Starting phenix.real_space_refine on Wed Mar 4 14:22:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pm4_20386/03_2026/6pm4_20386.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pm4_20386/03_2026/6pm4_20386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6pm4_20386/03_2026/6pm4_20386.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pm4_20386/03_2026/6pm4_20386.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pm4_20386/03_2026/6pm4_20386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pm4_20386/03_2026/6pm4_20386.map" } resolution = 4.0 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= 0.000 sd= 0.001 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 90 5.16 5 C 9140 2.51 5 N 2265 2.21 5 O 2560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14055 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2767 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 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: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Restraints were copied for chains: B, C, D, E, G, H, I, J Time building chain proxies: 2.29, per 1000 atoms: 0.16 Number of scatterers: 14055 At special positions: 0 Unit cell: (105.344, 105.344, 133.326, 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 90 16.00 O 2560 8.00 N 2265 7.00 C 9140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 168 " distance=2.04 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.02 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 168 " distance=2.04 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 168 " distance=2.04 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 168 " distance=2.04 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 168 " distance=2.04 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.02 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.02 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.02 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG F 1 " - " ASN A 54 " " NAG G 1 " - " ASN B 54 " " NAG H 1 " - " ASN C 54 " " NAG I 1 " - " ASN D 54 " " NAG J 1 " - " ASN E 54 " Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 522.6 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: 50 helices and 25 sheets defined 42.7% alpha, 37.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 25 through 34 Processing helix chain 'A' and resid 36 through 40 removed outlier: 4.398A pdb=" N TYR A 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 90 Processing helix chain 'A' and resid 102 through 109 removed outlier: 4.273A pdb=" N ASP A 107 " --> pdb=" O SER A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 163 Processing helix chain 'A' and resid 236 through 243 Processing helix chain 'A' and resid 243 through 257 removed outlier: 3.732A pdb=" N ILE A 250 " --> pdb=" O PRO A 246 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 287 removed outlier: 3.512A pdb=" N GLY A 272 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 327 removed outlier: 4.339A pdb=" N ILE A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 428 removed outlier: 3.694A pdb=" N LEU A 394 " --> pdb=" O GLU A 390 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 395 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) Proline residue: A 411 - end of helix removed outlier: 3.571A pdb=" N PHE A 414 " --> pdb=" O PHE A 410 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE A 423 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N THR A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR A 425 " --> pdb=" O TYR A 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 34 Processing helix chain 'B' and resid 36 through 40 removed outlier: 4.398A pdb=" N TYR B 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 102 through 109 removed outlier: 4.273A pdb=" N ASP B 107 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 163 Processing helix chain 'B' and resid 236 through 243 Processing helix chain 'B' and resid 243 through 257 removed outlier: 3.732A pdb=" N ILE B 250 " --> pdb=" O PRO B 246 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE B 252 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 287 removed outlier: 3.512A pdb=" N GLY B 272 " --> pdb=" O ARG B 268 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 327 removed outlier: 4.338A pdb=" N ILE B 301 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL B 305 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER B 312 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA B 313 " --> pdb=" O PHE B 309 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 428 removed outlier: 3.694A pdb=" N LEU B 394 " --> pdb=" O GLU B 390 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE B 395 " --> pdb=" O MET B 391 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) Proline residue: B 411 - end of helix removed outlier: 3.571A pdb=" N PHE B 414 " --> pdb=" O PHE B 410 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 419 " --> pdb=" O LEU B 415 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE B 423 " --> pdb=" O ILE B 419 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N THR B 424 " --> pdb=" O PHE B 420 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR B 425 " --> pdb=" O TYR B 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 34 Processing helix chain 'C' and resid 36 through 40 removed outlier: 4.397A pdb=" N TYR C 40 " --> pdb=" O VAL C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 90 Processing helix chain 'C' and resid 102 through 109 removed outlier: 4.273A pdb=" N ASP C 107 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 163 Processing helix chain 'C' and resid 236 through 243 Processing helix chain 'C' and resid 243 through 257 removed outlier: 3.732A pdb=" N ILE C 250 " --> pdb=" O PRO C 246 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 287 removed outlier: 3.511A pdb=" N GLY C 272 " --> pdb=" O ARG C 268 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR C 278 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG C 287 " --> pdb=" O SER C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 327 removed outlier: 4.339A pdb=" N ILE C 301 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL C 305 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER C 312 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA C 313 " --> pdb=" O PHE C 309 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE C 323 " --> pdb=" O ALA C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 428 removed outlier: 3.694A pdb=" N LEU C 394 " --> pdb=" O GLU C 390 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE C 395 " --> pdb=" O MET C 391 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) Proline residue: C 411 - end of helix removed outlier: 3.571A pdb=" N PHE C 414 " --> pdb=" O PHE C 410 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE C 419 " --> pdb=" O LEU C 415 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE C 423 " --> pdb=" O ILE C 419 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N THR C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR C 425 " --> pdb=" O TYR C 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 34 Processing helix chain 'D' and resid 36 through 40 removed outlier: 4.397A pdb=" N TYR D 40 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 90 Processing helix chain 'D' and resid 102 through 109 removed outlier: 4.273A pdb=" N ASP D 107 " --> pdb=" O SER D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 163 Processing helix chain 'D' and resid 236 through 243 Processing helix chain 'D' and resid 243 through 257 removed outlier: 3.732A pdb=" N ILE D 250 " --> pdb=" O PRO D 246 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 287 removed outlier: 3.511A pdb=" N GLY D 272 " --> pdb=" O ARG D 268 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR D 278 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG D 287 " --> pdb=" O SER D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 327 removed outlier: 4.339A pdb=" N ILE D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL D 305 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER D 312 " --> pdb=" O LEU D 308 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA D 313 " --> pdb=" O PHE D 309 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 428 removed outlier: 3.693A pdb=" N LEU D 394 " --> pdb=" O GLU D 390 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE D 395 " --> pdb=" O MET D 391 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL D 405 " --> pdb=" O ARG D 401 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER D 406 " --> pdb=" O ILE D 402 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL D 408 " --> pdb=" O THR D 404 " (cutoff:3.500A) Proline residue: D 411 - end of helix removed outlier: 3.571A pdb=" N PHE D 414 " --> pdb=" O PHE D 410 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE D 419 " --> pdb=" O LEU D 415 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE D 423 " --> pdb=" O ILE D 419 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N THR D 424 " --> pdb=" O PHE D 420 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR D 425 " --> pdb=" O TYR D 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 34 Processing helix chain 'E' and resid 36 through 40 removed outlier: 4.397A pdb=" N TYR E 40 " --> pdb=" O VAL E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 90 Processing helix chain 'E' and resid 102 through 109 removed outlier: 4.273A pdb=" N ASP E 107 " --> pdb=" O SER E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 163 Processing helix chain 'E' and resid 236 through 243 Processing helix chain 'E' and resid 243 through 257 removed outlier: 3.732A pdb=" N ILE E 250 " --> pdb=" O PRO E 246 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE E 252 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER E 257 " --> pdb=" O LEU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 287 removed outlier: 3.512A pdb=" N GLY E 272 " --> pdb=" O ARG E 268 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR E 278 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG E 287 " --> pdb=" O SER E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 327 removed outlier: 4.339A pdb=" N ILE E 301 " --> pdb=" O LYS E 297 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL E 305 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER E 312 " --> pdb=" O LEU E 308 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA E 313 " --> pdb=" O PHE E 309 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 428 removed outlier: 3.694A pdb=" N LEU E 394 " --> pdb=" O GLU E 390 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE E 395 " --> pdb=" O MET E 391 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL E 405 " --> pdb=" O ARG E 401 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER E 406 " --> pdb=" O ILE E 402 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL E 408 " --> pdb=" O THR E 404 " (cutoff:3.500A) Proline residue: E 411 - end of helix removed outlier: 3.571A pdb=" N PHE E 414 " --> pdb=" O PHE E 410 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE E 419 " --> pdb=" O LEU E 415 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE E 423 " --> pdb=" O ILE E 419 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N THR E 424 " --> pdb=" O PHE E 420 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR E 425 " --> pdb=" O TYR E 421 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 99 through 100 removed outlier: 6.620A pdb=" N PHE A 79 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ILE A 61 " --> pdb=" O PHE A 79 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG A 81 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE A 59 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLN A 83 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N CYS A 57 " --> pdb=" O GLN A 83 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N ASN A 85 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL A 55 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL A 55 " --> pdb=" O GLU A 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 123 removed outlier: 3.598A pdb=" N THR A 149 " --> pdb=" O ASN A 123 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE A 79 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ILE A 61 " --> pdb=" O PHE A 79 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG A 81 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE A 59 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLN A 83 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N CYS A 57 " --> pdb=" O GLN A 83 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N ASN A 85 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL A 55 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLN A 193 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 5.942A 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 99 through 100 removed outlier: 6.621A pdb=" N PHE B 79 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ILE B 61 " --> pdb=" O PHE B 79 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG B 81 " --> pdb=" O ILE B 59 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE B 59 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLN B 83 " --> pdb=" O CYS B 57 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N CYS B 57 " --> pdb=" O GLN B 83 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N ASN B 85 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL B 55 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 122 through 123 removed outlier: 3.597A pdb=" N THR B 149 " --> pdb=" O ASN B 123 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N PHE B 79 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ILE B 61 " --> pdb=" O PHE B 79 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG B 81 " --> pdb=" O ILE B 59 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE B 59 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLN B 83 " --> pdb=" O CYS B 57 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N CYS B 57 " --> pdb=" O GLN B 83 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N ASN B 85 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL B 55 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLN B 193 " --> pdb=" O CYS B 57 " (cutoff:3.500A) removed outlier: 5.942A 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 99 through 100 removed outlier: 6.620A pdb=" N PHE C 79 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ILE C 61 " --> pdb=" O PHE C 79 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG C 81 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ILE C 59 " --> pdb=" O ARG C 81 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLN C 83 " --> pdb=" O CYS C 57 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N CYS C 57 " --> pdb=" O GLN C 83 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N ASN C 85 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N VAL C 55 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 122 through 123 removed outlier: 3.598A pdb=" N THR C 149 " --> pdb=" O ASN C 123 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE C 79 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ILE C 61 " --> pdb=" O PHE C 79 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG C 81 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ILE C 59 " --> pdb=" O ARG C 81 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLN C 83 " --> pdb=" O CYS C 57 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N CYS C 57 " --> pdb=" O GLN C 83 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N ASN C 85 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N VAL C 55 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N GLN C 193 " --> pdb=" O CYS C 57 " (cutoff:3.500A) removed outlier: 5.943A 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 99 through 100 removed outlier: 6.621A pdb=" N PHE D 79 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ILE D 61 " --> pdb=" O PHE D 79 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG D 81 " --> pdb=" O ILE D 59 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE D 59 " --> pdb=" O ARG D 81 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLN D 83 " --> pdb=" O CYS D 57 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N CYS D 57 " --> pdb=" O GLN D 83 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N ASN D 85 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL D 55 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 122 through 123 removed outlier: 3.598A pdb=" N THR D 149 " --> pdb=" O ASN D 123 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N PHE D 79 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ILE D 61 " --> pdb=" O PHE D 79 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG D 81 " --> pdb=" O ILE D 59 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE D 59 " --> pdb=" O ARG D 81 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLN D 83 " --> pdb=" O CYS D 57 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N CYS D 57 " --> pdb=" O GLN D 83 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N ASN D 85 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL D 55 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N GLN D 193 " --> pdb=" O CYS D 57 " (cutoff:3.500A) removed outlier: 5.942A 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 99 through 100 removed outlier: 6.620A pdb=" N PHE E 79 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ILE E 61 " --> pdb=" O PHE E 79 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG E 81 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ILE E 59 " --> pdb=" O ARG E 81 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLN E 83 " --> pdb=" O CYS E 57 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N CYS E 57 " --> pdb=" O GLN E 83 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N ASN E 85 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL E 55 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL E 55 " --> pdb=" O GLU E 185 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 122 through 123 removed outlier: 3.597A pdb=" N THR E 149 " --> pdb=" O ASN E 123 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE E 79 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ILE E 61 " --> pdb=" O PHE E 79 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG E 81 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ILE E 59 " --> pdb=" O ARG E 81 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLN E 83 " --> pdb=" O CYS E 57 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N CYS E 57 " --> pdb=" O GLN E 83 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N ASN E 85 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL E 55 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLN E 193 " --> pdb=" O CYS E 57 " (cutoff:3.500A) removed outlier: 5.943A 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 217 740 hydrogen bonds defined for protein. 2085 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: 2.13 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4340 1.35 - 1.47: 3697 1.47 - 1.59: 6208 1.59 - 1.71: 0 1.71 - 1.84: 150 Bond restraints: 14395 Sorted by residual: bond pdb=" C1 BMA J 3 " pdb=" C2 BMA J 3 " ideal model delta sigma weight residual 1.519 1.551 -0.032 2.00e-02 2.50e+03 2.57e+00 bond pdb=" CB ARG B 234 " pdb=" CG ARG B 234 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.57e+00 bond pdb=" C1 BMA H 3 " pdb=" C2 BMA H 3 " ideal model delta sigma weight residual 1.519 1.551 -0.032 2.00e-02 2.50e+03 2.56e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.551 -0.032 2.00e-02 2.50e+03 2.56e+00 bond pdb=" CB ARG D 234 " pdb=" CG ARG D 234 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.53e+00 ... (remaining 14390 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 18592 1.94 - 3.88: 795 3.88 - 5.82: 107 5.82 - 7.75: 51 7.75 - 9.69: 10 Bond angle restraints: 19555 Sorted by residual: angle pdb=" C VAL D 127 " pdb=" N THR D 128 " pdb=" CA THR D 128 " ideal model delta sigma weight residual 121.54 131.23 -9.69 1.91e+00 2.74e-01 2.58e+01 angle pdb=" C VAL C 127 " pdb=" N THR C 128 " pdb=" CA THR C 128 " ideal model delta sigma weight residual 121.54 131.22 -9.68 1.91e+00 2.74e-01 2.57e+01 angle pdb=" C VAL E 127 " pdb=" N THR E 128 " pdb=" CA THR E 128 " ideal model delta sigma weight residual 121.54 131.21 -9.67 1.91e+00 2.74e-01 2.56e+01 angle pdb=" C VAL B 127 " pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta sigma weight residual 121.54 131.21 -9.67 1.91e+00 2.74e-01 2.56e+01 angle pdb=" C VAL A 127 " pdb=" N THR A 128 " pdb=" CA THR A 128 " ideal model delta sigma weight residual 121.54 131.20 -9.66 1.91e+00 2.74e-01 2.56e+01 ... (remaining 19550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.21: 8495 22.21 - 44.43: 210 44.43 - 66.64: 20 66.64 - 88.85: 40 88.85 - 111.06: 20 Dihedral angle restraints: 8785 sinusoidal: 3670 harmonic: 5115 Sorted by residual: dihedral pdb=" CB CYS D 154 " pdb=" SG CYS D 154 " pdb=" SG CYS D 168 " pdb=" CB CYS D 168 " ideal model delta sinusoidal sigma weight residual 93.00 52.72 40.28 1 1.00e+01 1.00e-02 2.28e+01 dihedral pdb=" CB CYS C 154 " pdb=" SG CYS C 154 " pdb=" SG CYS C 168 " pdb=" CB CYS C 168 " ideal model delta sinusoidal sigma weight residual 93.00 52.74 40.26 1 1.00e+01 1.00e-02 2.27e+01 dihedral pdb=" CB CYS A 154 " pdb=" SG CYS A 154 " pdb=" SG CYS A 168 " pdb=" CB CYS A 168 " ideal model delta sinusoidal sigma weight residual 93.00 52.75 40.25 1 1.00e+01 1.00e-02 2.27e+01 ... (remaining 8782 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1722 0.057 - 0.114: 447 0.114 - 0.170: 76 0.170 - 0.227: 5 0.227 - 0.284: 10 Chirality restraints: 2260 Sorted by residual: 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 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 0.28 2.00e-01 2.50e+01 2.02e+00 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 0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 2257 not shown) Planarity restraints: 2435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 127 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.60e+00 pdb=" C VAL E 127 " 0.037 2.00e-02 2.50e+03 pdb=" O VAL E 127 " -0.014 2.00e-02 2.50e+03 pdb=" N THR E 128 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 127 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.57e+00 pdb=" C VAL D 127 " -0.037 2.00e-02 2.50e+03 pdb=" O VAL D 127 " 0.014 2.00e-02 2.50e+03 pdb=" N THR D 128 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 127 " -0.010 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" C VAL A 127 " 0.037 2.00e-02 2.50e+03 pdb=" O VAL A 127 " -0.014 2.00e-02 2.50e+03 pdb=" N THR A 128 " -0.012 2.00e-02 2.50e+03 ... (remaining 2432 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3038 2.77 - 3.30: 13550 3.30 - 3.83: 24608 3.83 - 4.37: 29001 4.37 - 4.90: 47194 Nonbonded interactions: 117391 Sorted by model distance: nonbonded pdb=" OG1 THR E 178 " pdb=" OD1 ASN E 180 " model vdw 2.236 3.040 nonbonded pdb=" OG1 THR D 178 " pdb=" OD1 ASN D 180 " model vdw 2.237 3.040 nonbonded pdb=" OG1 THR A 178 " pdb=" OD1 ASN A 180 " model vdw 2.237 3.040 nonbonded pdb=" OG1 THR B 178 " pdb=" OD1 ASN B 180 " model vdw 2.237 3.040 nonbonded pdb=" OG1 THR C 178 " pdb=" OD1 ASN C 180 " model vdw 2.237 3.040 ... (remaining 117386 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 group one per residue 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: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 11.900 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 14420 Z= 0.324 Angle : 0.965 9.693 19620 Z= 0.504 Chirality : 0.053 0.284 2260 Planarity : 0.006 0.051 2430 Dihedral : 13.638 111.065 5435 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % 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: -4.33 (0.16), residues: 1710 helix: -3.47 (0.13), residues: 560 sheet: -2.49 (0.24), residues: 345 loop : -2.47 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 407 TYR 0.013 0.003 TYR E 425 PHE 0.014 0.003 PHE C 115 TRP 0.034 0.004 TRP B 110 HIS 0.004 0.002 HIS B 125 Details of bonding type rmsd covalent geometry : bond 0.00676 (14395) covalent geometry : angle 0.95852 (19555) SS BOND : bond 0.00760 ( 10) SS BOND : angle 1.72604 ( 20) hydrogen bonds : bond 0.30113 ( 610) hydrogen bonds : angle 10.14641 ( 2085) link_BETA1-4 : bond 0.00368 ( 10) link_BETA1-4 : angle 1.92197 ( 30) link_NAG-ASN : bond 0.00718 ( 5) link_NAG-ASN : angle 3.02247 ( 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 291 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ARG cc_start: 0.9587 (ttm-80) cc_final: 0.9386 (ttp80) REVERT: A 130 ASP cc_start: 0.9305 (m-30) cc_final: 0.8893 (m-30) REVERT: A 134 LEU cc_start: 0.9647 (tp) cc_final: 0.9431 (tt) REVERT: A 202 GLN cc_start: 0.9453 (mt0) cc_final: 0.8978 (tm-30) REVERT: A 262 MET cc_start: 0.8785 (tpt) cc_final: 0.8519 (tpt) REVERT: A 282 GLN cc_start: 0.9587 (mm-40) cc_final: 0.9347 (mt0) REVERT: A 311 PHE cc_start: 0.9593 (m-80) cc_final: 0.9379 (m-10) REVERT: A 391 MET cc_start: 0.8291 (mmm) cc_final: 0.7973 (ttp) REVERT: A 417 PHE cc_start: 0.9658 (t80) cc_final: 0.9390 (t80) REVERT: B 80 LEU cc_start: 0.9674 (tp) cc_final: 0.9398 (tp) REVERT: B 82 GLN cc_start: 0.9581 (mt0) cc_final: 0.9219 (mp10) REVERT: B 130 ASP cc_start: 0.9271 (m-30) cc_final: 0.8861 (m-30) REVERT: B 134 LEU cc_start: 0.9628 (tp) cc_final: 0.9401 (tt) REVERT: B 163 MET cc_start: 0.9251 (mpp) cc_final: 0.8660 (mpp) REVERT: B 202 GLN cc_start: 0.9518 (mt0) cc_final: 0.9010 (tm-30) REVERT: B 244 TYR cc_start: 0.9531 (m-10) cc_final: 0.8757 (m-80) REVERT: B 262 MET cc_start: 0.8846 (tpt) cc_final: 0.8533 (tpt) REVERT: B 282 GLN cc_start: 0.9585 (mm-40) cc_final: 0.9234 (mt0) REVERT: B 311 PHE cc_start: 0.9624 (m-80) cc_final: 0.9393 (m-10) REVERT: B 391 MET cc_start: 0.8322 (mmm) cc_final: 0.8074 (ttp) REVERT: B 417 PHE cc_start: 0.9616 (t80) cc_final: 0.9364 (t80) REVERT: C 130 ASP cc_start: 0.9276 (m-30) cc_final: 0.8826 (m-30) REVERT: C 134 LEU cc_start: 0.9585 (tp) cc_final: 0.9382 (tt) REVERT: C 202 GLN cc_start: 0.9495 (mt0) cc_final: 0.9014 (tm-30) REVERT: C 244 TYR cc_start: 0.9485 (m-10) cc_final: 0.8753 (m-80) REVERT: C 262 MET cc_start: 0.8834 (tpt) cc_final: 0.8539 (tpt) REVERT: C 282 GLN cc_start: 0.9563 (mm-40) cc_final: 0.9288 (mt0) REVERT: C 391 MET cc_start: 0.8258 (mmm) cc_final: 0.7969 (ttp) REVERT: C 417 PHE cc_start: 0.9619 (t80) cc_final: 0.9372 (t80) REVERT: D 130 ASP cc_start: 0.9264 (m-30) cc_final: 0.8826 (m-30) REVERT: D 163 MET cc_start: 0.9281 (mpp) cc_final: 0.8785 (mpp) REVERT: D 202 GLN cc_start: 0.9513 (mt0) cc_final: 0.9060 (tm-30) REVERT: D 244 TYR cc_start: 0.9499 (m-10) cc_final: 0.8696 (m-80) REVERT: D 262 MET cc_start: 0.8764 (tpt) cc_final: 0.8487 (tpt) REVERT: D 391 MET cc_start: 0.8370 (mmm) cc_final: 0.8097 (ttp) REVERT: D 417 PHE cc_start: 0.9611 (t80) cc_final: 0.9409 (t80) REVERT: E 80 LEU cc_start: 0.9690 (tp) cc_final: 0.9476 (tp) REVERT: E 82 GLN cc_start: 0.9632 (mt0) cc_final: 0.9233 (mp10) REVERT: E 130 ASP cc_start: 0.9220 (m-30) cc_final: 0.8880 (m-30) REVERT: E 163 MET cc_start: 0.9256 (mpp) cc_final: 0.8705 (mpp) REVERT: E 202 GLN cc_start: 0.9521 (mt0) cc_final: 0.9071 (tm-30) REVERT: E 262 MET cc_start: 0.8885 (tpt) cc_final: 0.8606 (tpt) REVERT: E 282 GLN cc_start: 0.9632 (mm-40) cc_final: 0.9351 (mt0) REVERT: E 391 MET cc_start: 0.8240 (mmm) cc_final: 0.7999 (ttp) REVERT: E 417 PHE cc_start: 0.9669 (t80) cc_final: 0.9402 (t80) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.1256 time to fit residues: 53.4481 Evaluate side-chains 161 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 40.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 ASN ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 GLN A 83 GLN A 141 ASN A 202 GLN A 231 HIS ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN B 141 ASN B 202 GLN B 231 HIS ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 ASN ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN C 83 GLN C 131 ASN C 141 ASN C 231 HIS ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 ASN ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN D 83 GLN D 131 ASN D 141 ASN D 231 HIS ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN E 83 GLN E 131 ASN E 141 ASN E 202 GLN E 231 HIS ** E 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.041051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.030627 restraints weight = 109782.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.031781 restraints weight = 69531.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.032593 restraints weight = 50391.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.033174 restraints weight = 39799.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.033601 restraints weight = 33487.762| |-----------------------------------------------------------------------------| r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 14420 Z= 0.261 Angle : 0.850 6.452 19620 Z= 0.434 Chirality : 0.045 0.192 2260 Planarity : 0.005 0.039 2430 Dihedral : 12.185 74.835 2185 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.46 % Allowed : 7.71 % Favored : 90.83 % 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: -3.18 (0.18), residues: 1710 helix: -1.66 (0.18), residues: 595 sheet: -2.04 (0.26), residues: 305 loop : -2.42 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 268 TYR 0.020 0.002 TYR E 238 PHE 0.015 0.002 PHE C 230 TRP 0.017 0.002 TRP C 110 HIS 0.003 0.001 HIS A 125 Details of bonding type rmsd covalent geometry : bond 0.00535 (14395) covalent geometry : angle 0.83606 (19555) SS BOND : bond 0.01693 ( 10) SS BOND : angle 2.78579 ( 20) hydrogen bonds : bond 0.06155 ( 610) hydrogen bonds : angle 6.01745 ( 2085) link_BETA1-4 : bond 0.00563 ( 10) link_BETA1-4 : angle 2.93909 ( 30) link_NAG-ASN : bond 0.00803 ( 5) link_NAG-ASN : angle 2.31441 ( 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 182 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.9315 (m-30) cc_final: 0.8755 (p0) REVERT: A 134 LEU cc_start: 0.9621 (tp) cc_final: 0.9328 (tt) REVERT: A 202 GLN cc_start: 0.9500 (mt0) cc_final: 0.9036 (tm-30) REVERT: A 391 MET cc_start: 0.8232 (mmm) cc_final: 0.7966 (ttp) REVERT: A 417 PHE cc_start: 0.9687 (t80) cc_final: 0.9478 (t80) REVERT: B 82 GLN cc_start: 0.9621 (mt0) cc_final: 0.9066 (mt0) REVERT: B 130 ASP cc_start: 0.9304 (m-30) cc_final: 0.8777 (p0) REVERT: B 134 LEU cc_start: 0.9608 (tp) cc_final: 0.9295 (tt) REVERT: B 202 GLN cc_start: 0.9559 (mt0) cc_final: 0.9117 (tm-30) REVERT: B 262 MET cc_start: 0.8651 (tpt) cc_final: 0.8425 (tpt) REVERT: B 417 PHE cc_start: 0.9699 (t80) cc_final: 0.9422 (t80) REVERT: C 130 ASP cc_start: 0.9328 (m-30) cc_final: 0.8735 (p0) REVERT: C 134 LEU cc_start: 0.9609 (tp) cc_final: 0.9339 (tt) REVERT: C 170 MET cc_start: 0.9321 (ppp) cc_final: 0.9071 (ppp) REVERT: C 202 GLN cc_start: 0.9555 (mt0) cc_final: 0.9081 (tm-30) REVERT: C 262 MET cc_start: 0.8598 (tpt) cc_final: 0.8389 (tpt) REVERT: C 417 PHE cc_start: 0.9651 (t80) cc_final: 0.9417 (t80) REVERT: D 82 GLN cc_start: 0.9630 (mt0) cc_final: 0.9288 (mp10) REVERT: D 130 ASP cc_start: 0.9226 (m-30) cc_final: 0.8717 (p0) REVERT: E 82 GLN cc_start: 0.9655 (mt0) cc_final: 0.9263 (mp-120) REVERT: E 130 ASP cc_start: 0.9307 (m-30) cc_final: 0.8807 (p0) outliers start: 22 outliers final: 17 residues processed: 175 average time/residue: 0.1040 time to fit residues: 28.6096 Evaluate side-chains 160 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 168 CYS Chi-restraints excluded: chain E residue 251 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 17 optimal weight: 6.9990 chunk 53 optimal weight: 0.5980 chunk 98 optimal weight: 40.0000 chunk 113 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 ASN ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 GLN ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.041248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.030651 restraints weight = 107563.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.031783 restraints weight = 68773.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.032584 restraints weight = 50225.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.033165 restraints weight = 39958.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.033574 restraints weight = 33781.913| |-----------------------------------------------------------------------------| r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14420 Z= 0.183 Angle : 0.745 8.989 19620 Z= 0.369 Chirality : 0.044 0.182 2260 Planarity : 0.004 0.035 2430 Dihedral : 9.431 53.259 2185 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.53 % Allowed : 7.11 % Favored : 91.36 % 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: -2.54 (0.19), residues: 1710 helix: -0.63 (0.20), residues: 590 sheet: -2.47 (0.23), residues: 370 loop : -2.02 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 75 TYR 0.017 0.002 TYR E 238 PHE 0.009 0.001 PHE A 161 TRP 0.011 0.001 TRP B 84 HIS 0.004 0.002 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00388 (14395) covalent geometry : angle 0.73299 (19555) SS BOND : bond 0.00649 ( 10) SS BOND : angle 2.30166 ( 20) hydrogen bonds : bond 0.04670 ( 610) hydrogen bonds : angle 5.29433 ( 2085) link_BETA1-4 : bond 0.00236 ( 10) link_BETA1-4 : angle 2.72910 ( 30) link_NAG-ASN : bond 0.00627 ( 5) link_NAG-ASN : angle 1.94151 ( 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 178 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.9078 (ttp) cc_final: 0.8775 (tmm) REVERT: A 130 ASP cc_start: 0.9390 (m-30) cc_final: 0.8777 (p0) REVERT: A 202 GLN cc_start: 0.9457 (mt0) cc_final: 0.9037 (tm-30) REVERT: A 415 LEU cc_start: 0.9338 (tp) cc_final: 0.9124 (pp) REVERT: A 417 PHE cc_start: 0.9709 (t80) cc_final: 0.9464 (t80) REVERT: B 72 MET cc_start: 0.9051 (ttp) cc_final: 0.8741 (tmm) REVERT: B 130 ASP cc_start: 0.9370 (m-30) cc_final: 0.8766 (p0) REVERT: B 134 LEU cc_start: 0.9648 (tp) cc_final: 0.9357 (tt) REVERT: B 202 GLN cc_start: 0.9511 (mt0) cc_final: 0.9068 (tm-30) REVERT: B 262 MET cc_start: 0.8615 (tpt) cc_final: 0.8408 (tpt) REVERT: B 417 PHE cc_start: 0.9703 (t80) cc_final: 0.9391 (t80) REVERT: C 72 MET cc_start: 0.9012 (ttp) cc_final: 0.8718 (tmm) REVERT: C 130 ASP cc_start: 0.9394 (m-30) cc_final: 0.8752 (p0) REVERT: C 134 LEU cc_start: 0.9609 (tp) cc_final: 0.9391 (tt) REVERT: C 170 MET cc_start: 0.9399 (ppp) cc_final: 0.9118 (ppp) REVERT: C 202 GLN cc_start: 0.9521 (mt0) cc_final: 0.9032 (tm-30) REVERT: C 262 MET cc_start: 0.8506 (tpt) cc_final: 0.8292 (tpt) REVERT: C 417 PHE cc_start: 0.9697 (t80) cc_final: 0.9447 (t80) REVERT: D 72 MET cc_start: 0.9069 (ttp) cc_final: 0.8792 (tmm) REVERT: D 130 ASP cc_start: 0.9308 (m-30) cc_final: 0.8729 (p0) REVERT: D 152 LEU cc_start: 0.9832 (mt) cc_final: 0.9290 (tt) REVERT: D 163 MET cc_start: 0.9284 (mmm) cc_final: 0.9075 (mmm) REVERT: D 202 GLN cc_start: 0.9507 (mt0) cc_final: 0.9077 (tm-30) REVERT: E 72 MET cc_start: 0.9049 (ttp) cc_final: 0.8666 (tmm) REVERT: E 82 GLN cc_start: 0.9652 (mt0) cc_final: 0.9146 (mt0) REVERT: E 130 ASP cc_start: 0.9336 (m-30) cc_final: 0.9026 (m-30) REVERT: E 202 GLN cc_start: 0.9476 (mt0) cc_final: 0.9056 (tm-30) REVERT: E 415 LEU cc_start: 0.9310 (tt) cc_final: 0.9108 (pp) outliers start: 23 outliers final: 12 residues processed: 173 average time/residue: 0.0989 time to fit residues: 27.3963 Evaluate side-chains 157 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 168 CYS Chi-restraints excluded: chain E residue 251 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 40.0000 chunk 15 optimal weight: 20.0000 chunk 117 optimal weight: 20.0000 chunk 76 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 102 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 154 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 GLN ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN C 202 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.040416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.030059 restraints weight = 110286.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.031135 restraints weight = 70570.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.031900 restraints weight = 51680.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.032452 restraints weight = 41251.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.032840 restraints weight = 35038.325| |-----------------------------------------------------------------------------| r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 14420 Z= 0.221 Angle : 0.740 11.581 19620 Z= 0.367 Chirality : 0.042 0.176 2260 Planarity : 0.005 0.041 2430 Dihedral : 7.237 55.950 2185 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 2.19 % Allowed : 7.64 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.19), residues: 1710 helix: -0.06 (0.21), residues: 590 sheet: -2.48 (0.23), residues: 370 loop : -1.88 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 43 TYR 0.015 0.002 TYR E 238 PHE 0.012 0.001 PHE D 161 TRP 0.010 0.001 TRP A 84 HIS 0.005 0.002 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00459 (14395) covalent geometry : angle 0.72812 (19555) SS BOND : bond 0.00523 ( 10) SS BOND : angle 2.02704 ( 20) hydrogen bonds : bond 0.04025 ( 610) hydrogen bonds : angle 5.06211 ( 2085) link_BETA1-4 : bond 0.00276 ( 10) link_BETA1-4 : angle 2.67992 ( 30) link_NAG-ASN : bond 0.00847 ( 5) link_NAG-ASN : angle 2.17870 ( 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 178 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.9231 (ttp) cc_final: 0.8818 (tmm) REVERT: A 130 ASP cc_start: 0.9379 (m-30) cc_final: 0.8861 (p0) REVERT: A 202 GLN cc_start: 0.9453 (mt0) cc_final: 0.8993 (tm-30) REVERT: A 391 MET cc_start: 0.7374 (ttm) cc_final: 0.7043 (ttp) REVERT: A 415 LEU cc_start: 0.9354 (tp) cc_final: 0.9115 (pp) REVERT: B 72 MET cc_start: 0.9197 (ttp) cc_final: 0.8820 (tmm) REVERT: B 130 ASP cc_start: 0.9367 (m-30) cc_final: 0.8829 (p0) REVERT: B 134 LEU cc_start: 0.9646 (tp) cc_final: 0.9365 (tt) REVERT: B 202 GLN cc_start: 0.9491 (mt0) cc_final: 0.9047 (tm-30) REVERT: B 262 MET cc_start: 0.8561 (tpt) cc_final: 0.8329 (tpt) REVERT: C 72 MET cc_start: 0.9202 (ttp) cc_final: 0.8796 (tmm) REVERT: C 130 ASP cc_start: 0.9392 (m-30) cc_final: 0.8831 (p0) REVERT: C 202 GLN cc_start: 0.9508 (mt0) cc_final: 0.9003 (tm-30) REVERT: C 262 MET cc_start: 0.8598 (tpt) cc_final: 0.8367 (tpt) REVERT: C 417 PHE cc_start: 0.9726 (t80) cc_final: 0.9470 (t80) REVERT: D 72 MET cc_start: 0.9226 (ttp) cc_final: 0.8841 (tmm) REVERT: D 119 GLU cc_start: 0.8507 (tp30) cc_final: 0.8280 (tp30) REVERT: D 130 ASP cc_start: 0.9312 (m-30) cc_final: 0.8783 (p0) REVERT: D 152 LEU cc_start: 0.9836 (mt) cc_final: 0.9312 (tt) REVERT: D 163 MET cc_start: 0.9263 (mmm) cc_final: 0.9024 (mmm) REVERT: D 202 GLN cc_start: 0.9471 (mt0) cc_final: 0.9059 (tm-30) REVERT: E 130 ASP cc_start: 0.9364 (m-30) cc_final: 0.8879 (p0) REVERT: E 202 GLN cc_start: 0.9446 (mt0) cc_final: 0.9005 (tm-30) REVERT: E 391 MET cc_start: 0.7696 (ttm) cc_final: 0.7342 (ttp) outliers start: 33 outliers final: 21 residues processed: 174 average time/residue: 0.1037 time to fit residues: 28.6563 Evaluate side-chains 163 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 225 CYS Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 168 CYS Chi-restraints excluded: chain E residue 225 CYS Chi-restraints excluded: chain E residue 251 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 52 optimal weight: 0.0370 chunk 46 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 chunk 115 optimal weight: 0.0030 chunk 47 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 overall best weight: 2.3672 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.040993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.030388 restraints weight = 108931.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.031483 restraints weight = 70289.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.032250 restraints weight = 51600.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.032807 restraints weight = 41363.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.033207 restraints weight = 35188.995| |-----------------------------------------------------------------------------| r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14420 Z= 0.149 Angle : 0.708 12.259 19620 Z= 0.351 Chirality : 0.043 0.175 2260 Planarity : 0.004 0.032 2430 Dihedral : 6.182 33.216 2185 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.53 % Allowed : 9.17 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.19), residues: 1710 helix: -0.05 (0.21), residues: 610 sheet: -2.35 (0.23), residues: 370 loop : -1.70 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 75 TYR 0.020 0.002 TYR E 144 PHE 0.015 0.001 PHE A 311 TRP 0.010 0.001 TRP A 84 HIS 0.002 0.001 HIS A 125 Details of bonding type rmsd covalent geometry : bond 0.00321 (14395) covalent geometry : angle 0.70095 (19555) SS BOND : bond 0.00416 ( 10) SS BOND : angle 1.81568 ( 20) hydrogen bonds : bond 0.03667 ( 610) hydrogen bonds : angle 4.79520 ( 2085) link_BETA1-4 : bond 0.00232 ( 10) link_BETA1-4 : angle 2.03854 ( 30) link_NAG-ASN : bond 0.00406 ( 5) link_NAG-ASN : angle 1.63402 ( 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 170 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.9233 (ttp) cc_final: 0.8828 (tmm) REVERT: A 130 ASP cc_start: 0.9377 (m-30) cc_final: 0.8809 (p0) REVERT: A 152 LEU cc_start: 0.9864 (mt) cc_final: 0.9348 (tt) REVERT: A 202 GLN cc_start: 0.9433 (mt0) cc_final: 0.8997 (tm-30) REVERT: A 391 MET cc_start: 0.7383 (ttm) cc_final: 0.7134 (ttp) REVERT: A 415 LEU cc_start: 0.9328 (tp) cc_final: 0.9089 (pp) REVERT: B 72 MET cc_start: 0.9256 (ttp) cc_final: 0.8894 (tmm) REVERT: B 130 ASP cc_start: 0.9365 (m-30) cc_final: 0.8828 (p0) REVERT: B 134 LEU cc_start: 0.9683 (tp) cc_final: 0.9298 (tt) REVERT: B 202 GLN cc_start: 0.9468 (mt0) cc_final: 0.9033 (tm-30) REVERT: B 262 MET cc_start: 0.8549 (tpt) cc_final: 0.8286 (tpp) REVERT: C 72 MET cc_start: 0.9235 (ttp) cc_final: 0.8844 (tmm) REVERT: C 130 ASP cc_start: 0.9399 (m-30) cc_final: 0.8800 (p0) REVERT: C 152 LEU cc_start: 0.9858 (mt) cc_final: 0.9397 (tt) REVERT: C 202 GLN cc_start: 0.9454 (mt0) cc_final: 0.8995 (tm-30) REVERT: C 391 MET cc_start: 0.7137 (ttp) cc_final: 0.6828 (ttp) REVERT: C 417 PHE cc_start: 0.9720 (t80) cc_final: 0.9449 (t80) REVERT: D 72 MET cc_start: 0.9256 (ttp) cc_final: 0.8879 (tmm) REVERT: D 119 GLU cc_start: 0.8613 (tp30) cc_final: 0.8412 (tp30) REVERT: D 130 ASP cc_start: 0.9323 (m-30) cc_final: 0.8787 (p0) REVERT: D 152 LEU cc_start: 0.9839 (mt) cc_final: 0.9375 (tt) REVERT: D 163 MET cc_start: 0.9260 (mmm) cc_final: 0.9029 (mmm) REVERT: D 202 GLN cc_start: 0.9473 (mt0) cc_final: 0.9054 (tm-30) REVERT: E 130 ASP cc_start: 0.9370 (m-30) cc_final: 0.8898 (p0) REVERT: E 156 MET cc_start: 0.8890 (mmt) cc_final: 0.8438 (mmt) REVERT: E 202 GLN cc_start: 0.9429 (mt0) cc_final: 0.9010 (tm-30) REVERT: E 391 MET cc_start: 0.7741 (ttm) cc_final: 0.7372 (ttp) outliers start: 23 outliers final: 21 residues processed: 168 average time/residue: 0.1118 time to fit residues: 29.1380 Evaluate side-chains 162 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 225 CYS Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 168 CYS Chi-restraints excluded: chain E residue 225 CYS Chi-restraints excluded: chain E residue 251 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 84 optimal weight: 0.5980 chunk 21 optimal weight: 8.9990 chunk 152 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.039882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.029626 restraints weight = 112123.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.030664 restraints weight = 71466.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.031409 restraints weight = 52455.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.031942 restraints weight = 42049.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.032326 restraints weight = 35842.314| |-----------------------------------------------------------------------------| r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 14420 Z= 0.220 Angle : 0.744 12.350 19620 Z= 0.367 Chirality : 0.042 0.173 2260 Planarity : 0.004 0.032 2430 Dihedral : 5.987 24.385 2185 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.59 % Allowed : 10.03 % Favored : 88.37 % 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: -1.80 (0.19), residues: 1710 helix: 0.13 (0.20), residues: 610 sheet: -2.28 (0.23), residues: 365 loop : -1.64 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 43 TYR 0.015 0.002 TYR A 94 PHE 0.024 0.002 PHE A 311 TRP 0.009 0.001 TRP E 84 HIS 0.004 0.002 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00454 (14395) covalent geometry : angle 0.73622 (19555) SS BOND : bond 0.00484 ( 10) SS BOND : angle 1.90870 ( 20) hydrogen bonds : bond 0.03639 ( 610) hydrogen bonds : angle 4.80507 ( 2085) link_BETA1-4 : bond 0.00276 ( 10) link_BETA1-4 : angle 1.97228 ( 30) link_NAG-ASN : bond 0.00874 ( 5) link_NAG-ASN : angle 2.19600 ( 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 160 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.9289 (ttp) cc_final: 0.8834 (tmm) REVERT: A 105 MET cc_start: 0.9313 (ptp) cc_final: 0.8865 (pmm) REVERT: A 130 ASP cc_start: 0.9366 (m-30) cc_final: 0.8877 (p0) REVERT: A 202 GLN cc_start: 0.9446 (mt0) cc_final: 0.8993 (tm-30) REVERT: A 391 MET cc_start: 0.7501 (ttm) cc_final: 0.7217 (ttp) REVERT: B 72 MET cc_start: 0.9295 (ttp) cc_final: 0.8873 (tmm) REVERT: B 130 ASP cc_start: 0.9366 (m-30) cc_final: 0.8911 (p0) REVERT: B 149 THR cc_start: 0.8911 (OUTLIER) cc_final: 0.8692 (m) REVERT: B 202 GLN cc_start: 0.9469 (mt0) cc_final: 0.9013 (tm-30) REVERT: B 262 MET cc_start: 0.8576 (tpt) cc_final: 0.8327 (tpp) REVERT: C 72 MET cc_start: 0.9290 (ttp) cc_final: 0.8870 (tmm) REVERT: C 130 ASP cc_start: 0.9392 (m-30) cc_final: 0.8868 (p0) REVERT: C 202 GLN cc_start: 0.9470 (mt0) cc_final: 0.8984 (tm-30) REVERT: D 72 MET cc_start: 0.9309 (ttp) cc_final: 0.8870 (tmm) REVERT: D 119 GLU cc_start: 0.8612 (tp30) cc_final: 0.8388 (tp30) REVERT: D 130 ASP cc_start: 0.9356 (m-30) cc_final: 0.8898 (p0) REVERT: D 152 LEU cc_start: 0.9835 (mt) cc_final: 0.9366 (tt) REVERT: D 202 GLN cc_start: 0.9473 (mt0) cc_final: 0.9038 (tm-30) REVERT: E 105 MET cc_start: 0.9209 (ptp) cc_final: 0.8978 (ptp) REVERT: E 130 ASP cc_start: 0.9371 (m-30) cc_final: 0.8956 (p0) REVERT: E 202 GLN cc_start: 0.9443 (mt0) cc_final: 0.9009 (tm-30) REVERT: E 391 MET cc_start: 0.7748 (ttm) cc_final: 0.7438 (ttp) outliers start: 24 outliers final: 22 residues processed: 158 average time/residue: 0.0990 time to fit residues: 24.5695 Evaluate side-chains 157 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 225 CYS Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 168 CYS Chi-restraints excluded: chain E residue 225 CYS Chi-restraints excluded: chain E residue 251 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 99 optimal weight: 1.9990 chunk 19 optimal weight: 0.0770 chunk 128 optimal weight: 0.9990 chunk 145 optimal weight: 0.6980 chunk 38 optimal weight: 0.0980 chunk 73 optimal weight: 5.9990 chunk 143 optimal weight: 20.0000 chunk 87 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.041864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.031226 restraints weight = 106424.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.032318 restraints weight = 68534.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.033106 restraints weight = 50553.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.033671 restraints weight = 40538.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.034079 restraints weight = 34514.971| |-----------------------------------------------------------------------------| r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14420 Z= 0.121 Angle : 0.740 16.232 19620 Z= 0.357 Chirality : 0.044 0.187 2260 Planarity : 0.004 0.034 2430 Dihedral : 5.670 21.936 2185 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.66 % Allowed : 10.03 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.20), residues: 1710 helix: 0.01 (0.21), residues: 610 sheet: -1.99 (0.25), residues: 370 loop : -1.49 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 43 TYR 0.018 0.002 TYR B 144 PHE 0.019 0.001 PHE B 184 TRP 0.013 0.001 TRP D 84 HIS 0.002 0.001 HIS D 125 Details of bonding type rmsd covalent geometry : bond 0.00264 (14395) covalent geometry : angle 0.73596 (19555) SS BOND : bond 0.00347 ( 10) SS BOND : angle 1.57863 ( 20) hydrogen bonds : bond 0.03441 ( 610) hydrogen bonds : angle 4.47596 ( 2085) link_BETA1-4 : bond 0.00297 ( 10) link_BETA1-4 : angle 1.57160 ( 30) link_NAG-ASN : bond 0.00019 ( 5) link_NAG-ASN : angle 1.32383 ( 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 171 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.9309 (ttp) cc_final: 0.8889 (tmm) REVERT: A 105 MET cc_start: 0.9355 (ptp) cc_final: 0.8910 (pmm) REVERT: A 130 ASP cc_start: 0.9404 (m-30) cc_final: 0.8853 (p0) REVERT: A 202 GLN cc_start: 0.9477 (mt0) cc_final: 0.9035 (tm-30) REVERT: A 391 MET cc_start: 0.7508 (ttm) cc_final: 0.7212 (ttp) REVERT: B 72 MET cc_start: 0.9319 (ttp) cc_final: 0.8897 (tmm) REVERT: B 130 ASP cc_start: 0.9402 (m-30) cc_final: 0.8848 (p0) REVERT: B 149 THR cc_start: 0.8814 (OUTLIER) cc_final: 0.8590 (m) REVERT: B 202 GLN cc_start: 0.9507 (mt0) cc_final: 0.9067 (tm-30) REVERT: B 262 MET cc_start: 0.8412 (tpt) cc_final: 0.8171 (tpp) REVERT: C 72 MET cc_start: 0.9268 (ttp) cc_final: 0.8879 (tmm) REVERT: C 105 MET cc_start: 0.9350 (ptp) cc_final: 0.8384 (ptp) REVERT: C 130 ASP cc_start: 0.9433 (m-30) cc_final: 0.8799 (p0) REVERT: C 149 THR cc_start: 0.8846 (OUTLIER) cc_final: 0.8625 (m) REVERT: C 202 GLN cc_start: 0.9487 (mt0) cc_final: 0.9022 (tm-30) REVERT: C 391 MET cc_start: 0.7009 (ttp) cc_final: 0.6612 (tmm) REVERT: D 72 MET cc_start: 0.9323 (ttp) cc_final: 0.8968 (tmm) REVERT: D 82 GLN cc_start: 0.9514 (mt0) cc_final: 0.9269 (mp10) REVERT: D 119 GLU cc_start: 0.8660 (tp30) cc_final: 0.8444 (tp30) REVERT: D 130 ASP cc_start: 0.9380 (m-30) cc_final: 0.8793 (p0) REVERT: D 152 LEU cc_start: 0.9829 (mt) cc_final: 0.9451 (tt) REVERT: D 163 MET cc_start: 0.9250 (mmm) cc_final: 0.9043 (mmm) REVERT: D 202 GLN cc_start: 0.9523 (mt0) cc_final: 0.9080 (tm-30) REVERT: E 105 MET cc_start: 0.9241 (ptp) cc_final: 0.8716 (ptp) REVERT: E 130 ASP cc_start: 0.9400 (m-30) cc_final: 0.8862 (p0) REVERT: E 149 THR cc_start: 0.8989 (OUTLIER) cc_final: 0.8779 (m) REVERT: E 202 GLN cc_start: 0.9474 (mt0) cc_final: 0.9029 (tm-30) REVERT: E 391 MET cc_start: 0.7736 (ttm) cc_final: 0.7416 (ttp) outliers start: 25 outliers final: 19 residues processed: 167 average time/residue: 0.1094 time to fit residues: 28.4376 Evaluate side-chains 159 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 225 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 168 CYS Chi-restraints excluded: chain E residue 225 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 76 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 142 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 133 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.041215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.030488 restraints weight = 108316.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.031567 restraints weight = 70344.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.032339 restraints weight = 51913.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.032906 restraints weight = 41692.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.033312 restraints weight = 35526.330| |-----------------------------------------------------------------------------| r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14420 Z= 0.145 Angle : 0.745 14.705 19620 Z= 0.360 Chirality : 0.042 0.205 2260 Planarity : 0.004 0.036 2430 Dihedral : 5.528 21.361 2185 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.73 % Allowed : 11.30 % Favored : 86.98 % 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: -1.58 (0.20), residues: 1710 helix: 0.09 (0.20), residues: 610 sheet: -1.63 (0.27), residues: 320 loop : -1.65 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 43 TYR 0.016 0.002 TYR E 144 PHE 0.018 0.001 PHE E 184 TRP 0.010 0.001 TRP D 84 HIS 0.004 0.001 HIS A 125 Details of bonding type rmsd covalent geometry : bond 0.00315 (14395) covalent geometry : angle 0.73963 (19555) SS BOND : bond 0.00348 ( 10) SS BOND : angle 1.75682 ( 20) hydrogen bonds : bond 0.03340 ( 610) hydrogen bonds : angle 4.49015 ( 2085) link_BETA1-4 : bond 0.00241 ( 10) link_BETA1-4 : angle 1.68810 ( 30) link_NAG-ASN : bond 0.00504 ( 5) link_NAG-ASN : angle 1.75754 ( 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 165 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.9292 (ttp) cc_final: 0.8829 (tmm) REVERT: A 105 MET cc_start: 0.9335 (ptp) cc_final: 0.8940 (pmm) REVERT: A 130 ASP cc_start: 0.9381 (m-30) cc_final: 0.8917 (p0) REVERT: A 202 GLN cc_start: 0.9454 (mt0) cc_final: 0.9037 (tm-30) REVERT: A 391 MET cc_start: 0.7558 (ttm) cc_final: 0.7254 (ttp) REVERT: B 72 MET cc_start: 0.9318 (ttp) cc_final: 0.8908 (tmm) REVERT: B 105 MET cc_start: 0.9078 (ptp) cc_final: 0.8839 (ptp) REVERT: B 130 ASP cc_start: 0.9383 (m-30) cc_final: 0.8845 (p0) REVERT: B 149 THR cc_start: 0.8888 (OUTLIER) cc_final: 0.8673 (m) REVERT: B 202 GLN cc_start: 0.9463 (mt0) cc_final: 0.9052 (tm-30) REVERT: B 262 MET cc_start: 0.8344 (tpt) cc_final: 0.8096 (tpp) REVERT: C 72 MET cc_start: 0.9291 (ttp) cc_final: 0.8871 (tmm) REVERT: C 105 MET cc_start: 0.9272 (ptp) cc_final: 0.8954 (ptp) REVERT: C 130 ASP cc_start: 0.9403 (m-30) cc_final: 0.8782 (p0) REVERT: C 202 GLN cc_start: 0.9447 (mt0) cc_final: 0.9012 (tm-30) REVERT: C 391 MET cc_start: 0.7128 (ttp) cc_final: 0.6741 (tmm) REVERT: D 72 MET cc_start: 0.9324 (ttp) cc_final: 0.8928 (tmm) REVERT: D 82 GLN cc_start: 0.9504 (mt0) cc_final: 0.9258 (mp10) REVERT: D 105 MET cc_start: 0.9313 (ptp) cc_final: 0.8958 (mpp) REVERT: D 119 GLU cc_start: 0.8661 (tp30) cc_final: 0.8431 (tp30) REVERT: D 130 ASP cc_start: 0.9354 (m-30) cc_final: 0.8861 (p0) REVERT: D 152 LEU cc_start: 0.9816 (mt) cc_final: 0.9390 (tt) REVERT: D 163 MET cc_start: 0.9265 (mmm) cc_final: 0.9054 (mmm) REVERT: D 202 GLN cc_start: 0.9497 (mt0) cc_final: 0.9079 (tm-30) REVERT: E 130 ASP cc_start: 0.9377 (m-30) cc_final: 0.8904 (p0) REVERT: E 149 THR cc_start: 0.9048 (OUTLIER) cc_final: 0.8834 (m) REVERT: E 202 GLN cc_start: 0.9430 (mt0) cc_final: 0.9010 (tm-30) REVERT: E 391 MET cc_start: 0.7783 (ttm) cc_final: 0.7454 (ttp) outliers start: 26 outliers final: 22 residues processed: 160 average time/residue: 0.0986 time to fit residues: 25.2198 Evaluate side-chains 159 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 225 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 225 CYS Chi-restraints excluded: chain E residue 251 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 31 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 139 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 130 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 106 optimal weight: 0.0980 chunk 133 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.041798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.031059 restraints weight = 108406.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.032168 restraints weight = 69687.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.032944 restraints weight = 51245.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.033522 restraints weight = 41073.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.033938 restraints weight = 34921.487| |-----------------------------------------------------------------------------| r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14420 Z= 0.126 Angle : 0.742 10.185 19620 Z= 0.359 Chirality : 0.043 0.177 2260 Planarity : 0.004 0.035 2430 Dihedral : 5.435 21.489 2185 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 1.79 % Allowed : 11.30 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.47 (0.20), residues: 1710 helix: 0.16 (0.21), residues: 610 sheet: -1.53 (0.27), residues: 320 loop : -1.61 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 43 TYR 0.018 0.001 TYR E 144 PHE 0.046 0.001 PHE B 311 TRP 0.012 0.001 TRP D 84 HIS 0.004 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00277 (14395) covalent geometry : angle 0.73732 (19555) SS BOND : bond 0.00332 ( 10) SS BOND : angle 1.69218 ( 20) hydrogen bonds : bond 0.03303 ( 610) hydrogen bonds : angle 4.40756 ( 2085) link_BETA1-4 : bond 0.00231 ( 10) link_BETA1-4 : angle 1.54508 ( 30) link_NAG-ASN : bond 0.00244 ( 5) link_NAG-ASN : angle 1.51512 ( 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 167 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.9311 (ttp) cc_final: 0.8855 (tmm) REVERT: A 105 MET cc_start: 0.9353 (ptp) cc_final: 0.8953 (pmm) REVERT: A 130 ASP cc_start: 0.9396 (m-30) cc_final: 0.8861 (p0) REVERT: A 202 GLN cc_start: 0.9492 (mt0) cc_final: 0.9039 (tm-30) REVERT: A 391 MET cc_start: 0.7599 (ttm) cc_final: 0.7305 (ttp) REVERT: B 72 MET cc_start: 0.9340 (ttp) cc_final: 0.8909 (tmm) REVERT: B 105 MET cc_start: 0.9089 (ptp) cc_final: 0.8850 (ptp) REVERT: B 130 ASP cc_start: 0.9414 (m-30) cc_final: 0.8825 (p0) REVERT: B 149 THR cc_start: 0.8868 (OUTLIER) cc_final: 0.8653 (m) REVERT: B 202 GLN cc_start: 0.9516 (mt0) cc_final: 0.9082 (tm-30) REVERT: B 262 MET cc_start: 0.8383 (tpt) cc_final: 0.8161 (tpp) REVERT: C 72 MET cc_start: 0.9318 (ttp) cc_final: 0.8880 (tmm) REVERT: C 105 MET cc_start: 0.9326 (ptp) cc_final: 0.8984 (ptp) REVERT: C 130 ASP cc_start: 0.9431 (m-30) cc_final: 0.8802 (p0) REVERT: C 202 GLN cc_start: 0.9489 (mt0) cc_final: 0.9042 (tm-30) REVERT: C 391 MET cc_start: 0.7075 (ttp) cc_final: 0.6691 (tmm) REVERT: D 72 MET cc_start: 0.9338 (ttp) cc_final: 0.8968 (tmm) REVERT: D 105 MET cc_start: 0.9352 (ptp) cc_final: 0.8396 (mpp) REVERT: D 119 GLU cc_start: 0.8725 (tp30) cc_final: 0.8480 (tp30) REVERT: D 130 ASP cc_start: 0.9395 (m-30) cc_final: 0.8873 (p0) REVERT: D 152 LEU cc_start: 0.9811 (mt) cc_final: 0.9400 (tt) REVERT: D 163 MET cc_start: 0.9273 (mmm) cc_final: 0.9063 (mmm) REVERT: D 202 GLN cc_start: 0.9535 (mt0) cc_final: 0.9085 (tm-30) REVERT: E 130 ASP cc_start: 0.9392 (m-30) cc_final: 0.8911 (p0) REVERT: E 149 THR cc_start: 0.9017 (OUTLIER) cc_final: 0.8807 (m) REVERT: E 152 LEU cc_start: 0.9850 (mt) cc_final: 0.9384 (tt) REVERT: E 202 GLN cc_start: 0.9470 (mt0) cc_final: 0.9035 (tm-30) REVERT: E 262 MET cc_start: 0.8330 (tpt) cc_final: 0.8083 (tpt) REVERT: E 391 MET cc_start: 0.7786 (ttm) cc_final: 0.7465 (ttp) outliers start: 27 outliers final: 24 residues processed: 161 average time/residue: 0.1045 time to fit residues: 26.7591 Evaluate side-chains 161 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 225 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 168 CYS Chi-restraints excluded: chain E residue 225 CYS Chi-restraints excluded: chain E residue 251 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 135 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 154 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 42 optimal weight: 0.5980 chunk 146 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 15 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 overall best weight: 4.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.040552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.029979 restraints weight = 111896.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.031026 restraints weight = 72107.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.031767 restraints weight = 53350.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.032304 restraints weight = 42973.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.032695 restraints weight = 36715.173| |-----------------------------------------------------------------------------| r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.4984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14420 Z= 0.204 Angle : 0.784 12.728 19620 Z= 0.381 Chirality : 0.042 0.173 2260 Planarity : 0.004 0.085 2430 Dihedral : 5.493 21.761 2185 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 1.79 % Allowed : 11.89 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.20), residues: 1710 helix: 0.30 (0.21), residues: 610 sheet: -1.49 (0.27), residues: 315 loop : -1.60 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 43 TYR 0.016 0.002 TYR B 144 PHE 0.011 0.001 PHE A 311 TRP 0.010 0.001 TRP E 84 HIS 0.004 0.002 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00425 (14395) covalent geometry : angle 0.77782 (19555) SS BOND : bond 0.00424 ( 10) SS BOND : angle 1.87702 ( 20) hydrogen bonds : bond 0.03340 ( 610) hydrogen bonds : angle 4.50292 ( 2085) link_BETA1-4 : bond 0.00217 ( 10) link_BETA1-4 : angle 1.69364 ( 30) link_NAG-ASN : bond 0.00770 ( 5) link_NAG-ASN : angle 2.11074 ( 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 159 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.9352 (ttp) cc_final: 0.8875 (tmm) REVERT: A 105 MET cc_start: 0.9327 (ptp) cc_final: 0.8907 (pmm) REVERT: A 130 ASP cc_start: 0.9393 (m-30) cc_final: 0.8929 (p0) REVERT: A 202 GLN cc_start: 0.9507 (mt0) cc_final: 0.9029 (tm-30) REVERT: A 391 MET cc_start: 0.7657 (ttm) cc_final: 0.7379 (ttp) REVERT: B 72 MET cc_start: 0.9371 (ttp) cc_final: 0.8887 (tmm) REVERT: B 105 MET cc_start: 0.9095 (ptp) cc_final: 0.8828 (ptp) REVERT: B 130 ASP cc_start: 0.9423 (m-30) cc_final: 0.8871 (p0) REVERT: B 149 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8727 (m) REVERT: B 202 GLN cc_start: 0.9520 (mt0) cc_final: 0.9068 (tm-30) REVERT: B 262 MET cc_start: 0.8454 (tpt) cc_final: 0.8225 (tpp) REVERT: C 72 MET cc_start: 0.9363 (ttp) cc_final: 0.8884 (tmm) REVERT: C 105 MET cc_start: 0.9352 (ptp) cc_final: 0.8964 (ptp) REVERT: C 130 ASP cc_start: 0.9430 (m-30) cc_final: 0.8842 (p0) REVERT: C 202 GLN cc_start: 0.9512 (mt0) cc_final: 0.9011 (tm-30) REVERT: C 391 MET cc_start: 0.7231 (ttp) cc_final: 0.6852 (tmm) REVERT: C 415 LEU cc_start: 0.9380 (tp) cc_final: 0.9142 (pp) REVERT: D 72 MET cc_start: 0.9365 (ttp) cc_final: 0.8944 (tmm) REVERT: D 130 ASP cc_start: 0.9393 (m-30) cc_final: 0.8870 (p0) REVERT: D 163 MET cc_start: 0.9290 (mmm) cc_final: 0.9077 (mmm) REVERT: D 202 GLN cc_start: 0.9540 (mt0) cc_final: 0.9070 (tm-30) REVERT: E 130 ASP cc_start: 0.9403 (m-30) cc_final: 0.8970 (p0) REVERT: E 149 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8856 (m) REVERT: E 202 GLN cc_start: 0.9481 (mt0) cc_final: 0.9019 (tm-30) REVERT: E 262 MET cc_start: 0.8374 (tpt) cc_final: 0.8167 (tpt) outliers start: 27 outliers final: 24 residues processed: 152 average time/residue: 0.0937 time to fit residues: 22.9957 Evaluate side-chains 159 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 225 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 168 CYS Chi-restraints excluded: chain E residue 225 CYS Chi-restraints excluded: chain E residue 251 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 115 optimal weight: 0.5980 chunk 13 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 114 optimal weight: 0.9990 chunk 133 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.040836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.030086 restraints weight = 109829.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.031160 restraints weight = 70762.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.031922 restraints weight = 52279.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.032480 restraints weight = 42049.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.032877 restraints weight = 35872.837| |-----------------------------------------------------------------------------| r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.5058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14420 Z= 0.145 Angle : 0.785 14.401 19620 Z= 0.375 Chirality : 0.043 0.183 2260 Planarity : 0.004 0.067 2430 Dihedral : 5.497 22.807 2185 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.59 % Allowed : 12.29 % Favored : 86.11 % 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: -1.32 (0.20), residues: 1710 helix: 0.28 (0.21), residues: 610 sheet: -1.48 (0.28), residues: 320 loop : -1.49 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 43 TYR 0.017 0.002 TYR A 144 PHE 0.058 0.001 PHE A 311 TRP 0.011 0.001 TRP E 84 HIS 0.003 0.001 HIS D 125 Details of bonding type rmsd covalent geometry : bond 0.00315 (14395) covalent geometry : angle 0.78016 (19555) SS BOND : bond 0.00369 ( 10) SS BOND : angle 1.74128 ( 20) hydrogen bonds : bond 0.03243 ( 610) hydrogen bonds : angle 4.41077 ( 2085) link_BETA1-4 : bond 0.00230 ( 10) link_BETA1-4 : angle 1.51208 ( 30) link_NAG-ASN : bond 0.00378 ( 5) link_NAG-ASN : angle 1.78263 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1926.59 seconds wall clock time: 34 minutes 31.21 seconds (2071.21 seconds total)