mm-30) REVERT: C 102 ASP cc_start: 0.8037 (t70) cc_final: 0.7629 (t70) REVERT: C 126 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7426 (mt-10) REVERT: C 206 LYS cc_start: 0.7815 (mtpt) cc_final: 0.6952 (mttp) REVERT: C 210 ASP cc_start: 0.7739 (m-30) cc_final: 0.7395 (m-30) REVERT: C 279 MET cc_start: 0.7301 (tpt) cc_final: 0.6928 (tpt) REVERT: C 303 MET cc_start: 0.8568 (mmt) cc_final: 0.8182 (mmt) REVERT: D 72 MET cc_start: 0.8198 (mtm) cc_final: 0.7947 (mtt) REVERT: D 102 ASP cc_start: 0.7882 (t70) cc_final: 0.7397 (t70) REVERT: D 171 GLN cc_start: 0.8296 (pt0) cc_final: 0.8087 (mt0) REVERT: D 173 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7422 (tt0) REVERT: D 206 LYS cc_start: 0.7766 (mtpt) cc_final: 0.7136 (mttp) REVERT: D 210 ASP cc_start: 0.7731 (m-30) cc_final: 0.7461 (m-30) REVERT: D 235 GLN cc_start: 0.7887 (mm-40) cc_final: 0.7518 (mt0) REVERT: E 24 MET cc_start: 0.7471 (ptt) cc_final: 0.7136 (ptt) REVERT: E 62 ASN cc_start: 0.8405 (m-40) cc_final: 0.8136 (m-40) REVERT: E 94 TYR cc_start: 0.7788 (t80) cc_final: 0.7453 (t80) REVERT: E 102 ASP cc_start: 0.7809 (t70) cc_final: 0.7299 (t70) REVERT: E 130 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7462 (t0) REVERT: E 164 ASP cc_start: 0.9077 (p0) cc_final: 0.8813 (p0) REVERT: E 206 LYS cc_start: 0.7767 (mtpt) cc_final: 0.7162 (mttp) REVERT: E 235 GLN cc_start: 0.7776 (mm110) cc_final: 0.7150 (mt0) outliers start: 65 outliers final: 18 residues processed: 351 average time/residue: 0.4780 time to fit residues: 187.3345 Evaluate side-chains 299 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 279 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 321 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 131 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 74 optimal weight: 0.2980 chunk 130 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 168 optimal weight: 0.0370 chunk 1 optimal weight: 0.0670 chunk 97 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 ASN A 321 ASN C 321 ASN E 321 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.135329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.098546 restraints weight = 17226.373| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.70 r_work: 0.2943 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14530 Z= 0.104 Angle : 0.581 8.766 19750 Z= 0.287 Chirality : 0.044 0.157 2260 Planarity : 0.003 0.028 2430 Dihedral : 4.611 21.772 1890 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.80 % Allowed : 18.89 % Favored : 77.31 % 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: -1.46 (0.20), residues: 1710 helix: -0.99 (0.21), residues: 610 sheet: 0.13 (0.29), residues: 340 loop : -1.38 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 268 TYR 0.011 0.001 TYR B 144 PHE 0.028 0.001 PHE E 322 TRP 0.009 0.001 TRP E 84 HIS 0.001 0.000 HIS D 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (14505) covalent geometry : angle 0.56602 / 0.28 (19685) SS BOND : bond 0.00402 / 0.21 ( 10) SS BOND : angle 1.34867 / 0.85 ( 20) hydrogen bonds : bond 0.03039 / 1.99 ( 540) hydrogen bonds : angle 3.89026 / 2.65 ( 1995) link_BETA1-4 : bond 0.00490 / 0.27 ( 10) link_BETA1-4 : angle 3.24181 / 2.36 ( 30) link_NAG-ASN : bond 0.00187 / 0.11 ( 5) link_NAG-ASN : angle 0.38759 / 0.22 ( 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: 58 poor density : 290 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.7785 (tttt) cc_final: 0.7357 (ttpt) REVERT: A 102 ASP cc_start: 0.8435 (t70) cc_final: 0.8096 (t70) REVERT: A 126 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7704 (mt-10) REVERT: A 206 LYS cc_start: 0.8264 (mtpt) cc_final: 0.7488 (mmtm) REVERT: A 210 ASP cc_start: 0.7882 (m-30) cc_final: 0.7600 (m-30) REVERT: A 235 GLN cc_start: 0.8165 (mm-40) cc_final: 0.7476 (mm-40) REVERT: A 279 MET cc_start: 0.7523 (tpt) cc_final: 0.7279 (tpp) REVERT: B 24 MET cc_start: 0.7487 (ptt) cc_final: 0.7270 (ptp) REVERT: B 62 ASN cc_start: 0.8610 (m-40) cc_final: 0.8235 (m110) REVERT: B 102 ASP cc_start: 0.8168 (t70) cc_final: 0.7728 (t70) REVERT: B 206 LYS cc_start: 0.8216 (mtpt) cc_final: 0.7478 (mttp) REVERT: B 210 ASP cc_start: 0.8041 (m-30) cc_final: 0.7533 (m-30) REVERT: B 323 ILE cc_start: 0.7168 (OUTLIER) cc_final: 0.6914 (mp) REVERT: C 28 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7137 (mm-30) REVERT: C 36 LYS cc_start: 0.7918 (tppt) cc_final: 0.7566 (tptm) REVERT: C 102 ASP cc_start: 0.8272 (t70) cc_final: 0.7918 (t70) REVERT: C 126 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7704 (mt-10) REVERT: C 206 LYS cc_start: 0.8263 (mtpt) cc_final: 0.7445 (mttp) REVERT: C 210 ASP cc_start: 0.7997 (m-30) cc_final: 0.7689 (m-30) REVERT: C 279 MET cc_start: 0.7807 (tpt) cc_final: 0.7469 (tpt) REVERT: C 303 MET cc_start: 0.8935 (mmt) cc_final: 0.8485 (mmt) REVERT: D 72 MET cc_start: 0.8612 (mtm) cc_final: 0.8395 (mtt) REVERT: D 102 ASP cc_start: 0.8189 (t70) cc_final: 0.7728 (t70) REVERT: D 206 LYS cc_start: 0.8182 (mtpt) cc_final: 0.7572 (mttp) REVERT: D 210 ASP cc_start: 0.7972 (m-30) cc_final: 0.7730 (m-30) REVERT: D 235 GLN cc_start: 0.8112 (mm-40) cc_final: 0.7776 (mt0) REVERT: D 398 ARG cc_start: 0.6835 (ttm170) cc_final: 0.6388 (mmm-85) REVERT: E 24 MET cc_start: 0.7599 (ptt) cc_final: 0.7363 (ptt) REVERT: E 62 ASN cc_start: 0.8622 (m-40) cc_final: 0.8391 (m-40) REVERT: E 94 TYR cc_start: 0.8049 (t80) cc_final: 0.7767 (t80) REVERT: E 102 ASP cc_start: 0.8099 (t70) cc_final: 0.7677 (t70) REVERT: E 206 LYS cc_start: 0.8168 (mtpt) cc_final: 0.7563 (mttp) REVERT: E 235 GLN cc_start: 0.7952 (mm110) cc_final: 0.7343 (mt0) REVERT: E 323 ILE cc_start: 0.7004 (OUTLIER) cc_final: 0.6769 (mp) REVERT: E 398 ARG cc_start: 0.7751 (mmm-85) cc_final: 0.6592 (ttm170) outliers start: 58 outliers final: 25 residues processed: 317 average time/residue: 0.4658 time to fit residues: 165.4280 Evaluate side-chains 296 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 269 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 420 PHE Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 321 ASN Chi-restraints excluded: chain E residue 323 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 56 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 ASN A 321 ASN C 321 ASN E 321 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.131359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.094526 restraints weight = 17198.977| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.67 r_work: 0.2816 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14530 Z= 0.161 Angle : 0.615 9.642 19750 Z= 0.305 Chirality : 0.045 0.173 2260 Planarity : 0.004 0.036 2430 Dihedral : 4.760 40.076 1890 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.93 % Allowed : 20.20 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.20), residues: 1710 helix: -0.62 (0.22), residues: 595 sheet: 0.43 (0.30), residues: 320 loop : -1.15 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 268 TYR 0.013 0.001 TYR A 144 PHE 0.036 0.002 PHE E 322 TRP 0.009 0.001 TRP B 302 HIS 0.001 0.001 HIS B 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (14505) covalent geometry : angle 0.59852 / 0.30 (19685) SS BOND : bond 0.00524 / 0.29 ( 10) SS BOND : angle 1.97559 / 1.09 ( 20) hydrogen bonds : bond 0.03180 / 2.07 ( 540) hydrogen bonds : angle 3.93574 / 2.69 ( 1995) link_BETA1-4 : bond 0.00485 / 0.27 ( 10) link_BETA1-4 : angle 3.32884 / 2.43 ( 30) link_NAG-ASN : bond 0.00134 / 0.08 ( 5) link_NAG-ASN : angle 0.53767 / 0.31 ( 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 345 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 285 time to evaluate : 0.481 Fit side-chains REVERT: A 32 LYS cc_start: 0.7362 (tttt) cc_final: 0.6961 (ttpt) REVERT: A 102 ASP cc_start: 0.8234 (t70) cc_final: 0.7801 (t70) REVERT: A 126 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7404 (mt-10) REVERT: A 206 LYS cc_start: 0.7947 (mtpt) cc_final: 0.7396 (mttp) REVERT: A 210 ASP cc_start: 0.7711 (m-30) cc_final: 0.7428 (m-30) REVERT: A 235 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7351 (mm-40) REVERT: B 24 MET cc_start: 0.7215 (ptt) cc_final: 0.6923 (ptp) REVERT: B 62 ASN cc_start: 0.8470 (m-40) cc_final: 0.7994 (m110) REVERT: B 102 ASP cc_start: 0.7881 (t70) cc_final: 0.7437 (t70) REVERT: B 206 LYS cc_start: 0.7846 (mtpt) cc_final: 0.7026 (mttp) REVERT: B 210 ASP cc_start: 0.7884 (m-30) cc_final: 0.7331 (m-30) REVERT: B 235 GLN cc_start: 0.7889 (mm-40) cc_final: 0.7484 (mm-40) REVERT: C 28 GLU cc_start: 0.7521 (tm-30) cc_final: 0.7034 (mm-30) REVERT: C 32 LYS cc_start: 0.7377 (tttm) cc_final: 0.7159 (ttpt) REVERT: C 36 LYS cc_start: 0.8082 (tppt) cc_final: 0.7669 (tptm) REVERT: C 126 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7591 (mt-10) REVERT: C 206 LYS cc_start: 0.7862 (mtpt) cc_final: 0.7023 (mttp) REVERT: C 210 ASP cc_start: 0.7822 (m-30) cc_final: 0.7510 (m-30) REVERT: C 279 MET cc_start: 0.7371 (tpt) cc_final: 0.7100 (tpt) REVERT: D 72 MET cc_start: 0.8126 (mtm) cc_final: 0.7873 (mtt) REVERT: D 102 ASP cc_start: 0.7980 (t70) cc_final: 0.7513 (t70) REVERT: D 206 LYS cc_start: 0.7775 (mtpt) cc_final: 0.7149 (mttp) REVERT: D 235 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7665 (mt0) REVERT: D 398 ARG cc_start: 0.6642 (ttm170) cc_final: 0.6241 (mmm-85) REVERT: E 24 MET cc_start: 0.7275 (ptt) cc_final: 0.7000 (ptt) REVERT: E 62 ASN cc_start: 0.8491 (m-40) cc_final: 0.8233 (m-40) REVERT: E 94 TYR cc_start: 0.7803 (t80) cc_final: 0.7523 (t80) REVERT: E 97 ASP cc_start: 0.7441 (m-30) cc_final: 0.6824 (t0) REVERT: E 102 ASP cc_start: 0.7923 (t70) cc_final: 0.7491 (t70) REVERT: E 164 ASP cc_start: 0.9124 (p0) cc_final: 0.8827 (p0) REVERT: E 206 LYS cc_start: 0.7851 (mtpt) cc_final: 0.7155 (mttp) REVERT: E 235 GLN cc_start: 0.7885 (mm110) cc_final: 0.7215 (mt0) outliers start: 60 outliers final: 27 residues processed: 309 average time/residue: 0.4989 time to fit residues: 172.3325 Evaluate side-chains 303 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 276 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 107 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 139 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 138 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 ASN C 321 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.130179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.093156 restraints weight = 17094.789| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.67 r_work: 0.2953 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14530 Z= 0.150 Angle : 0.615 8.299 19750 Z= 0.303 Chirality : 0.045 0.166 2260 Planarity : 0.004 0.036 2430 Dihedral : 4.798 45.953 1890 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.13 % Allowed : 19.80 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.20), residues: 1710 helix: -0.18 (0.23), residues: 575 sheet: 0.47 (0.30), residues: 320 loop : -0.93 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 268 TYR 0.012 0.001 TYR E 144 PHE 0.032 0.002 PHE C 322 TRP 0.008 0.001 TRP E 302 HIS 0.001 0.000 HIS B 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 (14505) covalent geometry : angle 0.59833 / 0.30 (19685) SS BOND : bond 0.00499 / 0.28 ( 10) SS BOND : angle 1.99869 / 1.07 ( 20) hydrogen bonds : bond 0.03144 / 2.03 ( 540) hydrogen bonds : angle 3.88426 / 2.66 ( 1995) link_BETA1-4 : bond 0.00438 / 0.24 ( 10) link_BETA1-4 : angle 3.32197 / 2.43 ( 30) link_NAG-ASN : bond 0.00154 / 0.09 ( 5) link_NAG-ASN : angle 0.53081 / 0.31 ( 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 352 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 289 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.7801 (tttt) cc_final: 0.7371 (ttpt) REVERT: A 102 ASP cc_start: 0.8432 (t70) cc_final: 0.8064 (t70) REVERT: A 126 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7723 (mt-10) REVERT: A 206 LYS cc_start: 0.8308 (mtpt) cc_final: 0.7757 (mttp) REVERT: A 210 ASP cc_start: 0.7945 (m-30) cc_final: 0.7692 (m-30) REVERT: B 62 ASN cc_start: 0.8665 (m-40) cc_final: 0.8307 (m110) REVERT: B 102 ASP cc_start: 0.8175 (t70) cc_final: 0.7793 (t70) REVERT: B 206 LYS cc_start: 0.8267 (mtpt) cc_final: 0.7497 (mttp) REVERT: B 210 ASP cc_start: 0.8027 (m-30) cc_final: 0.7482 (m-30) REVERT: B 235 GLN cc_start: 0.8156 (mm-40) cc_final: 0.7754 (mm-40) REVERT: C 28 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7337 (mm-30) REVERT: C 32 LYS cc_start: 0.7766 (tttm) cc_final: 0.7513 (ttpt) REVERT: C 36 LYS cc_start: 0.8021 (tppt) cc_final: 0.7700 (tptm) REVERT: C 102 ASP cc_start: 0.8355 (t70) cc_final: 0.7961 (t70) REVERT: C 126 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7778 (mt-10) REVERT: C 206 LYS cc_start: 0.8278 (mtpt) cc_final: 0.7449 (mttp) REVERT: C 210 ASP cc_start: 0.8014 (m-30) cc_final: 0.7721 (m-30) REVERT: C 279 MET cc_start: 0.7961 (tpt) cc_final: 0.7643 (tpt) REVERT: C 303 MET cc_start: 0.8889 (mmt) cc_final: 0.8681 (mmt) REVERT: C 398 ARG cc_start: 0.6647 (ttm170) cc_final: 0.6262 (mmm-85) REVERT: D 72 MET cc_start: 0.8666 (mtm) cc_final: 0.8431 (mtt) REVERT: D 102 ASP cc_start: 0.8303 (t70) cc_final: 0.7863 (t70) REVERT: D 206 LYS cc_start: 0.8235 (mtpt) cc_final: 0.7626 (mttp) REVERT: D 235 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7869 (mt0) REVERT: D 398 ARG cc_start: 0.6811 (ttm170) cc_final: 0.6430 (mmm-85) REVERT: D 415 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6817 (tm) REVERT: E 24 MET cc_start: 0.7533 (ptt) cc_final: 0.7236 (ptp) REVERT: E 28 GLU cc_start: 0.7332 (tm-30) cc_final: 0.6735 (mm-30) REVERT: E 62 ASN cc_start: 0.8694 (m-40) cc_final: 0.8462 (m110) REVERT: E 102 ASP cc_start: 0.8219 (t70) cc_final: 0.7842 (t70) REVERT: E 206 LYS cc_start: 0.8239 (mtpt) cc_final: 0.7480 (mttp) REVERT: E 208 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7411 (tt0) REVERT: E 398 ARG cc_start: 0.7808 (mmm-85) cc_final: 0.6559 (ttm170) outliers start: 63 outliers final: 34 residues processed: 318 average time/residue: 0.5011 time to fit residues: 177.7685 Evaluate side-chains 306 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 271 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 123 optimal weight: 4.9990 chunk 128 optimal weight: 0.0770 chunk 25 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 103 optimal weight: 0.0060 chunk 141 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 162 optimal weight: 0.9980 overall best weight: 0.5954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 ASN A 321 ASN C 171 GLN C 321 ASN D 321 ASN E 321 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.134826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.097389 restraints weight = 16837.988| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.73 r_work: 0.2828 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14530 Z= 0.116 Angle : 0.617 11.608 19750 Z= 0.302 Chirality : 0.044 0.156 2260 Planarity : 0.004 0.034 2430 Dihedral : 4.800 49.889 1890 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.28 % Allowed : 20.79 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.44 (0.20), residues: 1710 helix: 0.10 (0.23), residues: 575 sheet: 0.66 (0.31), residues: 315 loop : -0.90 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 268 TYR 0.011 0.001 TYR B 317 PHE 0.032 0.001 PHE C 322 TRP 0.008 0.001 TRP A 84 HIS 0.003 0.000 HIS D 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (14505) covalent geometry : angle 0.59584 / 0.30 (19685) SS BOND : bond 0.00433 / 0.23 ( 10) SS BOND : angle 3.20380 / 1.69 ( 20) hydrogen bonds : bond 0.02996 / 1.95 ( 540) hydrogen bonds : angle 3.78981 / 2.59 ( 1995) link_BETA1-4 : bond 0.00434 / 0.24 ( 10) link_BETA1-4 : angle 3.22488 / 2.35 ( 30) link_NAG-ASN : bond 0.00175 / 0.10 ( 5) link_NAG-ASN : angle 0.46844 / 0.27 ( 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 336 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 286 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.7337 (tttt) cc_final: 0.6961 (ttpt) REVERT: A 102 ASP cc_start: 0.8251 (t70) cc_final: 0.7781 (t70) REVERT: A 126 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7533 (mt-10) REVERT: A 206 LYS cc_start: 0.7968 (mtpt) cc_final: 0.7479 (mttp) REVERT: A 210 ASP cc_start: 0.7721 (m-30) cc_final: 0.7484 (m-30) REVERT: B 62 ASN cc_start: 0.8451 (m-40) cc_final: 0.8026 (m110) REVERT: B 102 ASP cc_start: 0.7927 (t70) cc_final: 0.7502 (t70) REVERT: B 206 LYS cc_start: 0.7893 (mtpt) cc_final: 0.7074 (mttp) REVERT: B 210 ASP cc_start: 0.7880 (m-30) cc_final: 0.7312 (m-30) REVERT: B 235 GLN cc_start: 0.7973 (mm-40) cc_final: 0.7539 (mm-40) REVERT: C 28 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7119 (mm-30) REVERT: C 32 LYS cc_start: 0.7366 (tttm) cc_final: 0.7110 (ttpt) REVERT: C 36 LYS cc_start: 0.8042 (tppt) cc_final: 0.7667 (tptm) REVERT: C 102 ASP cc_start: 0.8072 (t70) cc_final: 0.7643 (t70) REVERT: C 126 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7629 (mt-10) REVERT: C 171 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8121 (mt0) REVERT: C 206 LYS cc_start: 0.7917 (mtpt) cc_final: 0.7087 (mttp) REVERT: C 210 ASP cc_start: 0.7844 (m-30) cc_final: 0.7543 (m-30) REVERT: C 279 MET cc_start: 0.7457 (tpt) cc_final: 0.7247 (tpt) REVERT: C 398 ARG cc_start: 0.6473 (ttm170) cc_final: 0.6109 (mmm-85) REVERT: C 415 LEU cc_start: 0.6672 (OUTLIER) cc_final: 0.6295 (tm) REVERT: D 72 MET cc_start: 0.8216 (mtm) cc_final: 0.7973 (mtt) REVERT: D 102 ASP cc_start: 0.8017 (t70) cc_final: 0.7509 (t70) REVERT: D 206 LYS cc_start: 0.7849 (mtpt) cc_final: 0.7230 (mttp) REVERT: D 235 GLN cc_start: 0.8028 (mm-40) cc_final: 0.7646 (mt0) REVERT: D 398 ARG cc_start: 0.6658 (ttm170) cc_final: 0.6278 (mmm-85) REVERT: D 415 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.6434 (tm) REVERT: E 28 GLU cc_start: 0.6883 (tm-30) cc_final: 0.6283 (mm-30) REVERT: E 62 ASN cc_start: 0.8497 (m-40) cc_final: 0.8237 (m-40) REVERT: E 97 ASP cc_start: 0.7509 (m-30) cc_final: 0.6969 (t0) REVERT: E 102 ASP cc_start: 0.8074 (t70) cc_final: 0.7619 (t70) REVERT: E 206 LYS cc_start: 0.7818 (mtpt) cc_final: 0.7072 (mttp) REVERT: E 235 GLN cc_start: 0.8035 (mm-40) cc_final: 0.7304 (mt0) REVERT: E 398 ARG cc_start: 0.7654 (mmm-85) cc_final: 0.6425 (ttm170) outliers start: 50 outliers final: 26 residues processed: 308 average time/residue: 0.5110 time to fit residues: 175.4281 Evaluate side-chains 290 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 261 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 138 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 143 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 ASN A 321 ASN B 321 ASN C 171 GLN C 321 ASN E 321 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.132836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.095408 restraints weight = 16949.394| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.74 r_work: 0.2811 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14530 Z= 0.134 Angle : 0.615 9.904 19750 Z= 0.303 Chirality : 0.045 0.161 2260 Planarity : 0.004 0.039 2430 Dihedral : 4.831 49.527 1890 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.02 % Allowed : 21.77 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.38 (0.20), residues: 1710 helix: 0.22 (0.23), residues: 575 sheet: 0.55 (0.31), residues: 320 loop : -0.87 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 268 TYR 0.011 0.001 TYR D 144 PHE 0.032 0.001 PHE D 322 TRP 0.008 0.001 TRP E 302 HIS 0.002 0.000 HIS C 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.13 (14505) covalent geometry : angle 0.59490 / 0.30 (19685) SS BOND : bond 0.00459 / 0.25 ( 10) SS BOND : angle 3.12934 / 1.68 ( 20) hydrogen bonds : bond 0.03022 / 1.95 ( 540) hydrogen bonds : angle 3.78890 / 2.60 ( 1995) link_BETA1-4 : bond 0.00486 / 0.27 ( 10) link_BETA1-4 : angle 3.24151 / 2.36 ( 30) link_NAG-ASN : bond 0.00164 / 0.10 ( 5) link_NAG-ASN : angle 0.51142 / 0.30 ( 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 314 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 268 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.7629 (tttt) cc_final: 0.7229 (ttpt) REVERT: A 102 ASP cc_start: 0.8382 (t70) cc_final: 0.7983 (t70) REVERT: A 126 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7617 (mt-10) REVERT: A 206 LYS cc_start: 0.8162 (mtpt) cc_final: 0.7675 (mttp) REVERT: A 210 ASP cc_start: 0.7849 (m-30) cc_final: 0.7603 (m-30) REVERT: B 41 ASP cc_start: 0.8912 (t0) cc_final: 0.8625 (t0) REVERT: B 62 ASN cc_start: 0.8575 (m-40) cc_final: 0.8126 (m110) REVERT: B 102 ASP cc_start: 0.8090 (t70) cc_final: 0.7688 (t70) REVERT: B 206 LYS cc_start: 0.8122 (mtpt) cc_final: 0.7299 (mttp) REVERT: B 210 ASP cc_start: 0.7932 (m-30) cc_final: 0.7394 (m-30) REVERT: B 235 GLN cc_start: 0.8093 (mm-40) cc_final: 0.7651 (mm-40) REVERT: B 415 LEU cc_start: 0.7150 (OUTLIER) cc_final: 0.6760 (tm) REVERT: C 28 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7284 (mm-30) REVERT: C 32 LYS cc_start: 0.7603 (tttm) cc_final: 0.7354 (ttpt) REVERT: C 36 LYS cc_start: 0.8024 (tppt) cc_final: 0.7726 (tptm) REVERT: C 102 ASP cc_start: 0.8305 (t70) cc_final: 0.7869 (t70) REVERT: C 126 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7622 (mt-10) REVERT: C 206 LYS cc_start: 0.8149 (mtpt) cc_final: 0.7313 (mttp) REVERT: C 210 ASP cc_start: 0.7969 (m-30) cc_final: 0.7670 (m-30) REVERT: C 279 MET cc_start: 0.7787 (tpt) cc_final: 0.7518 (tpt) REVERT: C 398 ARG cc_start: 0.6564 (ttm170) cc_final: 0.6207 (mmm-85) REVERT: C 415 LEU cc_start: 0.6899 (OUTLIER) cc_final: 0.6514 (tm) REVERT: D 72 MET cc_start: 0.8543 (mtm) cc_final: 0.8292 (mtt) REVERT: D 102 ASP cc_start: 0.8192 (t70) cc_final: 0.7712 (t70) REVERT: D 206 LYS cc_start: 0.8102 (mtpt) cc_final: 0.7475 (mttp) REVERT: D 235 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7725 (mt0) REVERT: D 398 ARG cc_start: 0.6714 (ttm170) cc_final: 0.6300 (mmm-85) REVERT: D 415 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6627 (tm) REVERT: E 24 MET cc_start: 0.7907 (ptp) cc_final: 0.7672 (ptp) REVERT: E 62 ASN cc_start: 0.8622 (m-40) cc_final: 0.8374 (m110) REVERT: E 102 ASP cc_start: 0.8217 (t70) cc_final: 0.7794 (t70) REVERT: E 206 LYS cc_start: 0.8051 (mtpt) cc_final: 0.7273 (mttp) REVERT: E 235 GLN cc_start: 0.8133 (mm-40) cc_final: 0.7450 (mt0) REVERT: E 398 ARG cc_start: 0.7741 (mmm-85) cc_final: 0.6485 (ttm170) outliers start: 46 outliers final: 31 residues processed: 291 average time/residue: 0.4934 time to fit residues: 160.6590 Evaluate side-chains 311 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 277 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 56 THR 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 227 GLU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 321 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 127 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 152 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 104 optimal weight: 0.0270 chunk 61 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 ASN A 321 ASN C 321 ASN E 321 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.132134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.095111 restraints weight = 16750.873| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.70 r_work: 0.2831 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14530 Z= 0.116 Angle : 0.605 9.083 19750 Z= 0.298 Chirality : 0.044 0.188 2260 Planarity : 0.004 0.037 2430 Dihedral : 4.785 48.465 1890 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.82 % Allowed : 22.16 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.30 (0.20), residues: 1710 helix: 0.34 (0.23), residues: 575 sheet: 0.55 (0.31), residues: 320 loop : -0.85 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 268 TYR 0.010 0.001 TYR B 317 PHE 0.036 0.001 PHE B 322 TRP 0.008 0.001 TRP A 84 HIS 0.001 0.000 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (14505) covalent geometry : angle 0.58549 / 0.29 (19685) SS BOND : bond 0.00413 / 0.22 ( 10) SS BOND : angle 2.97923 / 1.58 ( 20) hydrogen bonds : bond 0.02965 / 1.91 ( 540) hydrogen bonds : angle 3.75505 / 2.57 ( 1995) link_BETA1-4 : bond 0.00480 / 0.27 ( 10) link_BETA1-4 : angle 3.19430 / 2.32 ( 30) link_NAG-ASN : bond 0.00172 / 0.10 ( 5) link_NAG-ASN : angle 0.47428 / 0.27 ( 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 319 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 276 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.7320 (tttt) cc_final: 0.6972 (ttpt) REVERT: A 102 ASP cc_start: 0.8255 (t70) cc_final: 0.7845 (t70) REVERT: A 126 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7580 (mt-10) REVERT: A 206 LYS cc_start: 0.7996 (mtpt) cc_final: 0.7457 (mttp) REVERT: A 210 ASP cc_start: 0.7756 (m-30) cc_final: 0.7518 (m-30) REVERT: B 62 ASN cc_start: 0.8484 (m-40) cc_final: 0.8063 (m110) REVERT: B 102 ASP cc_start: 0.7965 (t70) cc_final: 0.7442 (t70) REVERT: B 206 LYS cc_start: 0.7941 (mtpt) cc_final: 0.7116 (mttp) REVERT: B 210 ASP cc_start: 0.7897 (m-30) cc_final: 0.7321 (m-30) REVERT: B 235 GLN cc_start: 0.8039 (mm-40) cc_final: 0.7589 (mm-40) REVERT: B 415 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6574 (tm) REVERT: C 28 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7088 (mm-30) REVERT: C 32 LYS cc_start: 0.7411 (tttm) cc_final: 0.7171 (ttpt) REVERT: C 36 LYS cc_start: 0.8018 (tppt) cc_final: 0.7687 (tptm) REVERT: C 102 ASP cc_start: 0.8186 (t70) cc_final: 0.7699 (t70) REVERT: C 126 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7583 (mt-10) REVERT: C 206 LYS cc_start: 0.7961 (mtpt) cc_final: 0.7135 (mttp) REVERT: C 210 ASP cc_start: 0.7915 (m-30) cc_final: 0.7624 (m-30) REVERT: C 279 MET cc_start: 0.7517 (tpt) cc_final: 0.7316 (tpt) REVERT: C 398 ARG cc_start: 0.6533 (ttm170) cc_final: 0.6179 (mmm-85) REVERT: C 415 LEU cc_start: 0.6705 (OUTLIER) cc_final: 0.6317 (tm) REVERT: D 72 MET cc_start: 0.8287 (mtm) cc_final: 0.8039 (mtt) REVERT: D 102 ASP cc_start: 0.8054 (t70) cc_final: 0.7529 (t70) REVERT: D 206 LYS cc_start: 0.7900 (mtpt) cc_final: 0.7280 (mttp) REVERT: D 235 GLN cc_start: 0.8079 (mm-40) cc_final: 0.7698 (mt0) REVERT: D 398 ARG cc_start: 0.6634 (ttm170) cc_final: 0.6223 (mmm-85) REVERT: D 415 LEU cc_start: 0.6863 (OUTLIER) cc_final: 0.6481 (tm) REVERT: E 24 MET cc_start: 0.7680 (ptp) cc_final: 0.7246 (ptp) REVERT: E 28 GLU cc_start: 0.6957 (tm-30) cc_final: 0.6141 (mm-30) REVERT: E 62 ASN cc_start: 0.8532 (m-40) cc_final: 0.8272 (m-40) REVERT: E 97 ASP cc_start: 0.7566 (m-30) cc_final: 0.7045 (t0) REVERT: E 102 ASP cc_start: 0.8116 (t70) cc_final: 0.7667 (t70) REVERT: E 206 LYS cc_start: 0.7873 (mtpt) cc_final: 0.7146 (mttp) REVERT: E 235 GLN cc_start: 0.8136 (mm-40) cc_final: 0.7475 (mt0) REVERT: E 279 MET cc_start: 0.7017 (tpt) cc_final: 0.6606 (tpt) REVERT: E 398 ARG cc_start: 0.7661 (mmm-85) cc_final: 0.6421 (ttm170) outliers start: 43 outliers final: 29 residues processed: 294 average time/residue: 0.4889 time to fit residues: 160.7931 Evaluate side-chains 294 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 262 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 113 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 162 optimal weight: 0.9990 chunk 154 optimal weight: 0.0000 chunk 75 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 157 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 ASN A 321 ASN B 321 ASN C 321 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.134899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.097438 restraints weight = 16855.145| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.74 r_work: 0.2832 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14530 Z= 0.119 Angle : 0.598 8.904 19750 Z= 0.296 Chirality : 0.044 0.171 2260 Planarity : 0.004 0.033 2430 Dihedral : 4.728 47.635 1890 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.69 % Allowed : 22.10 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.26 (0.20), residues: 1710 helix: 0.44 (0.23), residues: 580 sheet: 0.57 (0.30), residues: 320 loop : -0.88 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 268 TYR 0.012 0.001 TYR E 317 PHE 0.032 0.002 PHE A 322 TRP 0.009 0.001 TRP E 302 HIS 0.001 0.000 HIS C 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (14505) covalent geometry : angle 0.57895 / 0.29 (19685) SS BOND : bond 0.00423 / 0.23 ( 10) SS BOND : angle 2.87215 / 1.53 ( 20) hydrogen bonds : bond 0.02897 / 1.86 ( 540) hydrogen bonds : angle 3.71369 / 2.54 ( 1995) link_BETA1-4 : bond 0.00474 / 0.27 ( 10) link_BETA1-4 : angle 3.17003 / 2.31 ( 30) link_NAG-ASN : bond 0.00155 / 0.09 ( 5) link_NAG-ASN : angle 0.49906 / 0.29 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4780.09 seconds wall clock time: 82 minutes 22.54 seconds (4942.54 seconds total)