Starting phenix.real_space_refine on Wed Mar 4 14:32:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6plq_20372/03_2026/6plq_20372.cif Found real_map, /net/cci-nas-00/data/ceres_data/6plq_20372/03_2026/6plq_20372.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6plq_20372/03_2026/6plq_20372.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6plq_20372/03_2026/6plq_20372.map" model { file = "/net/cci-nas-00/data/ceres_data/6plq_20372/03_2026/6plq_20372.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6plq_20372/03_2026/6plq_20372.cif" } resolution = 3.4 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 100 5.16 5 C 9270 2.51 5 N 2290 2.21 5 O 2580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14240 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E, G, H, I, J Time building chain proxies: 2.39, per 1000 atoms: 0.17 Number of scatterers: 14240 At special positions: 0 Unit cell: (105.786, 107.745, 135.824, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2580 8.00 N 2290 7.00 C 9270 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 168 " distance=2.19 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 168 " distance=2.19 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 168 " distance=2.19 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 168 " distance=2.19 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 168 " distance=2.19 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.03 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.03 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG F 1 " - " ASN A 54 " " NAG G 1 " - " ASN B 54 " " NAG H 1 " - " ASN C 54 " " NAG I 1 " - " ASN D 54 " " NAG J 1 " - " ASN E 54 " Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 584.7 milliseconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 25 sheets defined 39.3% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 25 through 30 Processing helix chain 'A' and resid 30 through 35 Processing helix chain 'A' and resid 36 through 40 removed outlier: 3.998A pdb=" N GLY A 39 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR A 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 36 through 40' Processing helix chain 'A' and resid 87 through 90 Processing helix chain 'A' and resid 102 through 106 removed outlier: 4.039A pdb=" N LEU A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 163 Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 245 through 256 removed outlier: 4.462A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 260 Processing helix chain 'A' and resid 264 through 285 removed outlier: 3.755A pdb=" N ARG A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY A 270 " --> pdb=" O PRO A 266 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN A 282 " --> pdb=" O THR A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 325 removed outlier: 3.575A pdb=" N MET A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 425 removed outlier: 4.052A pdb=" N PHE A 395 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) Proline residue: A 411 - end of helix removed outlier: 4.233A pdb=" N LEU A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TRP A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR A 425 " --> pdb=" O TYR A 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'B' and resid 36 through 40 removed outlier: 3.999A pdb=" N GLY B 39 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR B 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 36 through 40' Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 102 through 106 removed outlier: 4.039A pdb=" N LEU B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 163 Processing helix chain 'B' and resid 238 through 243 Processing helix chain 'B' and resid 245 through 256 removed outlier: 4.462A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 260 Processing helix chain 'B' and resid 264 through 285 removed outlier: 3.755A pdb=" N ARG B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY B 270 " --> pdb=" O PRO B 266 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR B 280 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN B 282 " --> pdb=" O THR B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 325 removed outlier: 3.575A pdb=" N MET B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 305 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 425 removed outlier: 4.053A pdb=" N PHE B 395 " --> pdb=" O MET B 391 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER B 397 " --> pdb=" O LYS B 393 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 402 " --> pdb=" O ARG B 398 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP B 403 " --> pdb=" O ALA B 399 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) Proline residue: B 411 - end of helix removed outlier: 4.234A pdb=" N LEU B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TRP B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR B 425 " --> pdb=" O TYR B 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 30 through 35 Processing helix chain 'C' and resid 36 through 40 removed outlier: 3.998A pdb=" N GLY C 39 " --> pdb=" O LYS C 36 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR C 40 " --> pdb=" O VAL C 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 36 through 40' Processing helix chain 'C' and resid 87 through 90 Processing helix chain 'C' and resid 102 through 106 removed outlier: 4.039A pdb=" N LEU C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 163 Processing helix chain 'C' and resid 238 through 243 Processing helix chain 'C' and resid 245 through 256 removed outlier: 4.461A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 260 Processing helix chain 'C' and resid 264 through 285 removed outlier: 3.755A pdb=" N ARG C 268 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY C 270 " --> pdb=" O PRO C 266 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR C 280 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN C 282 " --> pdb=" O THR C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 325 removed outlier: 3.575A pdb=" N MET C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL C 305 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE C 323 " --> pdb=" O ALA C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 425 removed outlier: 4.052A pdb=" N PHE C 395 " --> pdb=" O MET C 391 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER C 397 " --> pdb=" O LYS C 393 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE C 402 " --> pdb=" O ARG C 398 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP C 403 " --> pdb=" O ALA C 399 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) Proline residue: C 411 - end of helix removed outlier: 4.234A pdb=" N LEU C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE C 416 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TRP C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR C 425 " --> pdb=" O TYR C 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 30 Processing helix chain 'D' and resid 30 through 35 Processing helix chain 'D' and resid 36 through 40 removed outlier: 3.998A pdb=" N GLY D 39 " --> pdb=" O LYS D 36 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR D 40 " --> pdb=" O VAL D 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 36 through 40' Processing helix chain 'D' and resid 87 through 90 Processing helix chain 'D' and resid 102 through 106 removed outlier: 4.039A pdb=" N LEU D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 163 Processing helix chain 'D' and resid 238 through 243 Processing helix chain 'D' and resid 245 through 256 removed outlier: 4.462A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 260 Processing helix chain 'D' and resid 264 through 285 removed outlier: 3.755A pdb=" N ARG D 268 " --> pdb=" O ALA D 264 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY D 270 " --> pdb=" O PRO D 266 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL D 276 " --> pdb=" O GLY D 272 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR D 280 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR D 281 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN D 282 " --> pdb=" O THR D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 325 removed outlier: 3.575A pdb=" N MET D 303 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 305 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 425 removed outlier: 4.053A pdb=" N PHE D 395 " --> pdb=" O MET D 391 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER D 397 " --> pdb=" O LYS D 393 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE D 402 " --> pdb=" O ARG D 398 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP D 403 " --> pdb=" O ALA D 399 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG D 407 " --> pdb=" O ASP D 403 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL D 408 " --> pdb=" O THR D 404 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE D 410 " --> pdb=" O SER D 406 " (cutoff:3.500A) Proline residue: D 411 - end of helix removed outlier: 4.233A pdb=" N LEU D 415 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TRP D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR D 425 " --> pdb=" O TYR D 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 30 Processing helix chain 'E' and resid 30 through 35 Processing helix chain 'E' and resid 36 through 40 removed outlier: 3.999A pdb=" N GLY E 39 " --> pdb=" O LYS E 36 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR E 40 " --> pdb=" O VAL E 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 36 through 40' Processing helix chain 'E' and resid 87 through 90 Processing helix chain 'E' and resid 102 through 106 removed outlier: 4.040A pdb=" N LEU E 106 " --> pdb=" O PRO E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 163 Processing helix chain 'E' and resid 238 through 243 Processing helix chain 'E' and resid 245 through 256 removed outlier: 4.462A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 260 Processing helix chain 'E' and resid 264 through 285 removed outlier: 3.755A pdb=" N ARG E 268 " --> pdb=" O ALA E 264 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY E 270 " --> pdb=" O PRO E 266 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL E 276 " --> pdb=" O GLY E 272 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR E 280 " --> pdb=" O VAL E 276 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR E 281 " --> pdb=" O LEU E 277 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN E 282 " --> pdb=" O THR E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 325 removed outlier: 3.575A pdb=" N MET E 303 " --> pdb=" O ILE E 299 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL E 305 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 425 removed outlier: 4.052A pdb=" N PHE E 395 " --> pdb=" O MET E 391 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER E 397 " --> pdb=" O LYS E 393 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE E 402 " --> pdb=" O ARG E 398 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP E 403 " --> pdb=" O ALA E 399 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG E 407 " --> pdb=" O ASP E 403 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL E 408 " --> pdb=" O THR E 404 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE E 410 " --> pdb=" O SER E 406 " (cutoff:3.500A) Proline residue: E 411 - end of helix removed outlier: 4.233A pdb=" N LEU E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE E 416 " --> pdb=" O LEU E 412 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TRP E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR E 425 " --> pdb=" O TYR E 421 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 99 through 100 removed outlier: 3.566A pdb=" N LEU A 99 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP A 84 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL A 55 " --> pdb=" O GLU A 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 123 removed outlier: 3.721A pdb=" N ASN A 123 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP A 84 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N GLN A 193 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE A 59 " --> pdb=" O GLN A 193 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 116 removed outlier: 3.795A pdb=" N MET A 170 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A 228 " --> pdb=" O MET A 170 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 227 " --> pdb=" O ARG A 212 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG A 212 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 165 through 167 Processing sheet with id=AA5, first strand: chain 'A' and resid 216 through 217 removed outlier: 3.789A pdb=" N LYS A 216 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE A 223 " --> pdb=" O LYS A 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 99 through 100 removed outlier: 3.566A pdb=" N LEU B 99 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP B 84 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 122 through 123 removed outlier: 3.721A pdb=" N ASN B 123 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP B 84 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N GLN B 193 " --> pdb=" O CYS B 57 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE B 59 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 114 through 116 removed outlier: 3.794A pdb=" N MET B 170 " --> pdb=" O ALA B 228 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA B 228 " --> pdb=" O MET B 170 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B 227 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG B 212 " --> pdb=" O GLU B 227 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 165 through 167 Processing sheet with id=AB1, first strand: chain 'B' and resid 216 through 217 removed outlier: 3.789A pdb=" N LYS B 216 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE B 223 " --> pdb=" O LYS B 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 99 through 100 removed outlier: 3.565A pdb=" N LEU C 99 " --> pdb=" O ILE C 136 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP C 84 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 122 through 123 removed outlier: 3.721A pdb=" N ASN C 123 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP C 84 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N GLN C 193 " --> pdb=" O CYS C 57 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE C 59 " --> pdb=" O GLN C 193 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 114 through 116 removed outlier: 3.795A pdb=" N MET C 170 " --> pdb=" O ALA C 228 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 228 " --> pdb=" O MET C 170 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU C 227 " --> pdb=" O ARG C 212 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG C 212 " --> pdb=" O GLU C 227 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 165 through 167 Processing sheet with id=AB6, first strand: chain 'C' and resid 216 through 217 removed outlier: 3.789A pdb=" N LYS C 216 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE C 223 " --> pdb=" O LYS C 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 99 through 100 removed outlier: 3.566A pdb=" N LEU D 99 " --> pdb=" O ILE D 136 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP D 84 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 122 through 123 removed outlier: 3.721A pdb=" N ASN D 123 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP D 84 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N GLN D 193 " --> pdb=" O CYS D 57 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE D 59 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 114 through 116 removed outlier: 3.794A pdb=" N MET D 170 " --> pdb=" O ALA D 228 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA D 228 " --> pdb=" O MET D 170 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU D 227 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG D 212 " --> pdb=" O GLU D 227 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 165 through 167 Processing sheet with id=AC2, first strand: chain 'D' and resid 216 through 217 removed outlier: 3.789A pdb=" N LYS D 216 " --> pdb=" O PHE D 223 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE D 223 " --> pdb=" O LYS D 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 99 through 100 removed outlier: 3.566A pdb=" N LEU E 99 " --> pdb=" O ILE E 136 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP E 84 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL E 55 " --> pdb=" O GLU E 185 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 122 through 123 removed outlier: 3.721A pdb=" N ASN E 123 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP E 84 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N GLN E 193 " --> pdb=" O CYS E 57 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE E 59 " --> pdb=" O GLN E 193 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 114 through 116 removed outlier: 3.795A pdb=" N MET E 170 " --> pdb=" O ALA E 228 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA E 228 " --> pdb=" O MET E 170 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU E 227 " --> pdb=" O ARG E 212 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG E 212 " --> pdb=" O GLU E 227 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 165 through 167 Processing sheet with id=AC7, first strand: chain 'E' and resid 216 through 217 removed outlier: 3.790A pdb=" N LYS E 216 " --> pdb=" O PHE E 223 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE E 223 " --> pdb=" O LYS E 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 565 hydrogen bonds defined for protein. 1635 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.20 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4385 1.34 - 1.46: 3523 1.46 - 1.58: 6507 1.58 - 1.70: 0 1.70 - 1.81: 170 Bond restraints: 14585 Sorted by residual: bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.76e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.75e+00 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.75e+00 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.74e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.71e+00 ... (remaining 14580 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 19286 1.34 - 2.67: 354 2.67 - 4.01: 75 4.01 - 5.35: 45 5.35 - 6.69: 15 Bond angle restraints: 19775 Sorted by residual: angle pdb=" CB ABU C 504 " pdb=" CG ABU C 504 " pdb=" CD ABU C 504 " ideal model delta sigma weight residual 116.08 109.39 6.69 3.00e+00 1.11e-01 4.97e+00 angle pdb=" CB ABU B 504 " pdb=" CG ABU B 504 " pdb=" CD ABU B 504 " ideal model delta sigma weight residual 116.08 109.40 6.68 3.00e+00 1.11e-01 4.96e+00 angle pdb=" CB ABU A 504 " pdb=" CG ABU A 504 " pdb=" CD ABU A 504 " ideal model delta sigma weight residual 116.08 109.40 6.68 3.00e+00 1.11e-01 4.95e+00 angle pdb=" CB ABU D 504 " pdb=" CG ABU D 504 " pdb=" CD ABU D 504 " ideal model delta sigma weight residual 116.08 109.43 6.65 3.00e+00 1.11e-01 4.91e+00 angle pdb=" CB ABU E 504 " pdb=" CG ABU E 504 " pdb=" CD ABU E 504 " ideal model delta sigma weight residual 116.08 109.44 6.64 3.00e+00 1.11e-01 4.90e+00 ... (remaining 19770 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.75: 8725 21.75 - 43.50: 150 43.50 - 65.24: 5 65.24 - 86.99: 30 86.99 - 108.74: 20 Dihedral angle restraints: 8930 sinusoidal: 3815 harmonic: 5115 Sorted by residual: dihedral pdb=" CB CYS C 154 " pdb=" SG CYS C 154 " pdb=" SG CYS C 168 " pdb=" CB CYS C 168 " ideal model delta sinusoidal sigma weight residual 93.00 36.38 56.62 1 1.00e+01 1.00e-02 4.32e+01 dihedral pdb=" CB CYS D 154 " pdb=" SG CYS D 154 " pdb=" SG CYS D 168 " pdb=" CB CYS D 168 " ideal model delta sinusoidal sigma weight residual 93.00 36.39 56.61 1 1.00e+01 1.00e-02 4.32e+01 dihedral pdb=" CB CYS E 154 " pdb=" SG CYS E 154 " pdb=" SG CYS E 168 " pdb=" CB CYS E 168 " ideal model delta sinusoidal sigma weight residual 93.00 36.40 56.60 1 1.00e+01 1.00e-02 4.31e+01 ... (remaining 8927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2059 0.078 - 0.156: 196 0.156 - 0.235: 0 0.235 - 0.313: 5 0.313 - 0.391: 5 Chirality restraints: 2265 Sorted by residual: chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-02 2.50e+03 3.82e+02 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-02 2.50e+03 3.80e+02 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-02 2.50e+03 3.80e+02 ... (remaining 2262 not shown) Planarity restraints: 2455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 102 " 0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO D 103 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 410 " 0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO D 411 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO D 411 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 411 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 410 " 0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO C 411 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO C 411 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 411 " 0.016 5.00e-02 4.00e+02 ... (remaining 2452 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4025 2.81 - 3.33: 12257 3.33 - 3.85: 21913 3.85 - 4.38: 27100 4.38 - 4.90: 45477 Nonbonded interactions: 110772 Sorted by model distance: nonbonded pdb=" OG1 THR C 178 " pdb=" OD1 ASN C 180 " model vdw 2.285 3.040 nonbonded pdb=" OG1 THR E 178 " pdb=" OD1 ASN E 180 " model vdw 2.286 3.040 nonbonded pdb=" OG1 THR A 178 " pdb=" OD1 ASN A 180 " model vdw 2.286 3.040 nonbonded pdb=" OG1 THR D 178 " pdb=" OD1 ASN D 180 " model vdw 2.286 3.040 nonbonded pdb=" OG1 THR B 178 " pdb=" OD1 ASN B 180 " model vdw 2.286 3.040 ... (remaining 110767 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 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: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.870 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3725 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.162 14610 Z= 0.207 Angle : 0.756 24.210 19840 Z= 0.321 Chirality : 0.046 0.391 2265 Planarity : 0.003 0.028 2450 Dihedral : 11.125 108.738 5580 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.40 (0.15), residues: 1710 helix: -4.20 (0.11), residues: 465 sheet: -2.53 (0.24), residues: 335 loop : -2.31 (0.17), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 234 TYR 0.004 0.000 TYR D 74 PHE 0.003 0.001 PHE B 258 TRP 0.002 0.000 TRP A 422 HIS 0.001 0.000 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00210 (14585) covalent geometry : angle 0.52608 (19775) SS BOND : bond 0.11439 ( 10) SS BOND : angle 5.75362 ( 20) hydrogen bonds : bond 0.32624 ( 475) hydrogen bonds : angle 10.39129 ( 1635) link_BETA1-4 : bond 0.06465 ( 10) link_BETA1-4 : angle 13.15746 ( 30) link_NAG-ASN : bond 0.00136 ( 5) link_NAG-ASN : angle 0.71023 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 409 time to evaluate : 0.589 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 409 average time/residue: 0.1435 time to fit residues: 81.4030 Evaluate side-chains 242 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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: 8.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 77 ASN A 125 HIS ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 GLN B 62 ASN B 125 HIS B 131 ASN ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 ASN C 77 ASN C 125 HIS D 62 ASN D 77 ASN D 125 HIS D 131 ASN ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 GLN E 62 ASN E 77 ASN E 125 HIS E 131 ASN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.139654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.116130 restraints weight = 50238.439| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 7.37 r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4969 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14610 Z= 0.177 Angle : 0.783 6.682 19840 Z= 0.385 Chirality : 0.049 0.171 2265 Planarity : 0.005 0.040 2450 Dihedral : 9.338 60.183 2200 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.68 % Allowed : 14.00 % Favored : 84.32 % 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: -3.16 (0.17), residues: 1710 helix: -2.30 (0.19), residues: 495 sheet: -1.95 (0.23), residues: 400 loop : -1.92 (0.19), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 147 TYR 0.013 0.002 TYR E 425 PHE 0.038 0.002 PHE E 79 TRP 0.014 0.002 TRP A 302 HIS 0.018 0.004 HIS E 125 Details of bonding type rmsd covalent geometry : bond 0.00389 (14585) covalent geometry : angle 0.76860 (19775) SS BOND : bond 0.00403 ( 10) SS BOND : angle 0.89465 ( 20) hydrogen bonds : bond 0.05508 ( 475) hydrogen bonds : angle 6.16933 ( 1635) link_BETA1-4 : bond 0.00343 ( 10) link_BETA1-4 : angle 3.92873 ( 30) link_NAG-ASN : bond 0.00695 ( 5) link_NAG-ASN : angle 1.06721 ( 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 298 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 272 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.4718 (t80) cc_final: 0.4358 (t80) REVERT: A 119 GLU cc_start: 0.3303 (OUTLIER) cc_final: 0.2818 (tt0) REVERT: A 163 MET cc_start: 0.6943 (mmm) cc_final: 0.6385 (mmm) REVERT: A 171 GLN cc_start: 0.7723 (pt0) cc_final: 0.7192 (pm20) REVERT: A 218 TYR cc_start: 0.4326 (m-80) cc_final: 0.4032 (t80) REVERT: A 243 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.7337 (pmm) REVERT: A 418 ASN cc_start: 0.8662 (t0) cc_final: 0.8395 (m-40) REVERT: B 60 PHE cc_start: 0.4723 (t80) cc_final: 0.4376 (t80) REVERT: B 163 MET cc_start: 0.6921 (mmm) cc_final: 0.6529 (mmm) REVERT: B 171 GLN cc_start: 0.7502 (pt0) cc_final: 0.7054 (pm20) REVERT: B 418 ASN cc_start: 0.8679 (t0) cc_final: 0.8418 (m-40) REVERT: C 34 MET cc_start: 0.1354 (ptm) cc_final: 0.0679 (ptm) REVERT: C 60 PHE cc_start: 0.4654 (t80) cc_final: 0.4439 (t80) REVERT: C 133 LEU cc_start: 0.5718 (tp) cc_final: 0.4867 (tt) REVERT: C 171 GLN cc_start: 0.7680 (pt0) cc_final: 0.7277 (pm20) REVERT: C 418 ASN cc_start: 0.8654 (t0) cc_final: 0.8398 (m-40) REVERT: D 60 PHE cc_start: 0.4699 (t80) cc_final: 0.4432 (t80) REVERT: D 131 ASN cc_start: 0.6421 (m110) cc_final: 0.6104 (t0) REVERT: D 171 GLN cc_start: 0.7640 (pt0) cc_final: 0.7197 (pm20) REVERT: D 236 MET cc_start: 0.7745 (mpp) cc_final: 0.7450 (mpp) REVERT: D 243 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.7411 (pmm) REVERT: D 418 ASN cc_start: 0.8655 (t0) cc_final: 0.8348 (m-40) REVERT: E 171 GLN cc_start: 0.7675 (pt0) cc_final: 0.7124 (pm20) REVERT: E 243 MET cc_start: 0.7514 (OUTLIER) cc_final: 0.7271 (pmm) REVERT: E 418 ASN cc_start: 0.8659 (t0) cc_final: 0.8340 (m-40) outliers start: 26 outliers final: 11 residues processed: 288 average time/residue: 0.1097 time to fit residues: 47.2740 Evaluate side-chains 210 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 195 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 243 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.0570 chunk 146 optimal weight: 0.9980 chunk 140 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 chunk 167 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 overall best weight: 1.1500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN B 141 ASN B 171 GLN C 77 ASN C 83 GLN C 141 ASN D 77 ASN D 141 ASN E 77 ASN E 141 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.138155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.114996 restraints weight = 51987.466| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 7.84 r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5157 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14610 Z= 0.139 Angle : 0.775 8.936 19840 Z= 0.366 Chirality : 0.046 0.207 2265 Planarity : 0.004 0.035 2450 Dihedral : 7.422 58.738 2200 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.84 % Allowed : 14.71 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.18), residues: 1710 helix: -1.40 (0.21), residues: 525 sheet: -1.52 (0.23), residues: 430 loop : -1.99 (0.19), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 147 TYR 0.029 0.002 TYR A 317 PHE 0.024 0.002 PHE C 414 TRP 0.011 0.001 TRP C 84 HIS 0.003 0.001 HIS E 217 Details of bonding type rmsd covalent geometry : bond 0.00299 (14585) covalent geometry : angle 0.76018 (19775) SS BOND : bond 0.00228 ( 10) SS BOND : angle 0.80561 ( 20) hydrogen bonds : bond 0.04691 ( 475) hydrogen bonds : angle 5.37324 ( 1635) link_BETA1-4 : bond 0.00418 ( 10) link_BETA1-4 : angle 3.85862 ( 30) link_NAG-ASN : bond 0.00300 ( 5) link_NAG-ASN : angle 1.06572 ( 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 257 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 213 time to evaluate : 0.516 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: A 101 LEU cc_start: 0.0310 (OUTLIER) cc_final: -0.0957 (mt) REVERT: A 171 GLN cc_start: 0.7999 (pt0) cc_final: 0.7340 (pm20) REVERT: A 243 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7573 (pmm) REVERT: A 418 ASN cc_start: 0.8711 (t0) cc_final: 0.8260 (m-40) REVERT: B 101 LEU cc_start: 0.1086 (OUTLIER) cc_final: 0.0462 (mt) REVERT: B 133 LEU cc_start: 0.5878 (tp) cc_final: 0.5066 (tt) REVERT: B 163 MET cc_start: 0.6821 (mmm) cc_final: 0.6533 (mmm) REVERT: B 171 GLN cc_start: 0.7889 (pt0) cc_final: 0.7098 (pm20) REVERT: B 418 ASN cc_start: 0.8655 (t0) cc_final: 0.8162 (m-40) REVERT: C 106 LEU cc_start: 0.4268 (OUTLIER) cc_final: 0.3893 (mm) REVERT: C 171 GLN cc_start: 0.7875 (pt0) cc_final: 0.7228 (pm20) REVERT: C 418 ASN cc_start: 0.8659 (t0) cc_final: 0.8166 (m-40) REVERT: D 101 LEU cc_start: 0.1384 (OUTLIER) cc_final: 0.0683 (mt) REVERT: D 171 GLN cc_start: 0.7851 (pt0) cc_final: 0.7163 (pm20) REVERT: D 236 MET cc_start: 0.7946 (mpp) cc_final: 0.7636 (mpp) REVERT: D 243 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7543 (pmm) REVERT: D 418 ASN cc_start: 0.8611 (t0) cc_final: 0.8102 (m-40) REVERT: E 101 LEU cc_start: 0.0779 (OUTLIER) cc_final: -0.0533 (mt) REVERT: E 163 MET cc_start: 0.6801 (mmm) cc_final: 0.6557 (mmm) REVERT: E 171 GLN cc_start: 0.7872 (pt0) cc_final: 0.7079 (pm20) REVERT: E 243 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7569 (pmm) REVERT: E 418 ASN cc_start: 0.8681 (t0) cc_final: 0.8169 (m-40) outliers start: 44 outliers final: 16 residues processed: 242 average time/residue: 0.1006 time to fit residues: 37.6122 Evaluate side-chains 216 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 84 TRP Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain E residue 84 TRP Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 243 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 3 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 153 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 chunk 42 optimal weight: 0.0980 chunk 165 optimal weight: 1.9990 chunk 41 optimal weight: 40.0000 chunk 151 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 GLN A 131 ASN ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN B 131 ASN ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN D 171 GLN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 GLN E 171 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.134350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.110235 restraints weight = 54732.666| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 7.96 r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5651 moved from start: 0.7209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 14610 Z= 0.164 Angle : 0.773 10.241 19840 Z= 0.374 Chirality : 0.046 0.216 2265 Planarity : 0.004 0.055 2450 Dihedral : 5.722 46.446 2200 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.29 % Allowed : 15.42 % Favored : 81.29 % 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: -2.09 (0.19), residues: 1710 helix: -0.72 (0.23), residues: 520 sheet: -1.12 (0.25), residues: 410 loop : -1.94 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 268 TYR 0.027 0.002 TYR C 175 PHE 0.022 0.002 PHE B 161 TRP 0.014 0.002 TRP B 302 HIS 0.009 0.002 HIS A 217 Details of bonding type rmsd covalent geometry : bond 0.00364 (14585) covalent geometry : angle 0.76170 (19775) SS BOND : bond 0.00408 ( 10) SS BOND : angle 1.04040 ( 20) hydrogen bonds : bond 0.04037 ( 475) hydrogen bonds : angle 4.86578 ( 1635) link_BETA1-4 : bond 0.00402 ( 10) link_BETA1-4 : angle 3.31062 ( 30) link_NAG-ASN : bond 0.00452 ( 5) link_NAG-ASN : angle 1.57544 ( 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 285 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 234 time to evaluate : 0.513 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: A 156 MET cc_start: 0.7541 (mmt) cc_final: 0.6933 (mmm) REVERT: A 171 GLN cc_start: 0.8064 (pt0) cc_final: 0.7202 (pm20) REVERT: A 202 GLN cc_start: 0.7583 (pm20) cc_final: 0.6565 (mp-120) REVERT: A 243 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.8080 (pmm) REVERT: A 418 ASN cc_start: 0.8748 (t0) cc_final: 0.8345 (m110) REVERT: B 34 MET cc_start: 0.5363 (ptt) cc_final: 0.5092 (mpp) REVERT: B 86 ASP cc_start: 0.5818 (OUTLIER) cc_final: 0.5567 (t0) REVERT: B 133 LEU cc_start: 0.6689 (tp) cc_final: 0.6197 (tt) REVERT: B 163 MET cc_start: 0.7318 (mmm) cc_final: 0.7100 (mmm) REVERT: B 171 GLN cc_start: 0.7815 (pt0) cc_final: 0.6987 (pm20) REVERT: B 208 GLU cc_start: 0.7417 (tp30) cc_final: 0.6937 (tp30) REVERT: B 418 ASN cc_start: 0.8755 (t0) cc_final: 0.8351 (m110) REVERT: C 141 ASN cc_start: 0.7203 (OUTLIER) cc_final: 0.6933 (m-40) REVERT: C 156 MET cc_start: 0.8015 (mmm) cc_final: 0.7540 (mmm) REVERT: C 163 MET cc_start: 0.7208 (mmm) cc_final: 0.6889 (mmm) REVERT: C 171 GLN cc_start: 0.8148 (pt0) cc_final: 0.7120 (pm20) REVERT: C 418 ASN cc_start: 0.8801 (t0) cc_final: 0.8427 (m110) REVERT: D 86 ASP cc_start: 0.5597 (OUTLIER) cc_final: 0.5273 (t0) REVERT: D 133 LEU cc_start: 0.6487 (tt) cc_final: 0.5921 (tt) REVERT: D 156 MET cc_start: 0.7463 (mmt) cc_final: 0.6845 (mmm) REVERT: D 163 MET cc_start: 0.7510 (mmm) cc_final: 0.7205 (mmm) REVERT: D 171 GLN cc_start: 0.8103 (pt0) cc_final: 0.7136 (pm20) REVERT: D 236 MET cc_start: 0.7972 (mpp) cc_final: 0.7767 (mpp) REVERT: D 243 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7989 (pmm) REVERT: D 418 ASN cc_start: 0.8719 (t0) cc_final: 0.8305 (m110) REVERT: E 86 ASP cc_start: 0.5933 (OUTLIER) cc_final: 0.5705 (t0) REVERT: E 125 HIS cc_start: 0.4054 (m90) cc_final: 0.3746 (m90) REVERT: E 133 LEU cc_start: 0.6435 (tt) cc_final: 0.6011 (tt) REVERT: E 141 ASN cc_start: 0.7186 (OUTLIER) cc_final: 0.6822 (m-40) REVERT: E 142 VAL cc_start: 0.7263 (t) cc_final: 0.6717 (t) REVERT: E 171 GLN cc_start: 0.8094 (pt0) cc_final: 0.7070 (pm20) REVERT: E 202 GLN cc_start: 0.7805 (pm20) cc_final: 0.7324 (pm20) REVERT: E 243 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7988 (pmm) REVERT: E 418 ASN cc_start: 0.8723 (t0) cc_final: 0.8292 (m110) outliers start: 51 outliers final: 32 residues processed: 273 average time/residue: 0.0912 time to fit residues: 39.8886 Evaluate side-chains 248 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 208 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 391 MET Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 243 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 95 optimal weight: 0.0370 chunk 24 optimal weight: 7.9990 chunk 153 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 7 optimal weight: 30.0000 chunk 163 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 overall best weight: 3.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 ASN ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 GLN ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** 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 = 0.4241 r_free = 0.4241 target = 0.127902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.103423 restraints weight = 48764.587| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 7.67 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6334 moved from start: 0.9875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.128 14610 Z= 0.259 Angle : 0.922 12.513 19840 Z= 0.457 Chirality : 0.051 0.335 2265 Planarity : 0.005 0.080 2450 Dihedral : 6.395 56.368 2200 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.26 % Allowed : 16.58 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.20), residues: 1710 helix: -0.58 (0.23), residues: 520 sheet: -0.70 (0.28), residues: 385 loop : -1.48 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 268 TYR 0.028 0.003 TYR E 317 PHE 0.040 0.003 PHE B 29 TRP 0.016 0.002 TRP C 84 HIS 0.010 0.003 HIS B 217 Details of bonding type rmsd covalent geometry : bond 0.00590 (14585) covalent geometry : angle 0.90161 (19775) SS BOND : bond 0.00783 ( 10) SS BOND : angle 4.87310 ( 20) hydrogen bonds : bond 0.04898 ( 475) hydrogen bonds : angle 5.11371 ( 1635) link_BETA1-4 : bond 0.00810 ( 10) link_BETA1-4 : angle 2.88545 ( 30) link_NAG-ASN : bond 0.00075 ( 5) link_NAG-ASN : angle 2.36851 ( 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 332 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 266 time to evaluate : 0.530 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: symmetry clash REVERT: A 151 VAL cc_start: 0.7260 (OUTLIER) cc_final: 0.7054 (m) REVERT: A 156 MET cc_start: 0.8216 (mmt) cc_final: 0.7649 (mmm) REVERT: A 171 GLN cc_start: 0.8537 (pt0) cc_final: 0.7313 (pm20) REVERT: A 173 GLU cc_start: 0.7017 (mt-10) cc_final: 0.6773 (mt-10) REVERT: A 229 ARG cc_start: 0.7717 (mtt-85) cc_final: 0.7441 (mtp85) REVERT: A 243 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8641 (pmm) REVERT: A 418 ASN cc_start: 0.8942 (t0) cc_final: 0.8632 (m110) REVERT: B 151 VAL cc_start: 0.7162 (OUTLIER) cc_final: 0.6952 (m) REVERT: B 171 GLN cc_start: 0.8518 (pt0) cc_final: 0.7236 (pm20) REVERT: B 173 GLU cc_start: 0.7019 (mt-10) cc_final: 0.6768 (mt-10) REVERT: B 418 ASN cc_start: 0.8932 (t0) cc_final: 0.8658 (m110) REVERT: C 142 VAL cc_start: 0.8154 (t) cc_final: 0.7846 (m) REVERT: C 156 MET cc_start: 0.8483 (mmm) cc_final: 0.8078 (mmp) REVERT: C 171 GLN cc_start: 0.8657 (pt0) cc_final: 0.7427 (pm20) REVERT: C 418 ASN cc_start: 0.8958 (t0) cc_final: 0.8665 (m110) REVERT: D 82 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7789 (tm-30) REVERT: D 142 VAL cc_start: 0.8194 (t) cc_final: 0.7406 (m) REVERT: D 156 MET cc_start: 0.8247 (mmt) cc_final: 0.7680 (mmm) REVERT: D 171 GLN cc_start: 0.8542 (pt0) cc_final: 0.7039 (pm20) REVERT: D 236 MET cc_start: 0.8290 (mpp) cc_final: 0.8063 (mpp) REVERT: D 243 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8648 (pmm) REVERT: D 418 ASN cc_start: 0.8922 (t0) cc_final: 0.8614 (m110) REVERT: E 34 MET cc_start: 0.6985 (ptt) cc_final: 0.6695 (mtm) REVERT: E 82 GLN cc_start: 0.8200 (tm-30) cc_final: 0.7991 (tm-30) REVERT: E 142 VAL cc_start: 0.8007 (t) cc_final: 0.7393 (t) REVERT: E 171 GLN cc_start: 0.8560 (pt0) cc_final: 0.7267 (pm20) REVERT: E 173 GLU cc_start: 0.7069 (mt-10) cc_final: 0.6681 (mt-10) REVERT: E 243 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8594 (pmm) REVERT: E 418 ASN cc_start: 0.8986 (t0) cc_final: 0.8669 (m110) outliers start: 66 outliers final: 40 residues processed: 322 average time/residue: 0.0903 time to fit residues: 46.0874 Evaluate side-chains 283 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 238 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 131 ASN Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 17 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 121 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 7 optimal weight: 30.0000 chunk 35 optimal weight: 9.9990 chunk 160 optimal weight: 20.0000 chunk 167 optimal weight: 4.9990 chunk 75 optimal weight: 30.0000 chunk 39 optimal weight: 4.9990 chunk 41 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 ASN ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN D 141 ASN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.113257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.088647 restraints weight = 48886.462| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 7.01 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 1.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.131 14610 Z= 0.344 Angle : 1.158 14.471 19840 Z= 0.581 Chirality : 0.058 0.268 2265 Planarity : 0.008 0.137 2450 Dihedral : 7.616 48.514 2200 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 21.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 5.10 % Allowed : 17.81 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.25 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.20), residues: 1710 helix: -1.14 (0.21), residues: 520 sheet: -0.94 (0.26), residues: 405 loop : -1.77 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 147 TYR 0.053 0.003 TYR A 317 PHE 0.037 0.003 PHE B 161 TRP 0.018 0.002 TRP C 84 HIS 0.023 0.005 HIS C 217 Details of bonding type rmsd covalent geometry : bond 0.00793 (14585) covalent geometry : angle 1.14376 (19775) SS BOND : bond 0.02750 ( 10) SS BOND : angle 4.33815 ( 20) hydrogen bonds : bond 0.06073 ( 475) hydrogen bonds : angle 5.86101 ( 1635) link_BETA1-4 : bond 0.00452 ( 10) link_BETA1-4 : angle 2.45445 ( 30) link_NAG-ASN : bond 0.00512 ( 5) link_NAG-ASN : angle 3.30054 ( 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 336 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 257 time to evaluate : 0.505 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ASP cc_start: 0.8061 (t0) cc_final: 0.7855 (t0) REVERT: A 119 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7968 (tt0) REVERT: A 130 ASP cc_start: 0.7240 (p0) cc_final: 0.6938 (p0) REVERT: A 171 GLN cc_start: 0.8744 (pt0) cc_final: 0.8214 (tt0) REVERT: A 179 MET cc_start: 0.7803 (mmm) cc_final: 0.7451 (mmm) REVERT: A 202 GLN cc_start: 0.8552 (pm20) cc_final: 0.8081 (mp10) REVERT: B 24 MET cc_start: 0.4159 (OUTLIER) cc_final: 0.3448 (tmm) REVERT: B 105 MET cc_start: 0.5996 (tmm) cc_final: 0.5558 (tmm) REVERT: B 119 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7696 (tm-30) REVERT: B 144 TYR cc_start: 0.8015 (t80) cc_final: 0.7780 (t80) REVERT: B 156 MET cc_start: 0.8145 (mmt) cc_final: 0.7816 (mmp) REVERT: B 242 GLN cc_start: 0.8174 (tt0) cc_final: 0.7829 (tm-30) REVERT: C 202 GLN cc_start: 0.8816 (pm20) cc_final: 0.8293 (pm20) REVERT: C 242 GLN cc_start: 0.8225 (tt0) cc_final: 0.7982 (tm-30) REVERT: D 34 MET cc_start: 0.7962 (ptt) cc_final: 0.7484 (mtm) REVERT: D 156 MET cc_start: 0.8692 (mmt) cc_final: 0.8341 (mmm) REVERT: D 202 GLN cc_start: 0.8601 (pm20) cc_final: 0.8160 (mp10) REVERT: D 243 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8554 (mmm) REVERT: E 24 MET cc_start: 0.5314 (ttt) cc_final: 0.3281 (ttt) REVERT: E 105 MET cc_start: 0.5269 (tmm) cc_final: 0.4885 (tmm) REVERT: E 202 GLN cc_start: 0.8786 (pm20) cc_final: 0.8359 (pm20) REVERT: E 243 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8572 (mmm) outliers start: 79 outliers final: 43 residues processed: 316 average time/residue: 0.0942 time to fit residues: 46.0792 Evaluate side-chains 266 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 218 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 168 CYS Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 19 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 111 optimal weight: 0.9980 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN C 58 ASN C 77 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 ASN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 ASN D 418 ASN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 ASN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 418 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.107497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.082517 restraints weight = 50492.040| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 6.76 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 1.5780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14610 Z= 0.219 Angle : 0.910 12.338 19840 Z= 0.436 Chirality : 0.049 0.285 2265 Planarity : 0.005 0.048 2450 Dihedral : 6.718 59.599 2200 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.23 % Allowed : 21.61 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.20), residues: 1710 helix: -0.74 (0.22), residues: 530 sheet: -0.69 (0.27), residues: 360 loop : -1.63 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 45 TYR 0.022 0.002 TYR B 144 PHE 0.019 0.002 PHE E 48 TRP 0.014 0.002 TRP C 84 HIS 0.014 0.002 HIS A 217 Details of bonding type rmsd covalent geometry : bond 0.00496 (14585) covalent geometry : angle 0.89932 (19775) SS BOND : bond 0.00550 ( 10) SS BOND : angle 2.92280 ( 20) hydrogen bonds : bond 0.04942 ( 475) hydrogen bonds : angle 5.20537 ( 1635) link_BETA1-4 : bond 0.00494 ( 10) link_BETA1-4 : angle 2.15579 ( 30) link_NAG-ASN : bond 0.00146 ( 5) link_NAG-ASN : angle 2.99120 ( 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 290 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 240 time to evaluate : 0.552 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.8075 (p0) cc_final: 0.7608 (p0) REVERT: A 179 MET cc_start: 0.8256 (mmm) cc_final: 0.8021 (mmm) REVERT: A 202 GLN cc_start: 0.8722 (pm20) cc_final: 0.8430 (mp10) REVERT: A 236 MET cc_start: 0.8535 (mmm) cc_final: 0.8276 (mmp) REVERT: B 59 ILE cc_start: 0.8924 (mp) cc_final: 0.8693 (mm) REVERT: B 120 LYS cc_start: 0.9261 (ttmm) cc_final: 0.9022 (ttmm) REVERT: B 173 GLU cc_start: 0.6857 (pm20) cc_final: 0.6500 (pm20) REVERT: B 242 GLN cc_start: 0.8136 (tt0) cc_final: 0.7776 (tm-30) REVERT: C 24 MET cc_start: 0.4439 (tmm) cc_final: 0.3185 (tmm) REVERT: C 106 LEU cc_start: 0.8661 (mm) cc_final: 0.8350 (mm) REVERT: C 202 GLN cc_start: 0.8842 (pm20) cc_final: 0.8345 (pm20) REVERT: C 242 GLN cc_start: 0.8275 (tt0) cc_final: 0.7925 (tm-30) REVERT: D 24 MET cc_start: 0.5001 (tmm) cc_final: 0.4308 (tmm) REVERT: D 34 MET cc_start: 0.8186 (ptt) cc_final: 0.7892 (mtm) REVERT: D 156 MET cc_start: 0.8877 (mmm) cc_final: 0.8614 (mmm) REVERT: D 242 GLN cc_start: 0.8622 (tt0) cc_final: 0.8150 (mt0) REVERT: D 243 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8553 (mmm) REVERT: E 24 MET cc_start: 0.4595 (ttt) cc_final: 0.4138 (ttt) REVERT: E 60 PHE cc_start: 0.6099 (t80) cc_final: 0.5322 (t80) REVERT: E 105 MET cc_start: 0.6031 (tmm) cc_final: 0.5775 (tmm) REVERT: E 130 ASP cc_start: 0.8746 (m-30) cc_final: 0.8102 (p0) REVERT: E 202 GLN cc_start: 0.8774 (pm20) cc_final: 0.8304 (pm20) REVERT: E 243 MET cc_start: 0.9112 (OUTLIER) cc_final: 0.8654 (mmm) outliers start: 50 outliers final: 30 residues processed: 273 average time/residue: 0.0977 time to fit residues: 40.8390 Evaluate side-chains 229 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 197 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 60 optimal weight: 0.0050 chunk 143 optimal weight: 0.0040 chunk 27 optimal weight: 0.7980 chunk 132 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 142 optimal weight: 0.9980 chunk 58 optimal weight: 8.9990 chunk 113 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.4606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 GLN ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN E 242 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.110196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.085019 restraints weight = 51215.808| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 6.98 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 1.5969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14610 Z= 0.140 Angle : 0.883 16.614 19840 Z= 0.411 Chirality : 0.048 0.265 2265 Planarity : 0.004 0.053 2450 Dihedral : 6.085 55.746 2200 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.71 % Allowed : 23.48 % Favored : 73.81 % 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: -1.41 (0.21), residues: 1710 helix: -0.44 (0.23), residues: 530 sheet: -0.41 (0.26), residues: 405 loop : -1.52 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG E 45 TYR 0.018 0.001 TYR C 94 PHE 0.019 0.002 PHE E 60 TRP 0.021 0.002 TRP B 84 HIS 0.007 0.001 HIS E 217 Details of bonding type rmsd covalent geometry : bond 0.00312 (14585) covalent geometry : angle 0.87354 (19775) SS BOND : bond 0.00360 ( 10) SS BOND : angle 2.54084 ( 20) hydrogen bonds : bond 0.04209 ( 475) hydrogen bonds : angle 4.70350 ( 1635) link_BETA1-4 : bond 0.00534 ( 10) link_BETA1-4 : angle 2.09377 ( 30) link_NAG-ASN : bond 0.00136 ( 5) link_NAG-ASN : angle 2.67303 ( 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 256 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 214 time to evaluate : 0.525 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: 0.8256 (mmm) cc_final: 0.8017 (mmm) REVERT: A 202 GLN cc_start: 0.8671 (pm20) cc_final: 0.8322 (mp10) REVERT: B 59 ILE cc_start: 0.8905 (mp) cc_final: 0.8675 (mm) REVERT: B 173 GLU cc_start: 0.6919 (pm20) cc_final: 0.6714 (pm20) REVERT: B 236 MET cc_start: 0.8364 (mpp) cc_final: 0.8097 (mpp) REVERT: B 243 MET cc_start: 0.8842 (pmm) cc_final: 0.8561 (mmm) REVERT: C 202 GLN cc_start: 0.8812 (pm20) cc_final: 0.8323 (pm20) REVERT: C 243 MET cc_start: 0.8878 (pmm) cc_final: 0.8656 (mmm) REVERT: C 287 ARG cc_start: 0.8963 (mtm-85) cc_final: 0.8626 (ptp90) REVERT: D 34 MET cc_start: 0.8189 (ptt) cc_final: 0.7915 (mtm) REVERT: D 156 MET cc_start: 0.8783 (mmm) cc_final: 0.8473 (mmm) REVERT: D 171 GLN cc_start: 0.8975 (pt0) cc_final: 0.8604 (pt0) REVERT: D 236 MET cc_start: 0.8295 (mpp) cc_final: 0.7959 (mpp) REVERT: D 243 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8377 (mmm) REVERT: D 287 ARG cc_start: 0.8991 (mtm-85) cc_final: 0.8719 (ptp-170) REVERT: E 24 MET cc_start: 0.4698 (ttt) cc_final: 0.4268 (ttt) REVERT: E 119 GLU cc_start: 0.8544 (tt0) cc_final: 0.8180 (tt0) REVERT: E 156 MET cc_start: 0.8622 (mmm) cc_final: 0.8251 (mmm) REVERT: E 179 MET cc_start: 0.8364 (tpp) cc_final: 0.7933 (mpp) REVERT: E 202 GLN cc_start: 0.8756 (pm20) cc_final: 0.8349 (pm20) REVERT: E 242 GLN cc_start: 0.9024 (mm-40) cc_final: 0.8808 (mm110) REVERT: E 243 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8434 (mmm) REVERT: E 287 ARG cc_start: 0.9131 (mtm180) cc_final: 0.8467 (mtm-85) outliers start: 42 outliers final: 24 residues processed: 242 average time/residue: 0.0930 time to fit residues: 35.5679 Evaluate side-chains 225 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 199 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 75 optimal weight: 8.9990 chunk 113 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 GLN ** 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 = 0.3930 r_free = 0.3930 target = 0.105740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.080504 restraints weight = 51324.124| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 6.76 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 1.6783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14610 Z= 0.175 Angle : 0.867 14.855 19840 Z= 0.413 Chirality : 0.046 0.243 2265 Planarity : 0.004 0.051 2450 Dihedral : 6.161 58.576 2200 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.00 % Allowed : 24.26 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.21), residues: 1710 helix: -0.33 (0.23), residues: 530 sheet: -0.42 (0.26), residues: 395 loop : -1.41 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 45 TYR 0.018 0.002 TYR B 144 PHE 0.032 0.002 PHE D 60 TRP 0.018 0.002 TRP B 84 HIS 0.003 0.001 HIS E 217 Details of bonding type rmsd covalent geometry : bond 0.00392 (14585) covalent geometry : angle 0.85885 (19775) SS BOND : bond 0.00340 ( 10) SS BOND : angle 2.34317 ( 20) hydrogen bonds : bond 0.04435 ( 475) hydrogen bonds : angle 4.79191 ( 1635) link_BETA1-4 : bond 0.00560 ( 10) link_BETA1-4 : angle 2.08133 ( 30) link_NAG-ASN : bond 0.00152 ( 5) link_NAG-ASN : angle 2.39348 ( 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 227 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 196 time to evaluate : 0.539 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: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.5150 (ttt) cc_final: 0.4407 (tmm) REVERT: A 179 MET cc_start: 0.8339 (mmm) cc_final: 0.8061 (mmm) REVERT: A 202 GLN cc_start: 0.8698 (pm20) cc_final: 0.8324 (mp10) REVERT: A 287 ARG cc_start: 0.8836 (mtm-85) cc_final: 0.8225 (mtm-85) REVERT: B 59 ILE cc_start: 0.8989 (mp) cc_final: 0.8737 (mm) REVERT: B 151 VAL cc_start: 0.8790 (OUTLIER) cc_final: 0.8181 (m) REVERT: C 236 MET cc_start: 0.8226 (mpp) cc_final: 0.7925 (mpp) REVERT: D 24 MET cc_start: 0.5541 (tmm) cc_final: 0.5267 (tmm) REVERT: D 105 MET cc_start: 0.6617 (tmm) cc_final: 0.6294 (tmm) REVERT: D 156 MET cc_start: 0.8675 (mmm) cc_final: 0.8364 (mmm) REVERT: D 171 GLN cc_start: 0.9006 (pt0) cc_final: 0.8690 (pt0) REVERT: D 243 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8582 (mmm) REVERT: D 287 ARG cc_start: 0.8894 (mtm-85) cc_final: 0.8440 (mpp80) REVERT: E 24 MET cc_start: 0.5015 (ttt) cc_final: 0.4431 (ttt) REVERT: E 105 MET cc_start: 0.6506 (tmm) cc_final: 0.6131 (tmm) REVERT: E 179 MET cc_start: 0.8583 (tpp) cc_final: 0.7883 (mmm) REVERT: E 202 GLN cc_start: 0.8776 (pm20) cc_final: 0.8339 (pm20) REVERT: E 242 GLN cc_start: 0.9033 (mm-40) cc_final: 0.8762 (mm110) REVERT: E 243 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8564 (mmm) outliers start: 31 outliers final: 22 residues processed: 217 average time/residue: 0.0916 time to fit residues: 32.0205 Evaluate side-chains 214 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 139 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 148 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 65 optimal weight: 8.9990 chunk 1 optimal weight: 20.0000 chunk 99 optimal weight: 9.9990 chunk 126 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 64 optimal weight: 0.0970 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 GLN ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.105444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.080375 restraints weight = 50609.938| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 6.59 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 1.7380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14610 Z= 0.159 Angle : 0.873 21.757 19840 Z= 0.411 Chirality : 0.047 0.250 2265 Planarity : 0.004 0.049 2450 Dihedral : 5.994 58.553 2200 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.00 % Allowed : 24.65 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.21), residues: 1710 helix: -0.39 (0.23), residues: 555 sheet: -0.55 (0.25), residues: 425 loop : -1.22 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 45 TYR 0.023 0.002 TYR E 218 PHE 0.050 0.002 PHE D 60 TRP 0.017 0.001 TRP B 84 HIS 0.009 0.001 HIS E 217 Details of bonding type rmsd covalent geometry : bond 0.00366 (14585) covalent geometry : angle 0.86504 (19775) SS BOND : bond 0.00403 ( 10) SS BOND : angle 2.35837 ( 20) hydrogen bonds : bond 0.04369 ( 475) hydrogen bonds : angle 4.69161 ( 1635) link_BETA1-4 : bond 0.00603 ( 10) link_BETA1-4 : angle 2.01708 ( 30) link_NAG-ASN : bond 0.00043 ( 5) link_NAG-ASN : angle 2.44657 ( 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 222 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 191 time to evaluate : 0.476 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.5626 (ttt) cc_final: 0.5110 (tmm) REVERT: A 179 MET cc_start: 0.8442 (mmm) cc_final: 0.8150 (mmm) REVERT: A 202 GLN cc_start: 0.8716 (pm20) cc_final: 0.8470 (mp10) REVERT: A 262 MET cc_start: 0.1147 (mmm) cc_final: 0.0915 (tpt) REVERT: A 287 ARG cc_start: 0.8884 (mtm-85) cc_final: 0.8441 (ptp90) REVERT: B 24 MET cc_start: 0.5061 (tmm) cc_final: 0.4644 (tmm) REVERT: B 59 ILE cc_start: 0.8985 (mp) cc_final: 0.8712 (mm) REVERT: B 145 SER cc_start: 0.9245 (OUTLIER) cc_final: 0.8287 (t) REVERT: C 166 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8384 (mm-40) REVERT: C 236 MET cc_start: 0.8349 (mpp) cc_final: 0.8054 (mpp) REVERT: D 243 MET cc_start: 0.9196 (OUTLIER) cc_final: 0.8619 (mmm) REVERT: E 24 MET cc_start: 0.5405 (ttt) cc_final: 0.4707 (ttt) REVERT: E 69 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8168 (mm-30) REVERT: E 179 MET cc_start: 0.8593 (tpp) cc_final: 0.7865 (mmm) REVERT: E 202 GLN cc_start: 0.8844 (pm20) cc_final: 0.8436 (pm20) REVERT: E 243 MET cc_start: 0.9092 (OUTLIER) cc_final: 0.8685 (mmm) outliers start: 31 outliers final: 25 residues processed: 212 average time/residue: 0.0921 time to fit residues: 31.3397 Evaluate side-chains 210 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 391 MET Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 154 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 30 optimal weight: 40.0000 chunk 105 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 119 optimal weight: 0.5980 chunk 18 optimal weight: 7.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 GLN ** C 242 GLN ** 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 83 GLN ** 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 = 0.3914 r_free = 0.3914 target = 0.104417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.079351 restraints weight = 50183.958| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 6.60 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 1.7390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.199 14610 Z= 0.242 Angle : 1.022 59.200 19840 Z= 0.534 Chirality : 0.050 0.843 2265 Planarity : 0.004 0.048 2450 Dihedral : 5.990 58.506 2200 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.94 % Allowed : 25.16 % Favored : 72.90 % Cbeta Deviations : 0.06 % 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: -1.25 (0.21), residues: 1710 helix: -0.39 (0.23), residues: 555 sheet: -0.54 (0.25), residues: 425 loop : -1.22 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 45 TYR 0.018 0.001 TYR E 218 PHE 0.045 0.002 PHE D 60 TRP 0.015 0.001 TRP B 84 HIS 0.006 0.001 HIS E 217 Details of bonding type rmsd covalent geometry : bond 0.00530 (14585) covalent geometry : angle 1.01559 (19775) SS BOND : bond 0.00351 ( 10) SS BOND : angle 2.34718 ( 20) hydrogen bonds : bond 0.04381 ( 475) hydrogen bonds : angle 4.67591 ( 1635) link_BETA1-4 : bond 0.00606 ( 10) link_BETA1-4 : angle 2.01826 ( 30) link_NAG-ASN : bond 0.00066 ( 5) link_NAG-ASN : angle 2.43750 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2555.56 seconds wall clock time: 44 minutes 47.95 seconds (2687.95 seconds total)