Starting phenix.real_space_refine on Sat Sep 12 06:23:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pm4_20386/09_2026/6pm4_20386.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pm4_20386/09_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_20386/09_2026/6pm4_20386.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pm4_20386/09_2026/6pm4_20386.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6pm4_20386/09_2026/6pm4_20386.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pm4_20386/09_2026/6pm4_20386.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pm4_20386/09_2026/6pm4_20386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pm4_20386/09_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-2.2.1-6174/lib/python3.11/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 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: 2.66, per 1000 atoms: 0.19 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: 1.18 Conformation dependent library (CDL) restraints added in 583.6 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: 0.30 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: 2.37 Time building geometry restraints manager: 1.57 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 - 14.94: 7945 14.94 - 29.87: 410 29.87 - 44.81: 105 44.81 - 59.75: 5 59.75 - 74.68: 15 Dihedral angle restraints: 8480 sinusoidal: 3365 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 8477 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: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.090 Find NCS groups from input model: 0.130 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 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 : 10.221 74.684 5130 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/Z covalent geometry : bond 0.00676 / 0.32 (14395) covalent geometry : angle 0.95852 / 0.50 (19555) SS BOND : bond 0.00760 / 0.49 ( 10) SS BOND : angle 1.72604 / 1.27 ( 20) hydrogen bonds : bond 0.30113 / 20.39 ( 610) hydrogen bonds : angle 10.14641 / 7.02 ( 2085) link_BETA1-4 : bond 0.00368 / 0.20 ( 10) link_BETA1-4 : angle 1.92197 / 1.18 ( 30) link_NAG-ASN : bond 0.00718 / 0.41 ( 5) link_NAG-ASN : angle 3.02247 / 1.72 ( 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 : 0.565 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: 0.1143 time to fit residues: 49.4087 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 : 0.414 ------------------------------------------------------------------------------- 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... ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN B 202 GLN B 231 HIS ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.041020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.030621 restraints weight = 111054.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.031776 restraints weight = 70433.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.032596 restraints weight = 50972.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.033175 restraints weight = 40353.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.033584 restraints weight = 34009.583| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 14420 Z= 0.254 Angle : 0.828 6.577 19620 Z= 0.427 Chirality : 0.044 0.186 2260 Planarity : 0.005 0.038 2430 Dihedral : 6.868 47.542 1880 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.46 % Allowed : 7.77 % Favored : 90.76 % 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: -3.20 (0.18), residues: 1710 helix: -1.71 (0.18), residues: 595 sheet: -2.02 (0.26), residues: 305 loop : -2.43 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 268 TYR 0.021 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 E 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.25 (14395) covalent geometry : angle 0.81792 / 0.42 (19555) SS BOND : bond 0.00786 / 0.48 ( 10) SS BOND : angle 2.85599 / 1.64 ( 20) hydrogen bonds : bond 0.06225 / 4.05 ( 610) hydrogen bonds : angle 6.01770 / 4.18 ( 2085) link_BETA1-4 : bond 0.00367 / 0.22 ( 10) link_BETA1-4 : angle 2.07426 / 1.39 ( 30) link_NAG-ASN : bond 0.00687 / 0.40 ( 5) link_NAG-ASN : angle 2.20286 / 1.25 ( 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 180 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.9294 (m-30) cc_final: 0.8739 (p0) REVERT: A 202 GLN cc_start: 0.9501 (mt0) cc_final: 0.9040 (tm-30) REVERT: A 391 MET cc_start: 0.8232 (mmm) cc_final: 0.7963 (ttp) REVERT: A 417 PHE cc_start: 0.9676 (t80) cc_final: 0.9473 (t80) REVERT: B 82 GLN cc_start: 0.9605 (mt0) cc_final: 0.9058 (mt0) REVERT: B 130 ASP cc_start: 0.9294 (m-30) cc_final: 0.8769 (p0) REVERT: B 134 LEU cc_start: 0.9605 (tp) cc_final: 0.9293 (tt) REVERT: B 170 MET cc_start: 0.9220 (ppp) cc_final: 0.8980 (ppp) REVERT: B 202 GLN cc_start: 0.9549 (mt0) cc_final: 0.9115 (tm-30) REVERT: B 262 MET cc_start: 0.8636 (tpt) cc_final: 0.8411 (tpt) REVERT: B 417 PHE cc_start: 0.9695 (t80) cc_final: 0.9423 (t80) REVERT: C 130 ASP cc_start: 0.9319 (m-30) cc_final: 0.8729 (p0) REVERT: C 134 LEU cc_start: 0.9613 (tp) cc_final: 0.9345 (tt) REVERT: C 170 MET cc_start: 0.9276 (ppp) cc_final: 0.9033 (ppp) REVERT: C 202 GLN cc_start: 0.9557 (mt0) cc_final: 0.9081 (tm-30) REVERT: C 262 MET cc_start: 0.8612 (tpt) cc_final: 0.8405 (tpt) REVERT: C 417 PHE cc_start: 0.9647 (t80) cc_final: 0.9419 (t80) REVERT: D 82 GLN cc_start: 0.9625 (mt0) cc_final: 0.9304 (mp10) REVERT: D 130 ASP cc_start: 0.9228 (m-30) cc_final: 0.8715 (p0) REVERT: D 170 MET cc_start: 0.9142 (ppp) cc_final: 0.8926 (ppp) REVERT: D 391 MET cc_start: 0.8330 (mmm) cc_final: 0.8126 (ttp) REVERT: E 82 GLN cc_start: 0.9647 (mt0) cc_final: 0.9237 (mp10) REVERT: E 130 ASP cc_start: 0.9293 (m-30) cc_final: 0.8795 (p0) REVERT: E 202 GLN cc_start: 0.9506 (mt0) cc_final: 0.9109 (tm-30) outliers start: 22 outliers final: 17 residues processed: 173 average time/residue: 0.0960 time to fit residues: 26.5665 Evaluate side-chains 158 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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: 0.6980 chunk 53 optimal weight: 6.9990 chunk 98 optimal weight: 40.0000 chunk 113 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 146 optimal weight: 9.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** B 83 GLN ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.040927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.030443 restraints weight = 110899.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.031587 restraints weight = 69990.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.032397 restraints weight = 50736.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.032966 restraints weight = 40188.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.033388 restraints weight = 33919.699| |-----------------------------------------------------------------------------| r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14420 Z= 0.202 Angle : 0.737 8.166 19620 Z= 0.371 Chirality : 0.042 0.177 2260 Planarity : 0.004 0.034 2430 Dihedral : 6.209 33.101 1880 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.33 % Allowed : 7.51 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.19), residues: 1710 helix: -0.65 (0.20), residues: 590 sheet: -2.50 (0.23), residues: 370 loop : -2.02 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 75 TYR 0.017 0.002 TYR E 238 PHE 0.015 0.001 PHE E 223 TRP 0.011 0.001 TRP D 302 HIS 0.004 0.002 HIS E 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.20 (14395) covalent geometry : angle 0.72868 / 0.37 (19555) SS BOND : bond 0.00753 / 0.45 ( 10) SS BOND : angle 2.36764 / 1.37 ( 20) hydrogen bonds : bond 0.04738 / 3.09 ( 610) hydrogen bonds : angle 5.34847 / 3.70 ( 2085) link_BETA1-4 : bond 0.00204 / 0.11 ( 10) link_BETA1-4 : angle 1.81989 / 1.20 ( 30) link_NAG-ASN : bond 0.00679 / 0.39 ( 5) link_NAG-ASN : angle 1.97823 / 1.12 ( 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 173 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.9588 (mt0) cc_final: 0.9250 (mp10) REVERT: A 130 ASP cc_start: 0.9367 (m-30) cc_final: 0.8771 (p0) REVERT: A 202 GLN cc_start: 0.9470 (mt0) cc_final: 0.9039 (tm-30) REVERT: A 415 LEU cc_start: 0.9344 (tp) cc_final: 0.9112 (pp) REVERT: B 130 ASP cc_start: 0.9363 (m-30) cc_final: 0.8775 (p0) REVERT: B 134 LEU cc_start: 0.9650 (tp) cc_final: 0.9348 (tt) REVERT: B 170 MET cc_start: 0.9321 (ppp) cc_final: 0.8840 (ppp) REVERT: B 202 GLN cc_start: 0.9499 (mt0) cc_final: 0.9060 (tm-30) REVERT: B 262 MET cc_start: 0.8608 (tpt) cc_final: 0.8405 (tpt) REVERT: B 417 PHE cc_start: 0.9703 (t80) cc_final: 0.9402 (t80) REVERT: C 72 MET cc_start: 0.8990 (ttp) cc_final: 0.8773 (ttp) REVERT: C 130 ASP cc_start: 0.9381 (m-30) cc_final: 0.8738 (p0) REVERT: C 134 LEU cc_start: 0.9625 (tp) cc_final: 0.9407 (tt) REVERT: C 170 MET cc_start: 0.9387 (ppp) cc_final: 0.9055 (ppp) REVERT: C 202 GLN cc_start: 0.9523 (mt0) cc_final: 0.9033 (tm-30) REVERT: C 262 MET cc_start: 0.8603 (tpt) cc_final: 0.8373 (tpt) REVERT: C 417 PHE cc_start: 0.9692 (t80) cc_final: 0.9446 (t80) REVERT: D 130 ASP cc_start: 0.9292 (m-30) cc_final: 0.8735 (p0) REVERT: D 152 LEU cc_start: 0.9833 (mt) cc_final: 0.9267 (tt) REVERT: D 163 MET cc_start: 0.9328 (mmm) cc_final: 0.9126 (mmm) REVERT: D 202 GLN cc_start: 0.9542 (mt0) cc_final: 0.9081 (tm-30) REVERT: E 82 GLN cc_start: 0.9660 (mt0) cc_final: 0.9111 (mt0) REVERT: E 130 ASP cc_start: 0.9327 (m-30) cc_final: 0.9019 (m-30) REVERT: E 202 GLN cc_start: 0.9475 (mt0) cc_final: 0.9058 (tm-30) REVERT: E 391 MET cc_start: 0.6693 (ttp) cc_final: 0.6476 (tmm) REVERT: E 415 LEU cc_start: 0.9311 (tt) cc_final: 0.9106 (pp) outliers start: 20 outliers final: 12 residues processed: 169 average time/residue: 0.0985 time to fit residues: 26.4082 Evaluate side-chains 148 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 251 VAL Chi-restraints excluded: chain E residue 168 CYS Chi-restraints excluded: chain E residue 172 LEU 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: 10.0000 chunk 15 optimal weight: 10.0000 chunk 117 optimal weight: 20.0000 chunk 76 optimal weight: 0.0470 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 154 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 141 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 overall best weight: 4.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 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 82 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.040150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.029802 restraints weight = 113704.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.030928 restraints weight = 71951.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.031696 restraints weight = 52160.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.032253 restraints weight = 41379.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.032651 restraints weight = 34960.980| |-----------------------------------------------------------------------------| r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 14420 Z= 0.222 Angle : 0.738 12.448 19620 Z= 0.369 Chirality : 0.042 0.210 2260 Planarity : 0.005 0.039 2430 Dihedral : 5.924 24.652 1880 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 2.39 % Allowed : 7.44 % 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: -2.23 (0.19), residues: 1710 helix: -0.18 (0.20), residues: 610 sheet: -2.49 (0.23), residues: 370 loop : -1.96 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 75 TYR 0.017 0.002 TYR B 144 PHE 0.012 0.001 PHE D 161 TRP 0.009 0.001 TRP E 84 HIS 0.005 0.002 HIS D 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.22 (14395) covalent geometry : angle 0.73047 / 0.37 (19555) SS BOND : bond 0.00571 / 0.36 ( 10) SS BOND : angle 2.02634 / 1.19 ( 20) hydrogen bonds : bond 0.04037 / 2.64 ( 610) hydrogen bonds : angle 5.09792 / 3.51 ( 2085) link_BETA1-4 : bond 0.00283 / 0.17 ( 10) link_BETA1-4 : angle 1.84991 / 1.24 ( 30) link_NAG-ASN : bond 0.00890 / 0.52 ( 5) link_NAG-ASN : angle 2.16908 / 1.22 ( 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: 36 poor density : 142 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.9371 (m-30) cc_final: 0.8824 (p0) REVERT: A 202 GLN cc_start: 0.9474 (mt0) cc_final: 0.9001 (tm-30) REVERT: A 391 MET cc_start: 0.7281 (ttm) cc_final: 0.6961 (ttp) REVERT: B 130 ASP cc_start: 0.9375 (m-30) cc_final: 0.8833 (p0) REVERT: B 134 LEU cc_start: 0.9656 (tp) cc_final: 0.9331 (tt) REVERT: B 163 MET cc_start: 0.9331 (mmm) cc_final: 0.9126 (mmm) REVERT: B 202 GLN cc_start: 0.9498 (mt0) cc_final: 0.9053 (tm-30) REVERT: B 262 MET cc_start: 0.8580 (tpt) cc_final: 0.8342 (tpt) REVERT: C 72 MET cc_start: 0.9200 (ttp) cc_final: 0.8805 (tmm) REVERT: C 130 ASP cc_start: 0.9399 (m-30) cc_final: 0.8840 (p0) REVERT: C 170 MET cc_start: 0.9428 (ppp) cc_final: 0.9099 (ppp) REVERT: C 202 GLN cc_start: 0.9515 (mt0) cc_final: 0.9010 (tm-30) REVERT: C 262 MET cc_start: 0.8617 (tpt) cc_final: 0.8392 (tpt) REVERT: C 417 PHE cc_start: 0.9721 (t80) cc_final: 0.9463 (t80) REVERT: D 72 MET cc_start: 0.9381 (ttp) cc_final: 0.8929 (ttp) REVERT: D 130 ASP cc_start: 0.9338 (m-30) cc_final: 0.8789 (p0) REVERT: D 152 LEU cc_start: 0.9839 (mt) cc_final: 0.9299 (tt) REVERT: D 163 MET cc_start: 0.9309 (mmm) cc_final: 0.9077 (mmm) REVERT: D 202 GLN cc_start: 0.9515 (mt0) cc_final: 0.9065 (tm-30) REVERT: D 391 MET cc_start: 0.7746 (ttm) cc_final: 0.7344 (ttp) REVERT: E 130 ASP cc_start: 0.9370 (m-30) cc_final: 0.8881 (p0) REVERT: E 202 GLN cc_start: 0.9455 (mt0) cc_final: 0.9004 (tm-30) REVERT: E 391 MET cc_start: 0.6636 (ttp) cc_final: 0.6381 (tmm) outliers start: 36 outliers final: 25 residues processed: 173 average time/residue: 0.0992 time to fit residues: 27.3740 Evaluate side-chains 167 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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 109 ILE 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 119 GLU 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 D residue 415 LEU 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: 0.0980 chunk 46 optimal weight: 7.9990 chunk 69 optimal weight: 0.0470 chunk 15 optimal weight: 3.9990 chunk 165 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 overall best weight: 3.0284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** 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 = 0.3114 r_free = 0.3114 target = 0.040664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.030257 restraints weight = 112057.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.031372 restraints weight = 71087.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.032116 restraints weight = 51748.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.032686 restraints weight = 41253.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.033087 restraints weight = 34787.647| |-----------------------------------------------------------------------------| r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14420 Z= 0.166 Angle : 0.721 12.596 19620 Z= 0.356 Chirality : 0.042 0.174 2260 Planarity : 0.004 0.032 2430 Dihedral : 5.717 24.058 1880 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.59 % Allowed : 9.44 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.19), residues: 1710 helix: -0.05 (0.20), residues: 610 sheet: -2.36 (0.23), residues: 370 loop : -1.75 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 75 TYR 0.019 0.002 TYR E 144 PHE 0.014 0.001 PHE A 311 TRP 0.010 0.001 TRP A 84 HIS 0.003 0.001 HIS D 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 (14395) covalent geometry : angle 0.71509 / 0.35 (19555) SS BOND : bond 0.00482 / 0.31 ( 10) SS BOND : angle 1.80187 / 1.08 ( 20) hydrogen bonds : bond 0.03706 / 2.43 ( 610) hydrogen bonds : angle 4.85631 / 3.33 ( 2085) link_BETA1-4 : bond 0.00196 / 0.13 ( 10) link_BETA1-4 : angle 1.64523 / 1.08 ( 30) link_NAG-ASN : bond 0.00550 / 0.32 ( 5) link_NAG-ASN : angle 1.83674 / 1.04 ( 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: 24 poor density : 146 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.9362 (m-30) cc_final: 0.8792 (p0) REVERT: A 202 GLN cc_start: 0.9461 (mt0) cc_final: 0.9007 (tm-30) REVERT: A 391 MET cc_start: 0.7361 (ttm) cc_final: 0.7022 (ttp) REVERT: B 72 MET cc_start: 0.9372 (ttp) cc_final: 0.8833 (ttp) REVERT: B 105 MET cc_start: 0.9292 (ptp) cc_final: 0.7929 (ptp) REVERT: B 130 ASP cc_start: 0.9370 (m-30) cc_final: 0.8872 (p0) REVERT: B 163 MET cc_start: 0.9337 (mmm) cc_final: 0.9133 (mmm) REVERT: B 202 GLN cc_start: 0.9483 (mt0) cc_final: 0.9050 (tm-30) REVERT: B 262 MET cc_start: 0.8568 (tpt) cc_final: 0.8313 (tpp) REVERT: C 72 MET cc_start: 0.9248 (ttp) cc_final: 0.8821 (tmm) REVERT: C 130 ASP cc_start: 0.9412 (m-30) cc_final: 0.8822 (p0) REVERT: C 152 LEU cc_start: 0.9867 (mt) cc_final: 0.9396 (tt) REVERT: C 202 GLN cc_start: 0.9500 (mt0) cc_final: 0.9026 (tm-30) REVERT: C 391 MET cc_start: 0.7128 (ttp) cc_final: 0.6834 (ttp) REVERT: C 417 PHE cc_start: 0.9716 (t80) cc_final: 0.9448 (t80) REVERT: D 72 MET cc_start: 0.9395 (ttp) cc_final: 0.8940 (ttp) REVERT: D 119 GLU cc_start: 0.8679 (tp30) cc_final: 0.8344 (tm-30) REVERT: D 130 ASP cc_start: 0.9329 (m-30) cc_final: 0.8802 (p0) REVERT: D 152 LEU cc_start: 0.9851 (mt) cc_final: 0.9275 (tt) REVERT: D 163 MET cc_start: 0.9275 (mmm) cc_final: 0.9056 (mmm) REVERT: D 202 GLN cc_start: 0.9515 (mt0) cc_final: 0.9054 (tm-30) REVERT: D 391 MET cc_start: 0.7738 (ttm) cc_final: 0.7274 (ttp) REVERT: E 72 MET cc_start: 0.9390 (ttp) cc_final: 0.8908 (ttp) REVERT: E 130 ASP cc_start: 0.9369 (m-30) cc_final: 0.8865 (p0) REVERT: E 202 GLN cc_start: 0.9448 (mt0) cc_final: 0.9018 (tm-30) REVERT: E 391 MET cc_start: 0.6609 (ttp) cc_final: 0.6352 (tmm) outliers start: 24 outliers final: 23 residues processed: 167 average time/residue: 0.1080 time to fit residues: 28.0470 Evaluate side-chains 159 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 172 LEU 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 109 ILE 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: 0.7980 chunk 21 optimal weight: 0.8980 chunk 152 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 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 = 0.3116 r_free = 0.3116 target = 0.040880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.030387 restraints weight = 111088.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.031480 restraints weight = 70662.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.032245 restraints weight = 51520.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.032808 restraints weight = 41119.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.033217 restraints weight = 34869.029| |-----------------------------------------------------------------------------| r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14420 Z= 0.162 Angle : 0.729 13.766 19620 Z= 0.357 Chirality : 0.042 0.170 2260 Planarity : 0.004 0.033 2430 Dihedral : 5.647 23.157 1880 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.53 % Allowed : 10.76 % Favored : 87.71 % 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: -1.85 (0.20), residues: 1710 helix: 0.02 (0.20), residues: 610 sheet: -2.22 (0.24), residues: 370 loop : -1.66 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 43 TYR 0.016 0.002 TYR B 144 PHE 0.033 0.001 PHE A 311 TRP 0.010 0.001 TRP A 84 HIS 0.003 0.001 HIS D 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (14395) covalent geometry : angle 0.72332 / 0.36 (19555) SS BOND : bond 0.00425 / 0.27 ( 10) SS BOND : angle 1.80520 / 1.09 ( 20) hydrogen bonds : bond 0.03557 / 2.34 ( 610) hydrogen bonds : angle 4.70562 / 3.23 ( 2085) link_BETA1-4 : bond 0.00179 / 0.12 ( 10) link_BETA1-4 : angle 1.57785 / 1.03 ( 30) link_NAG-ASN : bond 0.00547 / 0.32 ( 5) link_NAG-ASN : angle 1.79779 / 1.02 ( 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 161 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.9539 (ttm) cc_final: 0.9176 (tpp) REVERT: A 105 MET cc_start: 0.9295 (ptp) cc_final: 0.8414 (ptp) REVERT: A 130 ASP cc_start: 0.9373 (m-30) cc_final: 0.8889 (p0) REVERT: A 202 GLN cc_start: 0.9456 (mt0) cc_final: 0.9002 (tm-30) REVERT: A 391 MET cc_start: 0.7425 (ttm) cc_final: 0.7173 (ttp) REVERT: B 72 MET cc_start: 0.9382 (ttp) cc_final: 0.8853 (ttp) REVERT: B 105 MET cc_start: 0.9245 (ptp) cc_final: 0.9033 (ptp) REVERT: B 130 ASP cc_start: 0.9360 (m-30) cc_final: 0.8877 (p0) REVERT: B 134 LEU cc_start: 0.9566 (tp) cc_final: 0.9324 (tt) REVERT: B 202 GLN cc_start: 0.9485 (mt0) cc_final: 0.9049 (tm-30) REVERT: B 262 MET cc_start: 0.8590 (tpt) cc_final: 0.8353 (tpp) REVERT: C 72 MET cc_start: 0.9289 (ttp) cc_final: 0.8888 (tmm) REVERT: C 130 ASP cc_start: 0.9408 (m-30) cc_final: 0.8844 (p0) REVERT: C 152 LEU cc_start: 0.9869 (mt) cc_final: 0.9407 (tt) REVERT: C 202 GLN cc_start: 0.9502 (mt0) cc_final: 0.9040 (tm-30) REVERT: C 391 MET cc_start: 0.7039 (ttp) cc_final: 0.6738 (ttp) REVERT: D 72 MET cc_start: 0.9402 (ttp) cc_final: 0.8963 (ttp) REVERT: D 119 GLU cc_start: 0.8662 (tp30) cc_final: 0.8308 (tm-30) REVERT: D 130 ASP cc_start: 0.9340 (m-30) cc_final: 0.8857 (p0) REVERT: D 152 LEU cc_start: 0.9847 (mt) cc_final: 0.9356 (tt) REVERT: D 202 GLN cc_start: 0.9501 (mt0) cc_final: 0.9058 (tm-30) REVERT: D 391 MET cc_start: 0.7793 (ttm) cc_final: 0.7473 (ttp) REVERT: E 72 MET cc_start: 0.9411 (ttp) cc_final: 0.8936 (ttp) REVERT: E 130 ASP cc_start: 0.9372 (m-30) cc_final: 0.8898 (p0) REVERT: E 202 GLN cc_start: 0.9430 (mt0) cc_final: 0.9017 (tm-30) REVERT: E 391 MET cc_start: 0.6641 (ttp) cc_final: 0.6394 (tmm) outliers start: 23 outliers final: 21 residues processed: 158 average time/residue: 0.1008 time to fit residues: 25.3676 Evaluate side-chains 156 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 19 optimal weight: 0.0970 chunk 128 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 143 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 56 optimal weight: 0.3980 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 118 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 = 0.3121 r_free = 0.3121 target = 0.041029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.030460 restraints weight = 108486.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.031543 restraints weight = 69578.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.032311 restraints weight = 51066.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.032878 restraints weight = 40796.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.033280 restraints weight = 34616.230| |-----------------------------------------------------------------------------| r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14420 Z= 0.142 Angle : 0.723 15.305 19620 Z= 0.352 Chirality : 0.042 0.170 2260 Planarity : 0.004 0.034 2430 Dihedral : 5.539 22.596 1880 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 1.73 % Allowed : 11.10 % Favored : 87.18 % 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: -1.71 (0.20), residues: 1710 helix: 0.05 (0.20), residues: 610 sheet: -2.02 (0.24), residues: 370 loop : -1.56 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 43 TYR 0.015 0.002 TYR E 144 PHE 0.018 0.001 PHE D 311 TRP 0.010 0.001 TRP C 84 HIS 0.002 0.001 HIS D 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (14395) covalent geometry : angle 0.71850 / 0.35 (19555) SS BOND : bond 0.00402 / 0.26 ( 10) SS BOND : angle 1.68638 / 1.03 ( 20) hydrogen bonds : bond 0.03424 / 2.26 ( 610) hydrogen bonds : angle 4.55703 / 3.12 ( 2085) link_BETA1-4 : bond 0.00193 / 0.13 ( 10) link_BETA1-4 : angle 1.47068 / 0.94 ( 30) link_NAG-ASN : bond 0.00389 / 0.23 ( 5) link_NAG-ASN : angle 1.65467 / 0.94 ( 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 161 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.9558 (ttm) cc_final: 0.9332 (mmm) REVERT: A 105 MET cc_start: 0.9303 (ptp) cc_final: 0.8972 (ptp) REVERT: A 130 ASP cc_start: 0.9360 (m-30) cc_final: 0.8874 (p0) REVERT: A 152 LEU cc_start: 0.9857 (mt) cc_final: 0.9338 (tt) REVERT: A 202 GLN cc_start: 0.9432 (mt0) cc_final: 0.9020 (tm-30) REVERT: A 391 MET cc_start: 0.7448 (ttm) cc_final: 0.7191 (ttp) REVERT: B 72 MET cc_start: 0.9385 (ttp) cc_final: 0.8853 (ttp) REVERT: B 105 MET cc_start: 0.9258 (ptp) cc_final: 0.8844 (ptp) REVERT: B 130 ASP cc_start: 0.9371 (m-30) cc_final: 0.8869 (p0) REVERT: B 134 LEU cc_start: 0.9575 (tp) cc_final: 0.9254 (tt) REVERT: B 149 THR cc_start: 0.8868 (OUTLIER) cc_final: 0.8654 (m) REVERT: B 202 GLN cc_start: 0.9451 (mt0) cc_final: 0.9038 (tm-30) REVERT: B 262 MET cc_start: 0.8409 (tpt) cc_final: 0.8166 (tpp) REVERT: C 72 MET cc_start: 0.9303 (ttp) cc_final: 0.8905 (tmm) REVERT: C 130 ASP cc_start: 0.9400 (m-30) cc_final: 0.8853 (p0) REVERT: C 149 THR cc_start: 0.8912 (OUTLIER) cc_final: 0.8570 (m) REVERT: C 202 GLN cc_start: 0.9458 (mt0) cc_final: 0.9051 (tm-30) REVERT: D 72 MET cc_start: 0.9404 (ttp) cc_final: 0.8966 (ttp) REVERT: D 119 GLU cc_start: 0.8637 (tp30) cc_final: 0.8347 (tm-30) REVERT: D 130 ASP cc_start: 0.9345 (m-30) cc_final: 0.8857 (p0) REVERT: D 202 GLN cc_start: 0.9471 (mt0) cc_final: 0.9064 (tm-30) REVERT: D 391 MET cc_start: 0.7853 (ttm) cc_final: 0.7514 (ttp) REVERT: E 72 MET cc_start: 0.9393 (ttp) cc_final: 0.8954 (ttp) REVERT: E 130 ASP cc_start: 0.9372 (m-30) cc_final: 0.8875 (p0) REVERT: E 202 GLN cc_start: 0.9400 (mt0) cc_final: 0.9013 (tm-30) REVERT: E 391 MET cc_start: 0.6678 (ttp) cc_final: 0.6435 (tmm) REVERT: E 415 LEU cc_start: 0.9312 (tt) cc_final: 0.9106 (pp) outliers start: 26 outliers final: 21 residues processed: 160 average time/residue: 0.0985 time to fit residues: 25.3001 Evaluate side-chains 158 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 149 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 149 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 76 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 72 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 142 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 146 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 133 optimal weight: 6.9990 chunk 127 optimal weight: 8.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3112 r_free = 0.3112 target = 0.040683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.030132 restraints weight = 110248.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.031191 restraints weight = 70459.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.031963 restraints weight = 51801.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.032530 restraints weight = 41402.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.032931 restraints weight = 35097.366| |-----------------------------------------------------------------------------| r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14420 Z= 0.161 Angle : 0.733 8.913 19620 Z= 0.359 Chirality : 0.042 0.201 2260 Planarity : 0.004 0.034 2430 Dihedral : 5.515 22.362 1880 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.46 % Allowed : 11.50 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.20), residues: 1710 helix: 0.21 (0.21), residues: 610 sheet: -1.61 (0.27), residues: 320 loop : -1.72 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 43 TYR 0.018 0.002 TYR E 144 PHE 0.020 0.001 PHE C 311 TRP 0.010 0.001 TRP C 84 HIS 0.006 0.002 HIS D 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (14395) covalent geometry : angle 0.72818 / 0.36 (19555) SS BOND : bond 0.00393 / 0.26 ( 10) SS BOND : angle 1.76948 / 1.07 ( 20) hydrogen bonds : bond 0.03337 / 2.19 ( 610) hydrogen bonds : angle 4.52062 / 3.10 ( 2085) link_BETA1-4 : bond 0.00185 / 0.12 ( 10) link_BETA1-4 : angle 1.49011 / 0.97 ( 30) link_NAG-ASN : bond 0.00533 / 0.31 ( 5) link_NAG-ASN : angle 1.78207 / 1.00 ( 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 160 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.9298 (ptp) cc_final: 0.8946 (ptp) REVERT: A 130 ASP cc_start: 0.9359 (m-30) cc_final: 0.8890 (p0) REVERT: A 202 GLN cc_start: 0.9450 (mt0) cc_final: 0.9030 (tm-30) REVERT: A 391 MET cc_start: 0.7549 (ttm) cc_final: 0.7243 (ttp) REVERT: B 72 MET cc_start: 0.9400 (ttp) cc_final: 0.8876 (ttp) REVERT: B 105 MET cc_start: 0.9246 (ptp) cc_final: 0.8792 (ptp) REVERT: B 130 ASP cc_start: 0.9376 (m-30) cc_final: 0.8867 (p0) REVERT: B 134 LEU cc_start: 0.9594 (tp) cc_final: 0.9260 (tt) REVERT: B 149 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8613 (m) REVERT: B 202 GLN cc_start: 0.9449 (mt0) cc_final: 0.9032 (tm-30) REVERT: B 262 MET cc_start: 0.8412 (tpt) cc_final: 0.8159 (tpp) REVERT: C 72 MET cc_start: 0.9318 (ttp) cc_final: 0.8892 (tmm) REVERT: C 130 ASP cc_start: 0.9410 (m-30) cc_final: 0.8875 (p0) REVERT: C 149 THR cc_start: 0.8889 (OUTLIER) cc_final: 0.8481 (m) REVERT: C 202 GLN cc_start: 0.9469 (mt0) cc_final: 0.9049 (tm-30) REVERT: C 391 MET cc_start: 0.7050 (ttp) cc_final: 0.6624 (tmm) REVERT: D 72 MET cc_start: 0.9408 (ttp) cc_final: 0.8966 (ttp) REVERT: D 119 GLU cc_start: 0.8651 (tp30) cc_final: 0.8306 (tm-30) REVERT: D 130 ASP cc_start: 0.9352 (m-30) cc_final: 0.8908 (p0) REVERT: D 202 GLN cc_start: 0.9466 (mt0) cc_final: 0.9055 (tm-30) REVERT: D 391 MET cc_start: 0.7871 (ttm) cc_final: 0.7530 (ttp) REVERT: E 72 MET cc_start: 0.9410 (ttp) cc_final: 0.8929 (ttp) REVERT: E 130 ASP cc_start: 0.9379 (m-30) cc_final: 0.8929 (p0) REVERT: E 202 GLN cc_start: 0.9407 (mt0) cc_final: 0.9010 (tm-30) REVERT: E 391 MET cc_start: 0.6702 (ttp) cc_final: 0.6457 (tmm) outliers start: 22 outliers final: 20 residues processed: 160 average time/residue: 0.1017 time to fit residues: 25.8461 Evaluate side-chains 155 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 149 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 149 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 31 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 139 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 9 optimal weight: 0.5980 chunk 130 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 106 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 145 optimal weight: 0.5980 overall best weight: 1.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3126 r_free = 0.3126 target = 0.041196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.030540 restraints weight = 109126.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.031629 restraints weight = 69980.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.032413 restraints weight = 51415.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.032978 restraints weight = 40981.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.033391 restraints weight = 34727.156| |-----------------------------------------------------------------------------| r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14420 Z= 0.134 Angle : 0.754 14.622 19620 Z= 0.363 Chirality : 0.043 0.222 2260 Planarity : 0.004 0.041 2430 Dihedral : 5.458 21.607 1880 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.53 % Allowed : 11.56 % 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: -1.52 (0.20), residues: 1710 helix: 0.18 (0.21), residues: 610 sheet: -1.90 (0.25), residues: 370 loop : -1.44 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 43 TYR 0.018 0.002 TYR D 144 PHE 0.018 0.001 PHE B 311 TRP 0.011 0.001 TRP C 84 HIS 0.003 0.001 HIS D 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (14395) covalent geometry : angle 0.74968 / 0.36 (19555) SS BOND : bond 0.00343 / 0.23 ( 10) SS BOND : angle 1.76334 / 1.07 ( 20) hydrogen bonds : bond 0.03251 / 2.15 ( 610) hydrogen bonds : angle 4.44039 / 3.05 ( 2085) link_BETA1-4 : bond 0.00178 / 0.11 ( 10) link_BETA1-4 : angle 1.38955 / 0.89 ( 30) link_NAG-ASN : bond 0.00306 / 0.18 ( 5) link_NAG-ASN : angle 1.57165 / 0.89 ( 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 159 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 105 MET cc_start: 0.9288 (ptp) cc_final: 0.8929 (ptp) REVERT: A 130 ASP cc_start: 0.9375 (m-30) cc_final: 0.8884 (p0) REVERT: A 202 GLN cc_start: 0.9468 (mt0) cc_final: 0.9037 (tm-30) REVERT: A 391 MET cc_start: 0.7586 (ttm) cc_final: 0.7288 (ttp) REVERT: B 72 MET cc_start: 0.9411 (ttp) cc_final: 0.8891 (ttp) REVERT: B 105 MET cc_start: 0.9241 (ptp) cc_final: 0.8768 (ptp) REVERT: B 130 ASP cc_start: 0.9398 (m-30) cc_final: 0.8850 (p0) REVERT: B 134 LEU cc_start: 0.9584 (tp) cc_final: 0.9264 (tt) REVERT: B 149 THR cc_start: 0.8836 (OUTLIER) cc_final: 0.8610 (m) REVERT: B 202 GLN cc_start: 0.9475 (mt0) cc_final: 0.9057 (tm-30) REVERT: B 262 MET cc_start: 0.8421 (tpt) cc_final: 0.8190 (tpp) REVERT: C 72 MET cc_start: 0.9335 (ttp) cc_final: 0.8887 (tmm) REVERT: C 82 GLN cc_start: 0.9481 (mt0) cc_final: 0.9254 (mp10) REVERT: C 130 ASP cc_start: 0.9418 (m-30) cc_final: 0.8855 (p0) REVERT: C 149 THR cc_start: 0.8891 (OUTLIER) cc_final: 0.8473 (m) REVERT: C 202 GLN cc_start: 0.9488 (mt0) cc_final: 0.9075 (tm-30) REVERT: C 391 MET cc_start: 0.7059 (ttp) cc_final: 0.6655 (tmm) REVERT: D 72 MET cc_start: 0.9429 (ttp) cc_final: 0.8975 (ttp) REVERT: D 119 GLU cc_start: 0.8579 (tp30) cc_final: 0.8292 (tm-30) REVERT: D 130 ASP cc_start: 0.9375 (m-30) cc_final: 0.8882 (p0) REVERT: D 202 GLN cc_start: 0.9490 (mt0) cc_final: 0.9068 (tm-30) REVERT: D 391 MET cc_start: 0.7889 (ttm) cc_final: 0.7551 (ttp) REVERT: E 72 MET cc_start: 0.9419 (ttp) cc_final: 0.8964 (ttp) REVERT: E 130 ASP cc_start: 0.9391 (m-30) cc_final: 0.8923 (p0) REVERT: E 202 GLN cc_start: 0.9441 (mt0) cc_final: 0.9036 (tm-30) REVERT: E 262 MET cc_start: 0.8331 (tpt) cc_final: 0.8080 (tpt) REVERT: E 391 MET cc_start: 0.6716 (ttp) cc_final: 0.6282 (ttp) outliers start: 23 outliers final: 20 residues processed: 158 average time/residue: 0.0996 time to fit residues: 24.9039 Evaluate side-chains 155 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 149 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 149 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 105 MET 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: 0.9990 chunk 112 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 154 optimal weight: 0.0000 chunk 73 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 146 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 17 optimal weight: 0.0470 chunk 15 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 overall best weight: 2.2088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** E 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.041230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.030613 restraints weight = 111174.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.031709 restraints weight = 71394.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.032474 restraints weight = 52535.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.033026 restraints weight = 42018.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.033447 restraints weight = 35746.789| |-----------------------------------------------------------------------------| r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.4913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14420 Z= 0.141 Angle : 0.752 10.332 19620 Z= 0.361 Chirality : 0.042 0.179 2260 Planarity : 0.004 0.034 2430 Dihedral : 5.434 21.762 1880 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.66 % Allowed : 11.83 % Favored : 86.51 % 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: -1.44 (0.20), residues: 1710 helix: 0.23 (0.21), residues: 610 sheet: -1.85 (0.25), residues: 370 loop : -1.38 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 43 TYR 0.017 0.002 TYR B 144 PHE 0.057 0.001 PHE A 311 TRP 0.014 0.001 TRP E 84 HIS 0.004 0.001 HIS A 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (14395) covalent geometry : angle 0.74765 / 0.36 (19555) SS BOND : bond 0.00334 / 0.22 ( 10) SS BOND : angle 1.80178 / 1.10 ( 20) hydrogen bonds : bond 0.03193 / 2.11 ( 610) hydrogen bonds : angle 4.38624 / 3.01 ( 2085) link_BETA1-4 : bond 0.00287 / 0.20 ( 10) link_BETA1-4 : angle 1.43765 / 0.93 ( 30) link_NAG-ASN : bond 0.00411 / 0.24 ( 5) link_NAG-ASN : angle 1.63461 / 0.92 ( 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 161 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.9250 (ptp) cc_final: 0.8849 (ptp) REVERT: A 130 ASP cc_start: 0.9367 (m-30) cc_final: 0.8885 (p0) REVERT: A 202 GLN cc_start: 0.9450 (mt0) cc_final: 0.9032 (tm-30) REVERT: A 391 MET cc_start: 0.7598 (ttm) cc_final: 0.7316 (ttp) REVERT: B 72 MET cc_start: 0.9424 (ttp) cc_final: 0.8905 (ttp) REVERT: B 105 MET cc_start: 0.9190 (ptp) cc_final: 0.8714 (ptp) REVERT: B 130 ASP cc_start: 0.9399 (m-30) cc_final: 0.8862 (p0) REVERT: B 134 LEU cc_start: 0.9588 (tp) cc_final: 0.9275 (tt) REVERT: B 149 THR cc_start: 0.8853 (OUTLIER) cc_final: 0.8634 (m) REVERT: B 202 GLN cc_start: 0.9480 (mt0) cc_final: 0.9077 (tm-30) REVERT: B 262 MET cc_start: 0.8416 (tpt) cc_final: 0.8189 (tpp) REVERT: C 72 MET cc_start: 0.9346 (ttp) cc_final: 0.8874 (tmm) REVERT: C 130 ASP cc_start: 0.9425 (m-30) cc_final: 0.8850 (p0) REVERT: C 149 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8580 (m) REVERT: C 202 GLN cc_start: 0.9473 (mt0) cc_final: 0.9074 (tm-30) REVERT: C 391 MET cc_start: 0.7079 (ttp) cc_final: 0.6672 (tmm) REVERT: C 415 LEU cc_start: 0.9360 (tp) cc_final: 0.9096 (pp) REVERT: D 72 MET cc_start: 0.9429 (ttp) cc_final: 0.8976 (ttp) REVERT: D 119 GLU cc_start: 0.8561 (tp30) cc_final: 0.8317 (tm-30) REVERT: D 130 ASP cc_start: 0.9370 (m-30) cc_final: 0.8883 (p0) REVERT: D 202 GLN cc_start: 0.9462 (mt0) cc_final: 0.9073 (tm-30) REVERT: D 391 MET cc_start: 0.7938 (ttm) cc_final: 0.7600 (ttp) REVERT: E 72 MET cc_start: 0.9422 (ttp) cc_final: 0.8977 (ttp) REVERT: E 130 ASP cc_start: 0.9381 (m-30) cc_final: 0.8943 (p0) REVERT: E 152 LEU cc_start: 0.9858 (mt) cc_final: 0.9375 (tt) REVERT: E 202 GLN cc_start: 0.9430 (mt0) cc_final: 0.9032 (tm-30) REVERT: E 391 MET cc_start: 0.6770 (ttp) cc_final: 0.6329 (ttp) outliers start: 25 outliers final: 22 residues processed: 158 average time/residue: 0.0955 time to fit residues: 24.1500 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 : 0.520 ------------------------------------------------------------------------------- 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 149 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 B residue 391 MET Chi-restraints excluded: chain C residue 71 THR 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 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 105 MET 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: 9.9990 chunk 13 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 58 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 133 optimal weight: 7.9990 chunk 76 optimal weight: 0.0470 overall best weight: 4.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3100 r_free = 0.3100 target = 0.040343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.029813 restraints weight = 111755.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.030856 restraints weight = 71997.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.031594 restraints weight = 53248.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.032116 restraints weight = 42893.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.032483 restraints weight = 36685.691| |-----------------------------------------------------------------------------| r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14420 Z= 0.203 Angle : 0.783 13.247 19620 Z= 0.379 Chirality : 0.042 0.169 2260 Planarity : 0.004 0.041 2430 Dihedral : 5.542 21.899 1880 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.66 % Allowed : 12.03 % 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: -1.35 (0.20), residues: 1710 helix: 0.34 (0.21), residues: 610 sheet: -1.48 (0.27), residues: 315 loop : -1.59 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 43 TYR 0.018 0.002 TYR B 144 PHE 0.031 0.001 PHE A 311 TRP 0.009 0.001 TRP C 110 HIS 0.004 0.002 HIS A 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.20 (14395) covalent geometry : angle 0.77731 / 0.38 (19555) SS BOND : bond 0.00425 / 0.29 ( 10) SS BOND : angle 1.94109 / 1.15 ( 20) hydrogen bonds : bond 0.03318 / 2.20 ( 610) hydrogen bonds : angle 4.48628 / 3.07 ( 2085) link_BETA1-4 : bond 0.00221 / 0.15 ( 10) link_BETA1-4 : angle 1.56177 / 1.06 ( 30) link_NAG-ASN : bond 0.00808 / 0.47 ( 5) link_NAG-ASN : angle 2.04938 / 1.15 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1928.94 seconds wall clock time: 34 minutes 38.90 seconds (2078.90 seconds total)