Starting phenix.real_space_refine on Wed Mar 4 14:45:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pm1_20383/03_2026/6pm1_20383.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pm1_20383/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6pm1_20383/03_2026/6pm1_20383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pm1_20383/03_2026/6pm1_20383.map" model { file = "/net/cci-nas-00/data/ceres_data/6pm1_20383/03_2026/6pm1_20383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pm1_20383/03_2026/6pm1_20383.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.045 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-dev-5986/lib/python3.9/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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'TAU': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E, G, H, I, J Time building chain proxies: 2.30, per 1000 atoms: 0.16 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: 0.81 Conformation dependent library (CDL) restraints added in 622.9 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: 0.46 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: 2.25 Time building geometry restraints manager: 1.18 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 - 22.01: 8605 22.01 - 44.02: 205 44.02 - 66.02: 0 66.02 - 88.03: 35 88.03 - 110.04: 20 Dihedral angle restraints: 8865 sinusoidal: 3750 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 8862 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.460 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.230 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 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 : 13.059 110.039 5515 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 covalent geometry : bond 0.00779 (14505) covalent geometry : angle 1.04076 (19685) SS BOND : bond 0.01480 ( 10) SS BOND : angle 3.61627 ( 20) hydrogen bonds : bond 0.27827 ( 540) hydrogen bonds : angle 10.19785 ( 1995) link_BETA1-4 : bond 0.00339 ( 10) link_BETA1-4 : angle 5.38573 ( 30) link_NAG-ASN : bond 0.00153 ( 5) link_NAG-ASN : angle 1.92842 ( 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 : 0.572 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: 0.5502 time to fit residues: 279.6911 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 : 0.531 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 62 ASN B 62 ASN 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.132819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.095308 restraints weight = 17142.144| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.69 r_work: 0.2850 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14530 Z= 0.142 Angle : 0.705 8.167 19750 Z= 0.353 Chirality : 0.047 0.166 2260 Planarity : 0.005 0.043 2430 Dihedral : 10.938 70.316 2197 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.69 % Allowed : 14.43 % 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: -3.66 (0.16), residues: 1710 helix: -3.38 (0.14), residues: 630 sheet: -0.95 (0.26), residues: 340 loop : -2.10 (0.19), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 229 TYR 0.012 0.002 TYR D 317 PHE 0.019 0.002 PHE D 322 TRP 0.011 0.002 TRP B 110 HIS 0.002 0.000 HIS B 125 Details of bonding type rmsd covalent geometry : bond 0.00315 (14505) covalent geometry : angle 0.68522 (19685) SS BOND : bond 0.00522 ( 10) SS BOND : angle 1.59616 ( 20) hydrogen bonds : bond 0.04744 ( 540) hydrogen bonds : angle 5.44243 ( 1995) link_BETA1-4 : bond 0.00487 ( 10) link_BETA1-4 : angle 4.18504 ( 30) link_NAG-ASN : bond 0.00392 ( 5) link_NAG-ASN : angle 0.73029 ( 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 365 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 324 time to evaluate : 0.418 Fit side-chains REVERT: A 102 ASP cc_start: 0.8084 (t70) cc_final: 0.7700 (t70) REVERT: A 126 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7245 (mt-10) REVERT: A 173 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7467 (tt0) REVERT: A 206 LYS cc_start: 0.7973 (mtpt) cc_final: 0.7366 (mttp) REVERT: A 210 ASP cc_start: 0.7612 (m-30) cc_final: 0.7312 (m-30) REVERT: A 235 GLN cc_start: 0.7815 (mm-40) cc_final: 0.7166 (mm-40) REVERT: B 24 MET cc_start: 0.8084 (ptt) cc_final: 0.7819 (ptt) REVERT: B 28 GLU cc_start: 0.7567 (tm-30) cc_final: 0.6876 (mm-30) REVERT: B 102 ASP cc_start: 0.8013 (t70) cc_final: 0.7617 (t70) REVERT: B 130 ASP cc_start: 0.7894 (m-30) cc_final: 0.7541 (t0) REVERT: B 206 LYS cc_start: 0.7808 (mtpt) cc_final: 0.6921 (mttp) REVERT: B 210 ASP cc_start: 0.7793 (m-30) cc_final: 0.7308 (m-30) REVERT: C 24 MET cc_start: 0.7750 (ptt) cc_final: 0.7487 (ptt) REVERT: C 28 GLU cc_start: 0.7581 (tm-30) cc_final: 0.7046 (mm-30) REVERT: C 36 LYS cc_start: 0.7917 (tppt) cc_final: 0.7504 (tptm) REVERT: C 102 ASP cc_start: 0.8046 (t70) cc_final: 0.7655 (t70) REVERT: C 126 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7426 (mt-10) REVERT: C 206 LYS cc_start: 0.7845 (mtpt) cc_final: 0.6919 (mttp) REVERT: C 210 ASP cc_start: 0.7806 (m-30) cc_final: 0.7474 (m-30) REVERT: C 235 GLN cc_start: 0.7954 (mm-40) cc_final: 0.7242 (mt0) REVERT: C 303 MET cc_start: 0.8548 (mmt) cc_final: 0.8330 (mmt) REVERT: C 316 GLU cc_start: 0.6097 (tm-30) cc_final: 0.5897 (tm-30) REVERT: D 72 MET cc_start: 0.8201 (mtm) cc_final: 0.7913 (mtt) REVERT: D 102 ASP cc_start: 0.7948 (t70) cc_final: 0.7497 (t70) REVERT: D 164 ASP cc_start: 0.8891 (p0) cc_final: 0.8558 (p0) REVERT: D 173 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7304 (tt0) REVERT: D 206 LYS cc_start: 0.7825 (mtpt) cc_final: 0.7203 (mttp) REVERT: D 210 ASP cc_start: 0.7816 (m-30) cc_final: 0.7554 (m-30) REVERT: D 235 GLN cc_start: 0.7930 (mm-40) cc_final: 0.7505 (mt0) REVERT: E 24 MET cc_start: 0.7500 (ptt) cc_final: 0.6992 (ptt) REVERT: E 28 GLU cc_start: 0.7631 (tm-30) cc_final: 0.6956 (mm-30) REVERT: E 31 ASP cc_start: 0.7982 (m-30) cc_final: 0.7774 (m-30) REVERT: E 94 TYR cc_start: 0.7714 (t80) cc_final: 0.7279 (t80) REVERT: E 164 ASP cc_start: 0.9057 (p0) cc_final: 0.8715 (p0) REVERT: E 206 LYS cc_start: 0.7850 (mtpt) cc_final: 0.7202 (mttp) REVERT: E 235 GLN cc_start: 0.7858 (mm110) cc_final: 0.7277 (mt0) REVERT: E 243 MET cc_start: 0.6149 (mtm) cc_final: 0.5948 (mtp) REVERT: E 303 MET cc_start: 0.8681 (mmt) cc_final: 0.8160 (mmt) outliers start: 41 outliers final: 9 residues processed: 338 average time/residue: 0.4986 time to fit residues: 186.9586 Evaluate side-chains 293 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 284 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 107 ASP 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: 0.6980 chunk 62 optimal weight: 0.8980 chunk 136 optimal weight: 0.0670 chunk 61 optimal weight: 0.4980 chunk 115 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 82 GLN A 321 ASN B 58 ASN B 82 GLN B 418 ASN C 321 ASN D 321 ASN E 321 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.153754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.114175 restraints weight = 16720.763| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.86 r_work: 0.3129 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14530 Z= 0.117 Angle : 0.641 6.775 19750 Z= 0.313 Chirality : 0.046 0.175 2260 Planarity : 0.004 0.034 2430 Dihedral : 8.190 48.363 2195 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.48 % Allowed : 16.85 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.58 (0.18), residues: 1710 helix: -2.21 (0.18), residues: 630 sheet: -0.39 (0.27), residues: 340 loop : -1.75 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 268 TYR 0.012 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 covalent geometry : bond 0.00261 (14505) covalent geometry : angle 0.61855 (19685) SS BOND : bond 0.00429 ( 10) SS BOND : angle 1.44000 ( 20) hydrogen bonds : bond 0.03726 ( 540) hydrogen bonds : angle 4.65861 ( 1995) link_BETA1-4 : bond 0.00391 ( 10) link_BETA1-4 : angle 4.25510 ( 30) link_NAG-ASN : bond 0.00191 ( 5) link_NAG-ASN : angle 0.59143 ( 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 376 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 323 time to evaluate : 0.344 Fit side-chains REVERT: A 102 ASP cc_start: 0.8284 (t70) cc_final: 0.7946 (t70) REVERT: A 126 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7589 (mt-10) REVERT: A 206 LYS cc_start: 0.8309 (mtpt) cc_final: 0.7761 (mttp) REVERT: A 210 ASP cc_start: 0.7959 (m-30) cc_final: 0.7661 (m-30) REVERT: A 235 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7419 (mm-40) REVERT: B 24 MET cc_start: 0.7937 (ptt) cc_final: 0.7702 (ptt) REVERT: B 28 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7035 (mm-30) REVERT: B 41 ASP cc_start: 0.8953 (t0) cc_final: 0.8713 (t0) REVERT: B 62 ASN cc_start: 0.8698 (m-40) cc_final: 0.8294 (m110) REVERT: B 102 ASP cc_start: 0.8219 (t70) cc_final: 0.7890 (t70) REVERT: B 164 ASP cc_start: 0.9037 (p0) cc_final: 0.8746 (p0) REVERT: B 206 LYS cc_start: 0.8114 (mtpt) cc_final: 0.7395 (mttp) REVERT: B 210 ASP cc_start: 0.8104 (m-30) cc_final: 0.7662 (m-30) REVERT: B 235 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7587 (mm-40) REVERT: B 420 PHE cc_start: 0.8212 (m-10) cc_final: 0.7248 (t80) REVERT: C 28 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7230 (mm-30) REVERT: C 36 LYS cc_start: 0.7914 (tppt) cc_final: 0.7541 (tptm) REVERT: C 102 ASP cc_start: 0.8287 (t70) cc_final: 0.7944 (t70) REVERT: C 126 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7693 (mt-10) REVERT: C 206 LYS cc_start: 0.8193 (mtpt) cc_final: 0.7353 (mttp) REVERT: C 210 ASP cc_start: 0.8030 (m-30) cc_final: 0.7737 (m-30) REVERT: C 235 GLN cc_start: 0.8176 (mm110) cc_final: 0.7485 (mt0) REVERT: C 303 MET cc_start: 0.8975 (mmt) cc_final: 0.8570 (mmt) REVERT: C 398 ARG cc_start: 0.6796 (ttm170) cc_final: 0.6246 (mmm-85) REVERT: C 420 PHE cc_start: 0.8232 (m-10) cc_final: 0.7295 (t80) REVERT: D 62 ASN cc_start: 0.8680 (m-40) cc_final: 0.8430 (m110) REVERT: D 69 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7099 (mt-10) REVERT: D 72 MET cc_start: 0.8581 (mtm) cc_final: 0.8344 (mtt) REVERT: D 102 ASP cc_start: 0.8235 (t70) cc_final: 0.7808 (t70) REVERT: D 173 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7732 (tt0) REVERT: D 206 LYS cc_start: 0.8177 (mtpt) cc_final: 0.7614 (mttp) REVERT: D 210 ASP cc_start: 0.8021 (m-30) cc_final: 0.7768 (m-30) REVERT: D 235 GLN cc_start: 0.8059 (mm-40) cc_final: 0.7681 (mt0) REVERT: E 24 MET cc_start: 0.7631 (ptt) cc_final: 0.7316 (ptt) REVERT: E 28 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7214 (mm-30) REVERT: E 62 ASN cc_start: 0.8683 (m-40) cc_final: 0.8452 (m110) REVERT: E 94 TYR cc_start: 0.8061 (t80) cc_final: 0.7717 (t80) REVERT: E 102 ASP cc_start: 0.8201 (t70) cc_final: 0.7816 (t70) REVERT: E 130 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7726 (t0) REVERT: E 206 LYS cc_start: 0.8185 (mtpt) cc_final: 0.7566 (mttp) REVERT: E 235 GLN cc_start: 0.8040 (mm110) cc_final: 0.7465 (mt0) outliers start: 53 outliers final: 15 residues processed: 348 average time/residue: 0.4800 time to fit residues: 185.9018 Evaluate side-chains 311 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 294 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 256 VAL 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 199 THR Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 69 GLU 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 129 THR Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 262 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 74 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 155 optimal weight: 0.3980 chunk 65 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 82 GLN A 321 ASN A 418 ASN C 62 ASN C 321 ASN E 171 GLN E 321 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.146129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.107663 restraints weight = 16606.896| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.74 r_work: 0.2983 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 14530 Z= 0.205 Angle : 0.697 7.928 19750 Z= 0.342 Chirality : 0.048 0.191 2260 Planarity : 0.004 0.033 2430 Dihedral : 6.062 34.488 2195 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 5.64 % Allowed : 16.39 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.20), residues: 1710 helix: -1.31 (0.21), residues: 585 sheet: 0.10 (0.29), residues: 325 loop : -1.17 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 45 TYR 0.018 0.002 TYR D 144 PHE 0.024 0.002 PHE A 322 TRP 0.012 0.002 TRP B 302 HIS 0.003 0.001 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00499 (14505) covalent geometry : angle 0.67568 (19685) SS BOND : bond 0.00680 ( 10) SS BOND : angle 1.80179 ( 20) hydrogen bonds : bond 0.03741 ( 540) hydrogen bonds : angle 4.24469 ( 1995) link_BETA1-4 : bond 0.00345 ( 10) link_BETA1-4 : angle 4.26651 ( 30) link_NAG-ASN : bond 0.00148 ( 5) link_NAG-ASN : angle 0.64746 ( 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 380 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 294 time to evaluate : 0.542 Fit side-chains REVERT: A 32 LYS cc_start: 0.7882 (tttt) cc_final: 0.7413 (ttpt) REVERT: A 36 LYS cc_start: 0.8093 (tptt) cc_final: 0.7600 (tptm) REVERT: A 102 ASP cc_start: 0.8433 (t70) cc_final: 0.8130 (t70) REVERT: A 126 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7663 (mt-10) REVERT: A 206 LYS cc_start: 0.8403 (mtpt) cc_final: 0.7816 (mttp) REVERT: A 210 ASP cc_start: 0.7978 (m-30) cc_final: 0.7726 (m-30) REVERT: A 235 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7649 (mm-40) REVERT: A 279 MET cc_start: 0.7791 (tpt) cc_final: 0.7534 (tpp) REVERT: A 420 PHE cc_start: 0.8222 (m-10) cc_final: 0.7247 (t80) REVERT: B 28 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7133 (tm-30) REVERT: B 62 ASN cc_start: 0.8773 (m-40) cc_final: 0.8347 (m110) REVERT: B 102 ASP cc_start: 0.8388 (t70) cc_final: 0.8127 (t70) REVERT: B 206 LYS cc_start: 0.8249 (mtpt) cc_final: 0.7421 (mttp) REVERT: B 210 ASP cc_start: 0.8131 (m-30) cc_final: 0.7629 (m-30) REVERT: B 235 GLN cc_start: 0.8193 (mm-40) cc_final: 0.7691 (mm-40) REVERT: B 420 PHE cc_start: 0.8224 (m-10) cc_final: 0.7506 (t80) REVERT: C 28 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7642 (tm-30) REVERT: C 36 LYS cc_start: 0.8023 (tppt) cc_final: 0.7661 (tptm) REVERT: C 69 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.6743 (mt-10) REVERT: C 126 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7841 (mt-10) REVERT: C 206 LYS cc_start: 0.8365 (mtpt) cc_final: 0.7535 (mttp) REVERT: C 210 ASP cc_start: 0.8085 (m-30) cc_final: 0.7800 (m-30) REVERT: D 72 MET cc_start: 0.8700 (mtm) cc_final: 0.8430 (mtt) REVERT: D 102 ASP cc_start: 0.8403 (t70) cc_final: 0.8028 (t70) REVERT: D 164 ASP cc_start: 0.9169 (p0) cc_final: 0.8917 (p0) REVERT: D 206 LYS cc_start: 0.8361 (mtpt) cc_final: 0.7783 (mttp) REVERT: D 210 ASP cc_start: 0.8039 (m-30) cc_final: 0.7815 (m-30) REVERT: D 235 GLN cc_start: 0.8181 (mm-40) cc_final: 0.7802 (mt0) REVERT: E 102 ASP cc_start: 0.8354 (t70) cc_final: 0.7964 (t70) REVERT: E 130 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7858 (t0) REVERT: E 164 ASP cc_start: 0.9185 (p0) cc_final: 0.8969 (p0) REVERT: E 206 LYS cc_start: 0.8370 (mtpt) cc_final: 0.7672 (mttp) REVERT: E 208 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7582 (tt0) outliers start: 86 outliers final: 34 residues processed: 337 average time/residue: 0.4811 time to fit residues: 180.3767 Evaluate side-chains 305 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 269 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 171 GLN 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 A residue 280 THR Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 56 THR 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 262 MET Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 69 GLU 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 280 THR 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 280 THR Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain E residue 56 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 262 MET Chi-restraints excluded: chain E residue 280 THR 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: 0.9990 chunk 34 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 168 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 321 ASN C 82 GLN C 321 ASN D 62 ASN D 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.149478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.109428 restraints weight = 16595.834| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.86 r_work: 0.3006 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14530 Z= 0.136 Angle : 0.624 8.188 19750 Z= 0.308 Chirality : 0.045 0.177 2260 Planarity : 0.004 0.029 2430 Dihedral : 5.425 26.087 2195 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.87 % Allowed : 19.61 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.20), residues: 1710 helix: -1.00 (0.22), residues: 595 sheet: 0.21 (0.30), residues: 325 loop : -1.20 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 268 TYR 0.012 0.001 TYR B 317 PHE 0.027 0.002 PHE C 322 TRP 0.009 0.001 TRP A 84 HIS 0.001 0.000 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00323 (14505) covalent geometry : angle 0.60312 (19685) SS BOND : bond 0.00505 ( 10) SS BOND : angle 1.52635 ( 20) hydrogen bonds : bond 0.03277 ( 540) hydrogen bonds : angle 4.01098 ( 1995) link_BETA1-4 : bond 0.00345 ( 10) link_BETA1-4 : angle 3.96437 ( 30) link_NAG-ASN : bond 0.00141 ( 5) link_NAG-ASN : angle 0.57897 ( 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 363 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 304 time to evaluate : 0.546 Fit side-chains REVERT: A 32 LYS cc_start: 0.7880 (tttt) cc_final: 0.7438 (ttpt) REVERT: A 36 LYS cc_start: 0.8114 (tptt) cc_final: 0.7633 (tptm) REVERT: A 102 ASP cc_start: 0.8416 (t70) cc_final: 0.8073 (t70) REVERT: A 126 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7673 (mt-10) REVERT: A 171 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8556 (mt0) REVERT: A 206 LYS cc_start: 0.8365 (mtpt) cc_final: 0.7787 (mttp) REVERT: A 210 ASP cc_start: 0.7978 (m-30) cc_final: 0.7722 (m-30) REVERT: A 323 ILE cc_start: 0.7110 (OUTLIER) cc_final: 0.6906 (mp) REVERT: A 420 PHE cc_start: 0.8067 (m-10) cc_final: 0.7285 (t80) REVERT: B 24 MET cc_start: 0.7588 (ptt) cc_final: 0.7078 (ptp) REVERT: B 28 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7085 (tm-30) REVERT: B 62 ASN cc_start: 0.8713 (m-40) cc_final: 0.8343 (m110) REVERT: B 102 ASP cc_start: 0.8309 (t70) cc_final: 0.7980 (t70) REVERT: B 164 ASP cc_start: 0.9141 (p0) cc_final: 0.8933 (p0) REVERT: B 206 LYS cc_start: 0.8232 (mtpt) cc_final: 0.7423 (mttp) REVERT: B 210 ASP cc_start: 0.8097 (m-30) cc_final: 0.7580 (m-30) REVERT: B 235 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7690 (mm-40) REVERT: C 24 MET cc_start: 0.7933 (ptt) cc_final: 0.7688 (ptm) REVERT: C 28 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7441 (mm-30) REVERT: C 36 LYS cc_start: 0.8024 (tppt) cc_final: 0.7658 (tptm) REVERT: C 69 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.6655 (mm-30) REVERT: C 126 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7805 (mt-10) REVERT: C 130 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.8081 (t0) REVERT: C 206 LYS cc_start: 0.8335 (mtpt) cc_final: 0.7610 (mttp) REVERT: C 210 ASP cc_start: 0.8055 (m-30) cc_final: 0.7767 (m-30) REVERT: C 303 MET cc_start: 0.8960 (mmt) cc_final: 0.8710 (mmt) REVERT: D 72 MET cc_start: 0.8688 (mtm) cc_final: 0.8442 (mtt) REVERT: D 102 ASP cc_start: 0.8380 (t70) cc_final: 0.7982 (t70) REVERT: D 206 LYS cc_start: 0.8312 (mtpt) cc_final: 0.7715 (mttp) REVERT: D 235 GLN cc_start: 0.8145 (mm-40) cc_final: 0.7774 (mt0) REVERT: D 398 ARG cc_start: 0.6841 (ttm170) cc_final: 0.6430 (mmm-85) REVERT: E 24 MET cc_start: 0.7548 (ptt) cc_final: 0.7164 (ptp) REVERT: E 62 ASN cc_start: 0.8713 (m-40) cc_final: 0.8476 (m110) REVERT: E 102 ASP cc_start: 0.8345 (t70) cc_final: 0.7961 (t70) REVERT: E 130 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7975 (t0) REVERT: E 206 LYS cc_start: 0.8278 (mtpt) cc_final: 0.7550 (mttp) REVERT: E 208 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7490 (tt0) REVERT: E 235 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7469 (mt0) REVERT: E 303 MET cc_start: 0.9044 (mmt) cc_final: 0.8606 (mmt) outliers start: 59 outliers final: 22 residues processed: 330 average time/residue: 0.4880 time to fit residues: 178.7313 Evaluate side-chains 290 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 263 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 256 VAL 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 412 LEU Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 256 VAL 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: 0.8980 chunk 18 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 112 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 321 ASN C 321 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.150205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.110543 restraints weight = 16607.009| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.84 r_work: 0.3075 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14530 Z= 0.129 Angle : 0.603 8.289 19750 Z= 0.298 Chirality : 0.045 0.164 2260 Planarity : 0.004 0.034 2430 Dihedral : 5.066 22.453 2195 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.66 % Allowed : 19.87 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.20), residues: 1710 helix: -0.64 (0.22), residues: 590 sheet: 0.40 (0.31), residues: 320 loop : -1.07 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 268 TYR 0.012 0.001 TYR E 144 PHE 0.032 0.002 PHE C 322 TRP 0.009 0.001 TRP A 84 HIS 0.001 0.000 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00307 (14505) covalent geometry : angle 0.58385 (19685) SS BOND : bond 0.00506 ( 10) SS BOND : angle 1.53714 ( 20) hydrogen bonds : bond 0.03136 ( 540) hydrogen bonds : angle 3.87545 ( 1995) link_BETA1-4 : bond 0.00342 ( 10) link_BETA1-4 : angle 3.72867 ( 30) link_NAG-ASN : bond 0.00146 ( 5) link_NAG-ASN : angle 0.57111 ( 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 358 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 287 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: A 32 LYS cc_start: 0.7798 (tttt) cc_final: 0.7357 (ttpt) REVERT: A 102 ASP cc_start: 0.8371 (t70) cc_final: 0.8021 (t70) REVERT: A 126 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7652 (mt-10) REVERT: A 171 GLN cc_start: 0.8762 (pt0) cc_final: 0.8559 (mt0) REVERT: A 206 LYS cc_start: 0.8284 (mtpt) cc_final: 0.7697 (mttp) REVERT: A 210 ASP cc_start: 0.7915 (m-30) cc_final: 0.7653 (m-30) REVERT: A 279 MET cc_start: 0.7778 (tpt) cc_final: 0.7522 (tpt) REVERT: A 323 ILE cc_start: 0.7002 (OUTLIER) cc_final: 0.6800 (mp) REVERT: B 24 MET cc_start: 0.7477 (ptt) cc_final: 0.7015 (ptp) REVERT: B 28 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7099 (tm-30) REVERT: B 62 ASN cc_start: 0.8692 (m-40) cc_final: 0.8274 (m110) REVERT: B 102 ASP cc_start: 0.8202 (t70) cc_final: 0.7818 (t70) REVERT: B 206 LYS cc_start: 0.8162 (mtpt) cc_final: 0.7373 (mttp) REVERT: B 210 ASP cc_start: 0.8042 (m-30) cc_final: 0.7520 (m-30) REVERT: B 235 GLN cc_start: 0.8161 (mm-40) cc_final: 0.7630 (mm-40) REVERT: C 24 MET cc_start: 0.7795 (ptt) cc_final: 0.7561 (ptm) REVERT: C 28 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7355 (mm-30) REVERT: C 36 LYS cc_start: 0.8070 (tppt) cc_final: 0.7702 (tptm) REVERT: C 69 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.6614 (mm-30) REVERT: C 102 ASP cc_start: 0.8330 (t70) cc_final: 0.7798 (t70) REVERT: C 126 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7764 (mt-10) REVERT: C 130 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.8005 (t0) REVERT: C 206 LYS cc_start: 0.8270 (mtpt) cc_final: 0.7448 (mttp) REVERT: C 210 ASP cc_start: 0.8025 (m-30) cc_final: 0.7730 (m-30) REVERT: C 279 MET cc_start: 0.7913 (tpt) cc_final: 0.7611 (tpt) REVERT: C 303 MET cc_start: 0.8886 (mmt) cc_final: 0.8610 (mmt) REVERT: C 398 ARG cc_start: 0.6603 (ttm170) cc_final: 0.6253 (mmm-85) REVERT: C 415 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6701 (tm) REVERT: D 72 MET cc_start: 0.8633 (mtm) cc_final: 0.8376 (mtt) REVERT: D 102 ASP cc_start: 0.8300 (t70) cc_final: 0.7843 (t70) REVERT: D 206 LYS cc_start: 0.8202 (mtpt) cc_final: 0.7628 (mttp) REVERT: D 235 GLN cc_start: 0.8143 (mm-40) cc_final: 0.7763 (mt0) REVERT: D 398 ARG cc_start: 0.6775 (ttm170) cc_final: 0.6415 (mmm-85) REVERT: D 415 LEU cc_start: 0.7196 (OUTLIER) cc_final: 0.6780 (tm) REVERT: E 24 MET cc_start: 0.7443 (ptt) cc_final: 0.7027 (ptp) REVERT: E 28 GLU cc_start: 0.7540 (tm-30) cc_final: 0.6789 (mm-30) REVERT: E 62 ASN cc_start: 0.8703 (m-40) cc_final: 0.8499 (m110) REVERT: E 97 ASP cc_start: 0.7887 (m-30) cc_final: 0.7356 (t0) REVERT: E 102 ASP cc_start: 0.8331 (t70) cc_final: 0.7933 (t70) REVERT: E 164 ASP cc_start: 0.9194 (p0) cc_final: 0.8894 (p0) REVERT: E 171 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8543 (mt0) REVERT: E 206 LYS cc_start: 0.8204 (mtpt) cc_final: 0.7512 (mttp) REVERT: E 208 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7430 (tt0) REVERT: E 235 GLN cc_start: 0.8079 (mm-40) cc_final: 0.7438 (mt0) outliers start: 71 outliers final: 27 residues processed: 327 average time/residue: 0.4491 time to fit residues: 164.3841 Evaluate side-chains 310 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 277 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 323 ILE 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 69 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 301 ILE 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 199 THR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 290 LEU 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 128 THR Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 171 GLN 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 323 ILE 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: 0.9990 chunk 139 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 138 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 321 ASN C 321 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.129902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.093402 restraints weight = 16977.432| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.67 r_work: 0.2803 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3478 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= 0.131 Angle : 0.616 10.071 19750 Z= 0.303 Chirality : 0.045 0.162 2260 Planarity : 0.004 0.031 2430 Dihedral : 5.008 40.069 2195 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.93 % Allowed : 20.00 % 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: -0.63 (0.20), residues: 1710 helix: -0.13 (0.23), residues: 575 sheet: 0.37 (0.31), residues: 325 loop : -0.89 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 268 TYR 0.011 0.001 TYR C 144 PHE 0.032 0.002 PHE C 322 TRP 0.009 0.001 TRP A 84 HIS 0.001 0.000 HIS D 217 Details of bonding type rmsd covalent geometry : bond 0.00316 (14505) covalent geometry : angle 0.59653 (19685) SS BOND : bond 0.00510 ( 10) SS BOND : angle 2.18519 ( 20) hydrogen bonds : bond 0.03113 ( 540) hydrogen bonds : angle 3.83419 ( 1995) link_BETA1-4 : bond 0.00384 ( 10) link_BETA1-4 : angle 3.61056 ( 30) link_NAG-ASN : bond 0.00154 ( 5) link_NAG-ASN : angle 0.58029 ( 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 342 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 282 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 32 LYS cc_start: 0.7356 (tttt) cc_final: 0.6969 (ttpt) REVERT: A 102 ASP cc_start: 0.8150 (t70) cc_final: 0.7720 (t70) REVERT: A 126 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7423 (mt-10) REVERT: A 171 GLN cc_start: 0.8528 (pt0) cc_final: 0.8276 (mt0) REVERT: A 206 LYS cc_start: 0.7979 (mtpt) cc_final: 0.7175 (mmtm) REVERT: A 210 ASP cc_start: 0.7693 (m-30) cc_final: 0.7451 (m-30) REVERT: B 24 MET cc_start: 0.7135 (ptt) cc_final: 0.6672 (ptp) REVERT: B 28 GLU cc_start: 0.7447 (tm-30) cc_final: 0.6758 (tm-30) REVERT: B 62 ASN cc_start: 0.8478 (m-40) cc_final: 0.8038 (m110) REVERT: B 102 ASP cc_start: 0.7897 (t70) cc_final: 0.7477 (t70) REVERT: B 206 LYS cc_start: 0.7809 (mtpt) cc_final: 0.7241 (mttm) REVERT: B 210 ASP cc_start: 0.7890 (m-30) cc_final: 0.7317 (m-30) REVERT: B 235 GLN cc_start: 0.8006 (mm-40) cc_final: 0.7447 (mm-40) REVERT: C 24 MET cc_start: 0.7503 (ptt) cc_final: 0.7259 (ptm) REVERT: C 28 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7051 (mm-30) REVERT: C 36 LYS cc_start: 0.8091 (tppt) cc_final: 0.7729 (tptm) REVERT: C 102 ASP cc_start: 0.8094 (t70) cc_final: 0.7463 (t70) REVERT: C 126 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7636 (mt-10) REVERT: C 130 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7850 (t0) REVERT: C 206 LYS cc_start: 0.7940 (mtpt) cc_final: 0.7090 (mttp) REVERT: C 210 ASP cc_start: 0.7806 (m-30) cc_final: 0.7511 (m-30) REVERT: C 279 MET cc_start: 0.7432 (tpt) cc_final: 0.7199 (tpt) REVERT: C 303 MET cc_start: 0.8539 (mmt) cc_final: 0.8281 (mmt) REVERT: C 398 ARG cc_start: 0.6468 (ttm170) cc_final: 0.6118 (mmm-85) REVERT: C 415 LEU cc_start: 0.6680 (OUTLIER) cc_final: 0.6287 (tm) REVERT: D 72 MET cc_start: 0.8202 (mtm) cc_final: 0.7941 (mtt) REVERT: D 102 ASP cc_start: 0.8006 (t70) cc_final: 0.7507 (t70) REVERT: D 206 LYS cc_start: 0.7887 (mtpt) cc_final: 0.7222 (mttp) REVERT: D 235 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7618 (mt0) REVERT: D 398 ARG cc_start: 0.6678 (ttm170) cc_final: 0.6295 (mmm-85) REVERT: D 415 LEU cc_start: 0.6825 (OUTLIER) cc_final: 0.6419 (tm) REVERT: E 24 MET cc_start: 0.7068 (ptt) cc_final: 0.6645 (ptp) REVERT: E 28 GLU cc_start: 0.7196 (tm-30) cc_final: 0.6404 (mm-30) REVERT: E 62 ASN cc_start: 0.8524 (m-40) cc_final: 0.8279 (m110) REVERT: E 102 ASP cc_start: 0.8068 (t70) cc_final: 0.7602 (t70) REVERT: E 206 LYS cc_start: 0.7828 (mtpt) cc_final: 0.7108 (mttp) REVERT: E 208 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7185 (tt0) REVERT: E 235 GLN cc_start: 0.7974 (mm-40) cc_final: 0.7295 (mt0) REVERT: E 303 MET cc_start: 0.8619 (mmt) cc_final: 0.8326 (mmt) outliers start: 60 outliers final: 30 residues processed: 312 average time/residue: 0.4691 time to fit residues: 163.4424 Evaluate side-chains 314 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 281 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 199 THR 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 171 GLN Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 130 ASP 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 301 ILE 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 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 412 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 423 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 123 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 321 ASN C 321 ASN D 82 GLN D 321 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.127347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.090604 restraints weight = 17051.173| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.70 r_work: 0.2959 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14530 Z= 0.192 Angle : 0.665 10.428 19750 Z= 0.327 Chirality : 0.047 0.163 2260 Planarity : 0.004 0.033 2430 Dihedral : 5.202 46.516 2195 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.80 % Allowed : 20.13 % Favored : 76.07 % 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: -0.60 (0.20), residues: 1710 helix: -0.07 (0.23), residues: 580 sheet: 0.42 (0.31), residues: 325 loop : -0.91 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 268 TYR 0.013 0.002 TYR E 144 PHE 0.034 0.002 PHE E 322 TRP 0.009 0.001 TRP B 255 HIS 0.002 0.001 HIS C 217 Details of bonding type rmsd covalent geometry : bond 0.00472 (14505) covalent geometry : angle 0.64555 (19685) SS BOND : bond 0.00626 ( 10) SS BOND : angle 2.54989 ( 20) hydrogen bonds : bond 0.03337 ( 540) hydrogen bonds : angle 3.95034 ( 1995) link_BETA1-4 : bond 0.00368 ( 10) link_BETA1-4 : angle 3.62546 ( 30) link_NAG-ASN : bond 0.00092 ( 5) link_NAG-ASN : angle 0.67563 ( 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 340 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 282 time to evaluate : 0.579 Fit side-chains REVERT: A 32 LYS cc_start: 0.7783 (tttt) cc_final: 0.7328 (ttpt) REVERT: A 36 LYS cc_start: 0.8072 (tptt) cc_final: 0.7761 (tptm) REVERT: A 102 ASP cc_start: 0.8393 (t70) cc_final: 0.8048 (t70) REVERT: A 126 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7663 (mt-10) REVERT: A 171 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8563 (mt0) REVERT: A 206 LYS cc_start: 0.8309 (mtpt) cc_final: 0.7819 (mttp) REVERT: A 208 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7524 (tt0) REVERT: A 210 ASP cc_start: 0.7940 (m-30) cc_final: 0.7737 (m-30) REVERT: A 415 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6875 (tm) REVERT: B 24 MET cc_start: 0.7400 (ptt) cc_final: 0.6944 (ptp) REVERT: B 28 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7051 (tm-30) REVERT: B 62 ASN cc_start: 0.8709 (m-40) cc_final: 0.8336 (m110) REVERT: B 102 ASP cc_start: 0.8232 (t70) cc_final: 0.7887 (t70) REVERT: B 107 ASP cc_start: 0.8683 (m-30) cc_final: 0.8416 (m-30) REVERT: B 206 LYS cc_start: 0.8240 (mtpt) cc_final: 0.7352 (mttp) REVERT: B 208 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7476 (tm-30) REVERT: B 210 ASP cc_start: 0.8015 (m-30) cc_final: 0.7436 (m-30) REVERT: B 235 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7635 (mm-40) REVERT: B 415 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.6891 (tm) REVERT: C 28 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7263 (mm-30) REVERT: C 36 LYS cc_start: 0.8087 (tppt) cc_final: 0.7765 (tptm) REVERT: C 126 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7764 (mt-10) REVERT: C 130 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.8083 (t0) REVERT: C 206 LYS cc_start: 0.8350 (mtpt) cc_final: 0.7511 (mttp) REVERT: C 210 ASP cc_start: 0.7969 (m-30) cc_final: 0.7688 (m-30) REVERT: C 279 MET cc_start: 0.7958 (tpt) cc_final: 0.7642 (tpt) REVERT: C 398 ARG cc_start: 0.6616 (ttm170) cc_final: 0.6241 (mmm-85) REVERT: C 415 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6716 (tm) REVERT: D 102 ASP cc_start: 0.8364 (t70) cc_final: 0.7977 (t70) REVERT: D 206 LYS cc_start: 0.8294 (mtpt) cc_final: 0.7724 (mttp) REVERT: D 208 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7517 (tt0) REVERT: D 235 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7814 (mt0) REVERT: D 398 ARG cc_start: 0.6727 (ttm170) cc_final: 0.6366 (mmm-85) REVERT: D 415 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6796 (tm) REVERT: E 24 MET cc_start: 0.7413 (ptt) cc_final: 0.7021 (ptp) REVERT: E 97 ASP cc_start: 0.7901 (m-30) cc_final: 0.7388 (t0) REVERT: E 102 ASP cc_start: 0.8334 (t70) cc_final: 0.7935 (t70) REVERT: E 206 LYS cc_start: 0.8284 (mtpt) cc_final: 0.7533 (mttp) REVERT: E 208 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7449 (tt0) REVERT: E 235 GLN cc_start: 0.8144 (mm-40) cc_final: 0.7454 (mt0) outliers start: 58 outliers final: 31 residues processed: 309 average time/residue: 0.4599 time to fit residues: 158.8967 Evaluate side-chains 305 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 268 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 171 GLN 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 301 ILE Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 130 ASP 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 301 ILE 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 188 GLU Chi-restraints excluded: chain D residue 199 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 128 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 Chi-restraints excluded: chain E residue 262 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 138 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 9 optimal weight: 0.0070 chunk 143 optimal weight: 0.5980 chunk 100 optimal weight: 0.0470 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN B 180 ASN C 171 GLN C 321 ASN D 82 GLN D 171 GLN D 180 ASN E 141 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.131071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.094540 restraints weight = 17031.310| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.72 r_work: 0.2826 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3700 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= 0.111 Angle : 0.615 9.989 19750 Z= 0.303 Chirality : 0.044 0.168 2260 Planarity : 0.004 0.031 2430 Dihedral : 5.109 54.905 2195 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.30 % Allowed : 22.23 % Favored : 75.48 % 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: -0.35 (0.20), residues: 1710 helix: 0.20 (0.23), residues: 580 sheet: 0.65 (0.31), residues: 315 loop : -0.86 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 268 TYR 0.011 0.001 TYR B 317 PHE 0.032 0.002 PHE E 322 TRP 0.010 0.001 TRP A 84 HIS 0.002 0.000 HIS D 217 Details of bonding type rmsd covalent geometry : bond 0.00257 (14505) covalent geometry : angle 0.59015 (19685) SS BOND : bond 0.00394 ( 10) SS BOND : angle 3.52666 ( 20) hydrogen bonds : bond 0.02976 ( 540) hydrogen bonds : angle 3.78084 ( 1995) link_BETA1-4 : bond 0.00453 ( 10) link_BETA1-4 : angle 3.41834 ( 30) link_NAG-ASN : bond 0.00180 ( 5) link_NAG-ASN : angle 0.53725 ( 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: 35 poor density : 279 time to evaluate : 0.536 Fit side-chains REVERT: A 32 LYS cc_start: 0.7290 (tttt) cc_final: 0.6908 (ttpt) REVERT: A 36 LYS cc_start: 0.8042 (tptt) cc_final: 0.7690 (tptm) REVERT: A 102 ASP cc_start: 0.8162 (t70) cc_final: 0.7854 (t70) REVERT: A 126 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7484 (mt-10) REVERT: A 171 GLN cc_start: 0.8507 (pt0) cc_final: 0.8204 (mt0) REVERT: A 206 LYS cc_start: 0.7908 (mtpt) cc_final: 0.7105 (mmtm) REVERT: A 210 ASP cc_start: 0.7683 (m-30) cc_final: 0.7442 (m-30) REVERT: A 415 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6399 (tm) REVERT: B 24 MET cc_start: 0.7059 (ptt) cc_final: 0.6710 (ptp) REVERT: B 28 GLU cc_start: 0.7390 (tm-30) cc_final: 0.6756 (tm-30) REVERT: B 62 ASN cc_start: 0.8456 (m-40) cc_final: 0.8000 (m110) REVERT: B 102 ASP cc_start: 0.7962 (t70) cc_final: 0.7515 (t70) REVERT: B 107 ASP cc_start: 0.8616 (m-30) cc_final: 0.8396 (m-30) REVERT: B 171 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.8130 (mt0) REVERT: B 206 LYS cc_start: 0.7817 (mtpt) cc_final: 0.7241 (mttm) REVERT: B 210 ASP cc_start: 0.7865 (m-30) cc_final: 0.7284 (m-30) REVERT: B 235 GLN cc_start: 0.8033 (mm-40) cc_final: 0.7395 (mm-40) REVERT: B 398 ARG cc_start: 0.6509 (ttm170) cc_final: 0.6193 (mmm-85) REVERT: B 415 LEU cc_start: 0.6903 (OUTLIER) cc_final: 0.6527 (tm) REVERT: C 24 MET cc_start: 0.6977 (ptm) cc_final: 0.6532 (ptp) REVERT: C 28 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7141 (mm-30) REVERT: C 36 LYS cc_start: 0.8062 (tppt) cc_final: 0.7696 (tptm) REVERT: C 102 ASP cc_start: 0.8100 (t70) cc_final: 0.7626 (t70) REVERT: C 126 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7626 (mt-10) REVERT: C 130 ASP cc_start: 0.8164 (OUTLIER) cc_final: 0.7899 (t0) REVERT: C 171 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8151 (mt0) REVERT: C 206 LYS cc_start: 0.7930 (mtpt) cc_final: 0.7067 (mttm) REVERT: C 210 ASP cc_start: 0.7832 (m-30) cc_final: 0.7537 (m-30) REVERT: C 279 MET cc_start: 0.7417 (tpt) cc_final: 0.7195 (tpt) REVERT: C 303 MET cc_start: 0.8513 (mmt) cc_final: 0.8209 (mmt) REVERT: C 398 ARG cc_start: 0.6458 (ttm170) cc_final: 0.6130 (mmm-85) REVERT: C 415 LEU cc_start: 0.6645 (OUTLIER) cc_final: 0.6272 (tm) REVERT: D 102 ASP cc_start: 0.8072 (t70) cc_final: 0.7554 (t70) REVERT: D 126 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.6829 (pp20) REVERT: D 206 LYS cc_start: 0.7878 (mtpt) cc_final: 0.7238 (mttp) REVERT: D 208 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7275 (tm-30) REVERT: D 235 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7647 (mt0) REVERT: D 398 ARG cc_start: 0.6592 (ttm170) cc_final: 0.6208 (mmm-85) REVERT: D 415 LEU cc_start: 0.6776 (OUTLIER) cc_final: 0.6396 (tm) REVERT: E 24 MET cc_start: 0.6916 (ptt) cc_final: 0.6513 (ptp) REVERT: E 28 GLU cc_start: 0.7067 (tm-30) cc_final: 0.6344 (mm-30) REVERT: E 62 ASN cc_start: 0.8516 (m-40) cc_final: 0.8251 (m-40) REVERT: E 102 ASP cc_start: 0.8081 (t70) cc_final: 0.7518 (t70) REVERT: E 206 LYS cc_start: 0.7854 (mtpt) cc_final: 0.7073 (mttp) REVERT: E 208 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7201 (tt0) REVERT: E 235 GLN cc_start: 0.8034 (mm110) cc_final: 0.7372 (mt0) REVERT: E 303 MET cc_start: 0.8602 (mmt) cc_final: 0.8361 (mmt) outliers start: 35 outliers final: 13 residues processed: 299 average time/residue: 0.4854 time to fit residues: 161.3891 Evaluate side-chains 295 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 274 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 171 GLN 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 56 THR Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 126 GLU 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 128 THR Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 227 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 127 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 51 optimal weight: 0.3980 chunk 152 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 26 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 321 ASN C 171 GLN C 321 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.133033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.095878 restraints weight = 16967.031| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.76 r_work: 0.2995 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14530 Z= 0.142 Angle : 0.633 10.702 19750 Z= 0.312 Chirality : 0.045 0.162 2260 Planarity : 0.004 0.037 2430 Dihedral : 5.083 52.261 2195 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.16 % Allowed : 22.82 % 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: -0.32 (0.20), residues: 1710 helix: 0.30 (0.23), residues: 580 sheet: 0.53 (0.31), residues: 320 loop : -0.85 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 268 TYR 0.011 0.001 TYR B 317 PHE 0.034 0.002 PHE C 322 TRP 0.009 0.001 TRP A 84 HIS 0.002 0.000 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00346 (14505) covalent geometry : angle 0.60821 (19685) SS BOND : bond 0.00528 ( 10) SS BOND : angle 3.68229 ( 20) hydrogen bonds : bond 0.03064 ( 540) hydrogen bonds : angle 3.82851 ( 1995) link_BETA1-4 : bond 0.00402 ( 10) link_BETA1-4 : angle 3.45457 ( 30) link_NAG-ASN : bond 0.00129 ( 5) link_NAG-ASN : angle 0.58851 ( 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 314 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 281 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: A 32 LYS cc_start: 0.7734 (tttt) cc_final: 0.7308 (ttpt) REVERT: A 36 LYS cc_start: 0.8045 (tptt) cc_final: 0.7749 (tptm) REVERT: A 102 ASP cc_start: 0.8445 (t70) cc_final: 0.8102 (t70) REVERT: A 126 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7692 (mt-10) REVERT: A 206 LYS cc_start: 0.8283 (mtpt) cc_final: 0.7510 (mmtm) REVERT: A 208 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7487 (tt0) REVERT: A 210 ASP cc_start: 0.7935 (m-30) cc_final: 0.7734 (m-30) REVERT: A 415 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6817 (tm) REVERT: B 24 MET cc_start: 0.7323 (ptt) cc_final: 0.6959 (ptp) REVERT: B 28 GLU cc_start: 0.7666 (tm-30) cc_final: 0.6987 (tm-30) REVERT: B 62 ASN cc_start: 0.8657 (m-40) cc_final: 0.8322 (m110) REVERT: B 102 ASP cc_start: 0.8219 (t70) cc_final: 0.7847 (t70) REVERT: B 107 ASP cc_start: 0.8668 (m-30) cc_final: 0.8412 (m-30) REVERT: B 206 LYS cc_start: 0.8212 (mtpt) cc_final: 0.7436 (mttp) REVERT: B 210 ASP cc_start: 0.7999 (m-30) cc_final: 0.7456 (m-30) REVERT: B 235 GLN cc_start: 0.8227 (mm-40) cc_final: 0.7607 (mm-40) REVERT: B 415 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.6896 (tm) REVERT: C 24 MET cc_start: 0.7384 (ptm) cc_final: 0.7132 (ptp) REVERT: C 28 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7364 (mm-30) REVERT: C 36 LYS cc_start: 0.8063 (tppt) cc_final: 0.7732 (tptm) REVERT: C 102 ASP cc_start: 0.8337 (t70) cc_final: 0.7884 (t70) REVERT: C 126 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7816 (mt-10) REVERT: C 130 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.8102 (t0) REVERT: C 206 LYS cc_start: 0.8312 (mtpt) cc_final: 0.7449 (mttm) REVERT: C 208 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7321 (tm-30) REVERT: C 210 ASP cc_start: 0.7995 (m-30) cc_final: 0.7636 (m-30) REVERT: C 279 MET cc_start: 0.7930 (tpt) cc_final: 0.7671 (tpt) REVERT: C 303 MET cc_start: 0.8914 (mmt) cc_final: 0.8498 (mmt) REVERT: C 398 ARG cc_start: 0.6536 (ttm170) cc_final: 0.6190 (mmm-85) REVERT: C 415 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6697 (tm) REVERT: D 102 ASP cc_start: 0.8337 (t70) cc_final: 0.7898 (t70) REVERT: D 126 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7293 (pp20) REVERT: D 206 LYS cc_start: 0.8283 (mtpt) cc_final: 0.7670 (mttp) REVERT: D 208 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7525 (tt0) REVERT: D 235 GLN cc_start: 0.8237 (mm-40) cc_final: 0.7836 (mt0) REVERT: D 398 ARG cc_start: 0.6784 (ttm170) cc_final: 0.6367 (mmm-85) REVERT: D 415 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6800 (tm) REVERT: E 24 MET cc_start: 0.7307 (ptt) cc_final: 0.6939 (ptp) REVERT: E 28 GLU cc_start: 0.7407 (tm-30) cc_final: 0.6676 (mm-30) REVERT: E 62 ASN cc_start: 0.8700 (m-40) cc_final: 0.8486 (m110) REVERT: E 97 ASP cc_start: 0.7895 (m-30) cc_final: 0.7410 (t0) REVERT: E 102 ASP cc_start: 0.8305 (t70) cc_final: 0.7912 (t70) REVERT: E 206 LYS cc_start: 0.8266 (mtpt) cc_final: 0.7523 (mttp) REVERT: E 208 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7455 (tt0) REVERT: E 235 GLN cc_start: 0.8120 (mm110) cc_final: 0.7525 (mt0) REVERT: E 303 MET cc_start: 0.8956 (mmt) cc_final: 0.8585 (mmt) outliers start: 33 outliers final: 18 residues processed: 297 average time/residue: 0.4855 time to fit residues: 160.1949 Evaluate side-chains 287 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 263 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 A residue 415 LEU Chi-restraints excluded: chain B residue 56 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 56 THR Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 126 GLU 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 E residue 128 THR Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 227 GLU 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: 2.9990 chunk 105 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 321 ASN B 82 GLN C 82 GLN C 321 ASN D 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.127038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.090161 restraints weight = 17102.533| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.72 r_work: 0.2954 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14530 Z= 0.209 Angle : 0.685 10.905 19750 Z= 0.339 Chirality : 0.047 0.162 2260 Planarity : 0.004 0.038 2430 Dihedral : 5.280 50.972 2195 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.62 % Allowed : 22.30 % Favored : 75.08 % 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: -0.32 (0.20), residues: 1710 helix: 0.24 (0.23), residues: 580 sheet: 0.48 (0.31), residues: 325 loop : -0.76 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 268 TYR 0.013 0.002 TYR B 317 PHE 0.035 0.002 PHE C 322 TRP 0.009 0.002 TRP E 302 HIS 0.002 0.001 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00517 (14505) covalent geometry : angle 0.65968 (19685) SS BOND : bond 0.00649 ( 10) SS BOND : angle 3.85826 ( 20) hydrogen bonds : bond 0.03329 ( 540) hydrogen bonds : angle 4.02493 ( 1995) link_BETA1-4 : bond 0.00419 ( 10) link_BETA1-4 : angle 3.59438 ( 30) link_NAG-ASN : bond 0.00062 ( 5) link_NAG-ASN : angle 0.75798 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4607.58 seconds wall clock time: 79 minutes 5.27 seconds (4745.27 seconds total)