Starting phenix.real_space_refine on Mon Jul 6 11:01:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mgz_23831/07_2026/7mgz_23831_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mgz_23831/07_2026/7mgz_23831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mgz_23831/07_2026/7mgz_23831_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mgz_23831/07_2026/7mgz_23831_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mgz_23831/07_2026/7mgz_23831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mgz_23831/07_2026/7mgz_23831.map" } resolution = 2.8 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= 0.263 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: 7 Type Number sf(0) Gaussians P 24 5.49 5 Mg 8 5.21 5 S 92 5.16 5 C 11104 2.51 5 N 2992 2.21 5 O 3316 1.98 5 H 17316 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34852 Number of models: 1 Model: "" Number of chains: 8 Chain: "F" Number of atoms: 8631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 8631 Classifications: {'peptide': 542} Modifications used: {'ACID-GLU': 2, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 513} Chain breaks: 2 Chain: "O" Number of atoms: 8631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 8631 Classifications: {'peptide': 542} Modifications used: {'ACID-GLU': 2, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 513} Chain breaks: 2 Chain: "P" Number of atoms: 8631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 8631 Classifications: {'peptide': 542} Modifications used: {'ACID-GLU': 2, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 513} Chain breaks: 2 Chain: "Q" Number of atoms: 8631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 8631 Classifications: {'peptide': 542} Modifications used: {'ACID-GLU': 2, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 513} Chain breaks: 2 Chain: "F" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 82 Unusual residues: {' MG': 2, 'ANP': 1, 'UTP': 1} Inner-chain residues flagged as termini: ['pdbres="GLN F 602 "'] Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 4} Chain: "O" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 82 Unusual residues: {' MG': 2, 'ANP': 1, 'UTP': 1} Inner-chain residues flagged as termini: ['pdbres="GLN O 602 "'] Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 4} Chain: "P" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 82 Unusual residues: {' MG': 2, 'ANP': 1, 'UTP': 1} Inner-chain residues flagged as termini: ['pdbres="GLN P 603 "'] Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 4} Chain: "Q" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 82 Unusual residues: {' MG': 2, 'ANP': 1, 'UTP': 1} Inner-chain residues flagged as termini: ['pdbres="GLN Q 603 "'] Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 4} Time building chain proxies: 5.27, per 1000 atoms: 0.15 Number of scatterers: 34852 At special positions: 0 Unit cell: (127.05, 135.45, 87.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 92 16.00 P 24 15.00 Mg 8 11.99 O 3316 8.00 N 2992 7.00 C 11104 6.00 H 17316 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 2.67 Conformation dependent library (CDL) restraints added in 714.0 milliseconds 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4016 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 16 sheets defined 47.0% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'F' and resid 15 through 30 Processing helix chain 'F' and resid 69 through 79 Processing helix chain 'F' and resid 83 through 85 No H-bonds generated for 'chain 'F' and resid 83 through 85' Processing helix chain 'F' and resid 90 through 103 Processing helix chain 'F' and resid 115 through 130 Processing helix chain 'F' and resid 156 through 170 removed outlier: 4.573A pdb=" N PHE F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 173 No H-bonds generated for 'chain 'F' and resid 171 through 173' Processing helix chain 'F' and resid 194 through 207 Processing helix chain 'F' and resid 223 through 235 Processing helix chain 'F' and resid 237 through 239 No H-bonds generated for 'chain 'F' and resid 237 through 239' Processing helix chain 'F' and resid 251 through 261 removed outlier: 4.450A pdb=" N LEU F 255 " --> pdb=" O TYR F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 270 removed outlier: 4.156A pdb=" N ARG F 268 " --> pdb=" O ASP F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 295 removed outlier: 3.929A pdb=" N TRP F 285 " --> pdb=" O MET F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 313 Processing helix chain 'F' and resid 314 through 328 Processing helix chain 'F' and resid 340 through 343 Processing helix chain 'F' and resid 345 through 349 Processing helix chain 'F' and resid 350 through 364 Processing helix chain 'F' and resid 377 through 391 Processing helix chain 'F' and resid 399 through 413 Processing helix chain 'F' and resid 462 through 468 Processing helix chain 'F' and resid 488 through 494 Processing helix chain 'F' and resid 526 through 531 removed outlier: 3.648A pdb=" N PHE F 529 " --> pdb=" O HIS F 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 548 Processing helix chain 'F' and resid 550 through 555 removed outlier: 3.613A pdb=" N LEU F 555 " --> pdb=" O LEU F 551 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 30 Processing helix chain 'O' and resid 69 through 79 Processing helix chain 'O' and resid 83 through 85 No H-bonds generated for 'chain 'O' and resid 83 through 85' Processing helix chain 'O' and resid 90 through 103 Processing helix chain 'O' and resid 115 through 130 Processing helix chain 'O' and resid 156 through 170 removed outlier: 4.573A pdb=" N PHE O 168 " --> pdb=" O ARG O 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 173 No H-bonds generated for 'chain 'O' and resid 171 through 173' Processing helix chain 'O' and resid 194 through 207 Processing helix chain 'O' and resid 223 through 235 Processing helix chain 'O' and resid 237 through 239 No H-bonds generated for 'chain 'O' and resid 237 through 239' Processing helix chain 'O' and resid 251 through 261 removed outlier: 4.449A pdb=" N LEU O 255 " --> pdb=" O TYR O 251 " (cutoff:3.500A) Processing helix chain 'O' and resid 261 through 270 removed outlier: 4.156A pdb=" N ARG O 268 " --> pdb=" O ASP O 264 " (cutoff:3.500A) Processing helix chain 'O' and resid 281 through 295 removed outlier: 3.929A pdb=" N TRP O 285 " --> pdb=" O MET O 281 " (cutoff:3.500A) Processing helix chain 'O' and resid 310 through 313 Processing helix chain 'O' and resid 314 through 328 Processing helix chain 'O' and resid 340 through 343 Processing helix chain 'O' and resid 345 through 349 Processing helix chain 'O' and resid 350 through 364 Processing helix chain 'O' and resid 377 through 391 Processing helix chain 'O' and resid 399 through 413 Processing helix chain 'O' and resid 462 through 468 Processing helix chain 'O' and resid 488 through 494 Processing helix chain 'O' and resid 526 through 531 removed outlier: 3.648A pdb=" N PHE O 529 " --> pdb=" O HIS O 526 " (cutoff:3.500A) Processing helix chain 'O' and resid 537 through 548 Processing helix chain 'O' and resid 550 through 555 removed outlier: 3.612A pdb=" N LEU O 555 " --> pdb=" O LEU O 551 " (cutoff:3.500A) Processing helix chain 'P' and resid 15 through 30 Processing helix chain 'P' and resid 69 through 79 Processing helix chain 'P' and resid 83 through 85 No H-bonds generated for 'chain 'P' and resid 83 through 85' Processing helix chain 'P' and resid 90 through 103 Processing helix chain 'P' and resid 115 through 130 Processing helix chain 'P' and resid 156 through 170 removed outlier: 4.573A pdb=" N PHE P 168 " --> pdb=" O ARG P 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 171 through 173 No H-bonds generated for 'chain 'P' and resid 171 through 173' Processing helix chain 'P' and resid 194 through 207 Processing helix chain 'P' and resid 223 through 235 Processing helix chain 'P' and resid 237 through 239 No H-bonds generated for 'chain 'P' and resid 237 through 239' Processing helix chain 'P' and resid 251 through 261 removed outlier: 4.451A pdb=" N LEU P 255 " --> pdb=" O TYR P 251 " (cutoff:3.500A) Processing helix chain 'P' and resid 261 through 270 removed outlier: 4.156A pdb=" N ARG P 268 " --> pdb=" O ASP P 264 " (cutoff:3.500A) Processing helix chain 'P' and resid 281 through 295 removed outlier: 3.928A pdb=" N TRP P 285 " --> pdb=" O MET P 281 " (cutoff:3.500A) Processing helix chain 'P' and resid 310 through 313 Processing helix chain 'P' and resid 314 through 328 Processing helix chain 'P' and resid 340 through 343 Processing helix chain 'P' and resid 345 through 349 Processing helix chain 'P' and resid 350 through 364 Processing helix chain 'P' and resid 377 through 391 Processing helix chain 'P' and resid 399 through 413 Processing helix chain 'P' and resid 462 through 468 Processing helix chain 'P' and resid 488 through 494 Processing helix chain 'P' and resid 526 through 531 removed outlier: 3.648A pdb=" N PHE P 529 " --> pdb=" O HIS P 526 " (cutoff:3.500A) Processing helix chain 'P' and resid 537 through 548 Processing helix chain 'P' and resid 550 through 555 removed outlier: 3.613A pdb=" N LEU P 555 " --> pdb=" O LEU P 551 " (cutoff:3.500A) Processing helix chain 'Q' and resid 15 through 30 Processing helix chain 'Q' and resid 69 through 79 Processing helix chain 'Q' and resid 83 through 85 No H-bonds generated for 'chain 'Q' and resid 83 through 85' Processing helix chain 'Q' and resid 90 through 103 Processing helix chain 'Q' and resid 115 through 130 Processing helix chain 'Q' and resid 156 through 170 removed outlier: 4.573A pdb=" N PHE Q 168 " --> pdb=" O ARG Q 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 171 through 173 No H-bonds generated for 'chain 'Q' and resid 171 through 173' Processing helix chain 'Q' and resid 194 through 207 Processing helix chain 'Q' and resid 223 through 235 Processing helix chain 'Q' and resid 237 through 239 No H-bonds generated for 'chain 'Q' and resid 237 through 239' Processing helix chain 'Q' and resid 251 through 261 removed outlier: 4.450A pdb=" N LEU Q 255 " --> pdb=" O TYR Q 251 " (cutoff:3.500A) Processing helix chain 'Q' and resid 261 through 270 removed outlier: 4.157A pdb=" N ARG Q 268 " --> pdb=" O ASP Q 264 " (cutoff:3.500A) Processing helix chain 'Q' and resid 281 through 295 removed outlier: 3.928A pdb=" N TRP Q 285 " --> pdb=" O MET Q 281 " (cutoff:3.500A) Processing helix chain 'Q' and resid 310 through 313 Processing helix chain 'Q' and resid 314 through 328 Processing helix chain 'Q' and resid 340 through 343 Processing helix chain 'Q' and resid 345 through 349 Processing helix chain 'Q' and resid 350 through 364 Processing helix chain 'Q' and resid 377 through 391 Processing helix chain 'Q' and resid 399 through 413 Processing helix chain 'Q' and resid 462 through 468 Processing helix chain 'Q' and resid 488 through 494 Processing helix chain 'Q' and resid 526 through 531 removed outlier: 3.648A pdb=" N PHE Q 529 " --> pdb=" O HIS Q 526 " (cutoff:3.500A) Processing helix chain 'Q' and resid 537 through 548 Processing helix chain 'Q' and resid 550 through 555 removed outlier: 3.612A pdb=" N LEU Q 555 " --> pdb=" O LEU Q 551 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 87 through 89 removed outlier: 4.185A pdb=" N GLY F 8 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TYR F 3 " --> pdb=" O CYS F 176 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ILE F 178 " --> pdb=" O TYR F 3 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU F 5 " --> pdb=" O ILE F 178 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL F 180 " --> pdb=" O LEU F 5 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR F 7 " --> pdb=" O VAL F 180 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N LEU F 182 " --> pdb=" O THR F 7 " (cutoff:3.500A) removed outlier: 9.459A pdb=" N LEU F 213 " --> pdb=" O PHE F 175 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASN F 177 " --> pdb=" O LEU F 213 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N VAL F 215 " --> pdb=" O ASN F 177 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N HIS F 179 " --> pdb=" O VAL F 215 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ARG F 217 " --> pdb=" O HIS F 179 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N SER F 181 " --> pdb=" O ARG F 217 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS F 218 " --> pdb=" O VAL F 244 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 59 through 60 Processing sheet with id=AA3, first strand: chain 'F' and resid 331 through 338 removed outlier: 6.666A pdb=" N CYS F 299 " --> pdb=" O GLU F 333 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LYS F 335 " --> pdb=" O CYS F 299 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE F 301 " --> pdb=" O LYS F 335 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ILE F 337 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU F 303 " --> pdb=" O ILE F 337 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N GLY F 366 " --> pdb=" O THR F 298 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N SER F 300 " --> pdb=" O GLY F 366 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N LEU F 368 " --> pdb=" O SER F 300 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ALA F 302 " --> pdb=" O LEU F 368 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL F 367 " --> pdb=" O LEU F 396 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N VAL F 398 " --> pdb=" O VAL F 367 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL F 369 " --> pdb=" O VAL F 398 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE F 395 " --> pdb=" O VAL F 521 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N VAL F 523 " --> pdb=" O PHE F 395 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLY F 397 " --> pdb=" O VAL F 523 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N PHE F 520 " --> pdb=" O LEU F 514 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N MET F 509 " --> pdb=" O GLN F 502 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLN F 502 " --> pdb=" O MET F 509 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE F 511 " --> pdb=" O VAL F 500 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 420 through 421 removed outlier: 7.125A pdb=" N ASN F 420 " --> pdb=" O VAL F 433 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N ASP F 435 " --> pdb=" O ASN F 420 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'O' and resid 87 through 89 removed outlier: 4.186A pdb=" N GLY O 8 " --> pdb=" O LEU O 147 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TYR O 3 " --> pdb=" O CYS O 176 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ILE O 178 " --> pdb=" O TYR O 3 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU O 5 " --> pdb=" O ILE O 178 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL O 180 " --> pdb=" O LEU O 5 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR O 7 " --> pdb=" O VAL O 180 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N LEU O 182 " --> pdb=" O THR O 7 " (cutoff:3.500A) removed outlier: 9.460A pdb=" N LEU O 213 " --> pdb=" O PHE O 175 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ASN O 177 " --> pdb=" O LEU O 213 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N VAL O 215 " --> pdb=" O ASN O 177 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N HIS O 179 " --> pdb=" O VAL O 215 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ARG O 217 " --> pdb=" O HIS O 179 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N SER O 181 " --> pdb=" O ARG O 217 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS O 218 " --> pdb=" O VAL O 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'O' and resid 59 through 60 Processing sheet with id=AA7, first strand: chain 'O' and resid 331 through 338 removed outlier: 6.666A pdb=" N CYS O 299 " --> pdb=" O GLU O 333 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LYS O 335 " --> pdb=" O CYS O 299 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE O 301 " --> pdb=" O LYS O 335 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ILE O 337 " --> pdb=" O ILE O 301 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU O 303 " --> pdb=" O ILE O 337 " (cutoff:3.500A) removed outlier: 9.624A pdb=" N GLY O 366 " --> pdb=" O THR O 298 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER O 300 " --> pdb=" O GLY O 366 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N LEU O 368 " --> pdb=" O SER O 300 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ALA O 302 " --> pdb=" O LEU O 368 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL O 367 " --> pdb=" O LEU O 396 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N VAL O 398 " --> pdb=" O VAL O 367 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL O 369 " --> pdb=" O VAL O 398 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE O 395 " --> pdb=" O VAL O 521 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N VAL O 523 " --> pdb=" O PHE O 395 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLY O 397 " --> pdb=" O VAL O 523 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N PHE O 520 " --> pdb=" O LEU O 514 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N MET O 509 " --> pdb=" O GLN O 502 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLN O 502 " --> pdb=" O MET O 509 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE O 511 " --> pdb=" O VAL O 500 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 420 through 421 removed outlier: 7.125A pdb=" N ASN O 420 " --> pdb=" O VAL O 433 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N ASP O 435 " --> pdb=" O ASN O 420 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'P' and resid 87 through 89 removed outlier: 4.185A pdb=" N GLY P 8 " --> pdb=" O LEU P 147 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TYR P 3 " --> pdb=" O CYS P 176 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ILE P 178 " --> pdb=" O TYR P 3 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU P 5 " --> pdb=" O ILE P 178 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL P 180 " --> pdb=" O LEU P 5 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR P 7 " --> pdb=" O VAL P 180 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N LEU P 182 " --> pdb=" O THR P 7 " (cutoff:3.500A) removed outlier: 9.459A pdb=" N LEU P 213 " --> pdb=" O PHE P 175 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASN P 177 " --> pdb=" O LEU P 213 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N VAL P 215 " --> pdb=" O ASN P 177 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N HIS P 179 " --> pdb=" O VAL P 215 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ARG P 217 " --> pdb=" O HIS P 179 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER P 181 " --> pdb=" O ARG P 217 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS P 218 " --> pdb=" O VAL P 244 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'P' and resid 59 through 60 Processing sheet with id=AB2, first strand: chain 'P' and resid 331 through 338 removed outlier: 6.666A pdb=" N CYS P 299 " --> pdb=" O GLU P 333 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LYS P 335 " --> pdb=" O CYS P 299 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE P 301 " --> pdb=" O LYS P 335 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ILE P 337 " --> pdb=" O ILE P 301 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU P 303 " --> pdb=" O ILE P 337 " (cutoff:3.500A) removed outlier: 9.623A pdb=" N GLY P 366 " --> pdb=" O THR P 298 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N SER P 300 " --> pdb=" O GLY P 366 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N LEU P 368 " --> pdb=" O SER P 300 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ALA P 302 " --> pdb=" O LEU P 368 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL P 367 " --> pdb=" O LEU P 396 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N VAL P 398 " --> pdb=" O VAL P 367 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL P 369 " --> pdb=" O VAL P 398 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE P 395 " --> pdb=" O VAL P 521 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N VAL P 523 " --> pdb=" O PHE P 395 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLY P 397 " --> pdb=" O VAL P 523 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N PHE P 520 " --> pdb=" O LEU P 514 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N MET P 509 " --> pdb=" O GLN P 502 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLN P 502 " --> pdb=" O MET P 509 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE P 511 " --> pdb=" O VAL P 500 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 420 through 421 removed outlier: 7.124A pdb=" N ASN P 420 " --> pdb=" O VAL P 433 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N ASP P 435 " --> pdb=" O ASN P 420 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Q' and resid 87 through 89 removed outlier: 4.186A pdb=" N GLY Q 8 " --> pdb=" O LEU Q 147 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TYR Q 3 " --> pdb=" O CYS Q 176 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ILE Q 178 " --> pdb=" O TYR Q 3 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU Q 5 " --> pdb=" O ILE Q 178 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL Q 180 " --> pdb=" O LEU Q 5 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR Q 7 " --> pdb=" O VAL Q 180 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N LEU Q 182 " --> pdb=" O THR Q 7 " (cutoff:3.500A) removed outlier: 9.460A pdb=" N LEU Q 213 " --> pdb=" O PHE Q 175 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ASN Q 177 " --> pdb=" O LEU Q 213 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N VAL Q 215 " --> pdb=" O ASN Q 177 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N HIS Q 179 " --> pdb=" O VAL Q 215 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ARG Q 217 " --> pdb=" O HIS Q 179 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N SER Q 181 " --> pdb=" O ARG Q 217 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS Q 218 " --> pdb=" O VAL Q 244 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Q' and resid 59 through 60 Processing sheet with id=AB6, first strand: chain 'Q' and resid 331 through 338 removed outlier: 6.666A pdb=" N CYS Q 299 " --> pdb=" O GLU Q 333 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LYS Q 335 " --> pdb=" O CYS Q 299 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE Q 301 " --> pdb=" O LYS Q 335 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ILE Q 337 " --> pdb=" O ILE Q 301 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU Q 303 " --> pdb=" O ILE Q 337 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N GLY Q 366 " --> pdb=" O THR Q 298 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N SER Q 300 " --> pdb=" O GLY Q 366 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N LEU Q 368 " --> pdb=" O SER Q 300 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ALA Q 302 " --> pdb=" O LEU Q 368 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL Q 367 " --> pdb=" O LEU Q 396 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N VAL Q 398 " --> pdb=" O VAL Q 367 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL Q 369 " --> pdb=" O VAL Q 398 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE Q 395 " --> pdb=" O VAL Q 521 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N VAL Q 523 " --> pdb=" O PHE Q 395 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLY Q 397 " --> pdb=" O VAL Q 523 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N PHE Q 520 " --> pdb=" O LEU Q 514 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N MET Q 509 " --> pdb=" O GLN Q 502 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLN Q 502 " --> pdb=" O MET Q 509 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE Q 511 " --> pdb=" O VAL Q 500 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Q' and resid 420 through 421 removed outlier: 7.125A pdb=" N ASN Q 420 " --> pdb=" O VAL Q 433 " (cutoff:3.500A) removed outlier: 8.915A pdb=" N ASP Q 435 " --> pdb=" O ASN Q 420 " (cutoff:3.500A) 756 hydrogen bonds defined for protein. 2172 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: 7.92 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.85 - 1.05: 3780 1.05 - 1.24: 15856 1.24 - 1.43: 5192 1.43 - 1.62: 10240 1.62 - 1.82: 164 Bond restraints: 35232 Sorted by residual: bond pdb=" C2' UTP F 601 " pdb=" C3' UTP F 601 " ideal model delta sigma weight residual 1.533 1.345 0.188 2.00e-02 2.50e+03 8.79e+01 bond pdb=" C2' UTP Q 602 " pdb=" C3' UTP Q 602 " ideal model delta sigma weight residual 1.533 1.346 0.187 2.00e-02 2.50e+03 8.77e+01 bond pdb=" C2' UTP O 601 " pdb=" C3' UTP O 601 " ideal model delta sigma weight residual 1.533 1.347 0.186 2.00e-02 2.50e+03 8.69e+01 bond pdb=" C2' UTP P 602 " pdb=" C3' UTP P 602 " ideal model delta sigma weight residual 1.533 1.347 0.186 2.00e-02 2.50e+03 8.69e+01 bond pdb=" N ASP P 136 " pdb=" H ASP P 136 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.81e+01 ... (remaining 35227 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.05: 63058 7.05 - 14.11: 686 14.11 - 21.16: 28 21.16 - 28.22: 4 28.22 - 35.27: 8 Bond angle restraints: 63784 Sorted by residual: angle pdb=" CG1 VAL Q 487 " pdb=" CB VAL Q 487 " pdb=" HB VAL Q 487 " ideal model delta sigma weight residual 108.00 72.73 35.27 3.00e+00 1.11e-01 1.38e+02 angle pdb=" CG1 VAL F 487 " pdb=" CB VAL F 487 " pdb=" HB VAL F 487 " ideal model delta sigma weight residual 108.00 72.73 35.27 3.00e+00 1.11e-01 1.38e+02 angle pdb=" CG1 VAL P 487 " pdb=" CB VAL P 487 " pdb=" HB VAL P 487 " ideal model delta sigma weight residual 108.00 72.73 35.27 3.00e+00 1.11e-01 1.38e+02 angle pdb=" CG1 VAL O 487 " pdb=" CB VAL O 487 " pdb=" HB VAL O 487 " ideal model delta sigma weight residual 108.00 72.73 35.27 3.00e+00 1.11e-01 1.38e+02 angle pdb=" CA VAL F 487 " pdb=" CB VAL F 487 " pdb=" HB VAL F 487 " ideal model delta sigma weight residual 109.00 75.36 33.64 3.00e+00 1.11e-01 1.26e+02 ... (remaining 63779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 14972 17.96 - 35.92: 1012 35.92 - 53.88: 392 53.88 - 71.84: 216 71.84 - 89.80: 64 Dihedral angle restraints: 16656 sinusoidal: 9304 harmonic: 7352 Sorted by residual: dihedral pdb=" CA LYS Q 460 " pdb=" C LYS Q 460 " pdb=" N ASN Q 461 " pdb=" CA ASN Q 461 " ideal model delta harmonic sigma weight residual -180.00 -153.23 -26.77 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA LYS P 460 " pdb=" C LYS P 460 " pdb=" N ASN P 461 " pdb=" CA ASN P 461 " ideal model delta harmonic sigma weight residual -180.00 -153.25 -26.75 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA LYS F 460 " pdb=" C LYS F 460 " pdb=" N ASN F 461 " pdb=" CA ASN F 461 " ideal model delta harmonic sigma weight residual -180.00 -153.25 -26.75 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 16653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 2313 0.161 - 0.321: 352 0.321 - 0.482: 11 0.482 - 0.643: 0 0.643 - 0.803: 4 Chirality restraints: 2680 Sorted by residual: chirality pdb=" CB VAL Q 487 " pdb=" CA VAL Q 487 " pdb=" CG1 VAL Q 487 " pdb=" CG2 VAL Q 487 " both_signs ideal model delta sigma weight residual False -2.63 -1.83 -0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" CB VAL O 487 " pdb=" CA VAL O 487 " pdb=" CG1 VAL O 487 " pdb=" CG2 VAL O 487 " both_signs ideal model delta sigma weight residual False -2.63 -1.83 -0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" CB VAL P 487 " pdb=" CA VAL P 487 " pdb=" CG1 VAL P 487 " pdb=" CG2 VAL P 487 " both_signs ideal model delta sigma weight residual False -2.63 -1.83 -0.80 2.00e-01 2.50e+01 1.61e+01 ... (remaining 2677 not shown) Planarity restraints: 5148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN P 603 " -0.156 2.00e-02 2.50e+03 1.70e-01 4.33e+02 pdb=" CD GLN P 603 " 0.015 2.00e-02 2.50e+03 pdb=" OE1 GLN P 603 " 0.146 2.00e-02 2.50e+03 pdb=" NE2 GLN P 603 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN P 603 " 0.249 2.00e-02 2.50e+03 pdb="HE22 GLN P 603 " -0.255 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN Q 603 " -0.156 2.00e-02 2.50e+03 1.70e-01 4.33e+02 pdb=" CD GLN Q 603 " 0.015 2.00e-02 2.50e+03 pdb=" OE1 GLN Q 603 " 0.146 2.00e-02 2.50e+03 pdb=" NE2 GLN Q 603 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN Q 603 " 0.249 2.00e-02 2.50e+03 pdb="HE22 GLN Q 603 " -0.255 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN O 602 " 0.156 2.00e-02 2.50e+03 1.70e-01 4.32e+02 pdb=" CD GLN O 602 " -0.015 2.00e-02 2.50e+03 pdb=" OE1 GLN O 602 " -0.146 2.00e-02 2.50e+03 pdb=" NE2 GLN O 602 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN O 602 " -0.248 2.00e-02 2.50e+03 pdb="HE22 GLN O 602 " 0.255 2.00e-02 2.50e+03 ... (remaining 5145 not shown) Histogram of nonbonded interaction distances: 1.01 - 1.73: 92 1.73 - 2.44: 15008 2.44 - 3.16: 115564 3.16 - 3.88: 153248 3.88 - 4.60: 240169 Nonbonded interactions: 524081 Sorted by model distance: nonbonded pdb=" HE2 MET O 448 " pdb=" HG3 ARG O 481 " model vdw 1.008 2.440 nonbonded pdb=" HE2 MET P 448 " pdb=" HG3 ARG P 481 " model vdw 1.008 2.440 nonbonded pdb=" HE2 MET F 448 " pdb=" HG3 ARG F 481 " model vdw 1.008 2.440 nonbonded pdb=" HE2 MET Q 448 " pdb=" HG3 ARG Q 481 " model vdw 1.008 2.440 nonbonded pdb=" HG3 MET Q 448 " pdb=" HG2 ARG Q 481 " model vdw 1.236 2.440 ... (remaining 524076 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 'F' and resid 1 through 555) selection = (chain 'O' and resid 1 through 555) selection = (chain 'P' and resid 1 through 555) selection = (chain 'Q' and resid 1 through 555) } 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: 1.810 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: 0.150 Extract box with map and model: 0.360 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 29.250 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 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 : 0.014 0.188 17916 Z= 0.835 Angle : 2.071 14.805 24292 Z= 1.335 Chirality : 0.112 0.803 2680 Planarity : 0.018 0.174 3104 Dihedral : 17.680 89.798 6916 Min Nonbonded Distance : 1.574 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.36 % Favored : 96.46 % Rotamer: Outliers : 1.66 % Allowed : 7.28 % Favored : 91.06 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 3.57 % 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 (0.16), residues: 2144 helix: -1.39 (0.14), residues: 912 sheet: -0.17 (0.28), residues: 320 loop : -0.49 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG F 389 TYR 0.122 0.022 TYR P 292 PHE 0.057 0.014 PHE Q 233 TRP 0.073 0.021 TRP P 285 HIS 0.014 0.004 HIS F 439 Details of bonding type rmsd/Z covalent geometry : bond 0.01396 / 0.84 (17916) covalent geometry : angle 2.07073 / 1.34 (24292) hydrogen bonds : bond 0.15426 / 10.22 ( 756) hydrogen bonds : angle 7.19840 / 5.01 ( 2172) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 649 time to evaluate : 0.957 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 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: F 66 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8066 (mt-10) REVERT: F 107 LEU cc_start: 0.7952 (mt) cc_final: 0.7640 (mt) REVERT: F 161 GLU cc_start: 0.8152 (tp30) cc_final: 0.7666 (mm-30) REVERT: F 335 LYS cc_start: 0.8294 (mttm) cc_final: 0.8041 (mtpt) REVERT: F 476 GLU cc_start: 0.8480 (mm-30) cc_final: 0.7262 (mm-30) REVERT: O 66 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8019 (mt-10) REVERT: O 107 LEU cc_start: 0.8006 (mt) cc_final: 0.7631 (mt) REVERT: O 161 GLU cc_start: 0.8172 (tp30) cc_final: 0.7673 (mm-30) REVERT: O 335 LYS cc_start: 0.8289 (mttm) cc_final: 0.8052 (mtpt) REVERT: O 476 GLU cc_start: 0.8464 (mm-30) cc_final: 0.7243 (mm-30) REVERT: O 482 PHE cc_start: 0.8461 (m-80) cc_final: 0.8209 (m-80) REVERT: P 66 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8098 (mt-10) REVERT: P 107 LEU cc_start: 0.7939 (mt) cc_final: 0.7644 (mt) REVERT: P 161 GLU cc_start: 0.8126 (tp30) cc_final: 0.7423 (mm-30) REVERT: P 335 LYS cc_start: 0.8296 (mttm) cc_final: 0.8035 (mtpt) REVERT: P 476 GLU cc_start: 0.8475 (mm-30) cc_final: 0.7277 (mm-30) REVERT: P 482 PHE cc_start: 0.8465 (m-80) cc_final: 0.8203 (m-80) REVERT: Q 66 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8043 (mt-10) REVERT: Q 107 LEU cc_start: 0.7989 (mt) cc_final: 0.7626 (mt) REVERT: Q 161 GLU cc_start: 0.8170 (tp30) cc_final: 0.7694 (mm-30) REVERT: Q 335 LYS cc_start: 0.8277 (mttm) cc_final: 0.8075 (mttt) REVERT: Q 476 GLU cc_start: 0.8469 (mm-30) cc_final: 0.7254 (mm-30) REVERT: Q 482 PHE cc_start: 0.8396 (m-80) cc_final: 0.8132 (m-80) outliers start: 32 outliers final: 7 residues processed: 657 average time/residue: 1.1095 time to fit residues: 824.4179 Evaluate side-chains 504 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 497 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain O residue 367 VAL Chi-restraints excluded: chain P residue 136 ASP Chi-restraints excluded: chain P residue 367 VAL Chi-restraints excluded: chain Q residue 136 ASP Chi-restraints excluded: chain Q residue 367 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 0.9980 chunk 212 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 87 ASN F 99 ASN ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 87 ASN O 99 ASN ** O 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 87 ASN P 99 ASN ** P 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 87 ASN Q 99 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.153415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.117915 restraints weight = 57219.351| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.01 r_work: 0.3092 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17916 Z= 0.189 Angle : 0.724 9.609 24292 Z= 0.380 Chirality : 0.069 1.359 2680 Planarity : 0.006 0.059 3104 Dihedral : 13.237 123.013 2638 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.40 % Favored : 98.41 % Rotamer: Outliers : 3.07 % Allowed : 15.33 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.43 (0.17), residues: 2144 helix: -0.08 (0.16), residues: 924 sheet: -0.44 (0.26), residues: 368 loop : -0.20 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 294 TYR 0.013 0.002 TYR P 42 PHE 0.012 0.002 PHE O 541 TRP 0.005 0.001 TRP Q 358 HIS 0.006 0.001 HIS O 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 (17916) covalent geometry : angle 0.72421 / 0.38 (24292) hydrogen bonds : bond 0.04767 / 3.19 ( 756) hydrogen bonds : angle 5.32996 / 3.71 ( 2172) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 538 time to evaluate : 0.977 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: F 79 ASP cc_start: 0.7798 (t0) cc_final: 0.7467 (t0) REVERT: F 103 LYS cc_start: 0.8099 (mtpp) cc_final: 0.7641 (mtmp) REVERT: F 219 SER cc_start: 0.8922 (m) cc_final: 0.8643 (p) REVERT: F 231 SER cc_start: 0.9116 (m) cc_final: 0.8912 (p) REVERT: F 232 MET cc_start: 0.7753 (mmm) cc_final: 0.7336 (tmm) REVERT: F 294 ARG cc_start: 0.7288 (mtm110) cc_final: 0.6759 (ptp-170) REVERT: F 322 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8343 (mt-10) REVERT: F 333 GLU cc_start: 0.7763 (tt0) cc_final: 0.7450 (tm-30) REVERT: F 335 LYS cc_start: 0.8171 (mttm) cc_final: 0.7800 (mttt) REVERT: F 389 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.7007 (mtm110) REVERT: F 476 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8217 (mm-30) REVERT: F 535 LYS cc_start: 0.7757 (tttm) cc_final: 0.7468 (ttpt) REVERT: O 79 ASP cc_start: 0.7896 (t0) cc_final: 0.7574 (t0) REVERT: O 103 LYS cc_start: 0.8115 (mtpp) cc_final: 0.7654 (mtmp) REVERT: O 219 SER cc_start: 0.8971 (m) cc_final: 0.8695 (p) REVERT: O 231 SER cc_start: 0.9180 (m) cc_final: 0.8910 (p) REVERT: O 286 LYS cc_start: 0.7910 (tptm) cc_final: 0.7660 (mmmt) REVERT: O 291 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.7321 (mtp85) REVERT: O 294 ARG cc_start: 0.7086 (mtm110) cc_final: 0.6516 (ptp-170) REVERT: O 322 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8262 (mt-10) REVERT: O 333 GLU cc_start: 0.7792 (tt0) cc_final: 0.7465 (tm-30) REVERT: O 335 LYS cc_start: 0.8179 (mttm) cc_final: 0.7807 (mttt) REVERT: O 387 TRP cc_start: 0.7733 (t-100) cc_final: 0.7339 (t-100) REVERT: O 389 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.7016 (mtm110) REVERT: O 475 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8134 (mt-10) REVERT: O 476 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8225 (mm-30) REVERT: O 535 LYS cc_start: 0.7761 (tttm) cc_final: 0.7443 (ttpt) REVERT: P 103 LYS cc_start: 0.8054 (mmmm) cc_final: 0.7658 (mttp) REVERT: P 232 MET cc_start: 0.7803 (mmm) cc_final: 0.7344 (tmm) REVERT: P 291 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.7060 (mtp85) REVERT: P 294 ARG cc_start: 0.7135 (mtp180) cc_final: 0.6574 (ptp-170) REVERT: P 310 PHE cc_start: 0.7172 (m-80) cc_final: 0.6956 (m-80) REVERT: P 322 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8356 (mt-10) REVERT: P 333 GLU cc_start: 0.7777 (tt0) cc_final: 0.7439 (tm-30) REVERT: P 335 LYS cc_start: 0.8154 (mttm) cc_final: 0.7785 (mttt) REVERT: P 387 TRP cc_start: 0.7736 (t-100) cc_final: 0.7333 (t-100) REVERT: P 389 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.7024 (mtm110) REVERT: P 476 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8382 (mm-30) REVERT: P 502 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7420 (mt0) REVERT: P 535 LYS cc_start: 0.7862 (tttm) cc_final: 0.7577 (ttpt) REVERT: Q 103 LYS cc_start: 0.8155 (mtpp) cc_final: 0.7692 (mtmp) REVERT: Q 231 SER cc_start: 0.9177 (m) cc_final: 0.8931 (p) REVERT: Q 232 MET cc_start: 0.7731 (mmm) cc_final: 0.7227 (tmm) REVERT: Q 286 LYS cc_start: 0.7921 (tptm) cc_final: 0.7583 (mmmt) REVERT: Q 288 MET cc_start: 0.8090 (mtm) cc_final: 0.7820 (mtp) REVERT: Q 294 ARG cc_start: 0.7142 (mtp180) cc_final: 0.6566 (ptp-170) REVERT: Q 322 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8405 (mt-10) REVERT: Q 335 LYS cc_start: 0.8151 (mttm) cc_final: 0.7800 (mttt) REVERT: Q 353 ARG cc_start: 0.6801 (tpp80) cc_final: 0.6582 (ttm-80) REVERT: Q 389 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.7041 (mtm110) REVERT: Q 475 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8278 (mt-10) REVERT: Q 476 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8354 (mm-30) REVERT: Q 502 GLN cc_start: 0.7901 (mt0) cc_final: 0.7664 (mt0) REVERT: Q 509 MET cc_start: 0.8273 (mmp) cc_final: 0.7903 (mmp) REVERT: O 602 GLN cc_start: 0.8034 (pt0) cc_final: 0.7785 (pt0) REVERT: Q 603 GLN cc_start: 0.8095 (pt0) cc_final: 0.7803 (pt0) outliers start: 59 outliers final: 14 residues processed: 547 average time/residue: 1.2522 time to fit residues: 770.2761 Evaluate side-chains 464 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 443 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 291 ARG Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 389 ARG Chi-restraints excluded: chain F residue 503 ASP Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 291 ARG Chi-restraints excluded: chain O residue 367 VAL Chi-restraints excluded: chain O residue 389 ARG Chi-restraints excluded: chain O residue 503 ASP Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 291 ARG Chi-restraints excluded: chain P residue 367 VAL Chi-restraints excluded: chain P residue 389 ARG Chi-restraints excluded: chain P residue 502 GLN Chi-restraints excluded: chain P residue 503 ASP Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 291 ARG Chi-restraints excluded: chain Q residue 367 VAL Chi-restraints excluded: chain Q residue 389 ARG Chi-restraints excluded: chain Q residue 503 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 99 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 175 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 87 optimal weight: 0.0770 chunk 8 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 189 optimal weight: 0.8980 overall best weight: 0.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 260 GLN F 365 HIS O 365 HIS P 260 GLN P 365 HIS Q 365 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.154572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.120457 restraints weight = 58734.536| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.94 r_work: 0.3059 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17916 Z= 0.166 Angle : 0.639 10.862 24292 Z= 0.336 Chirality : 0.071 1.427 2680 Planarity : 0.006 0.052 3104 Dihedral : 8.453 54.013 2632 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.23 % Allowed : 16.74 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.13 (0.18), residues: 2144 helix: 0.61 (0.17), residues: 924 sheet: -0.60 (0.25), residues: 380 loop : 0.04 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 353 TYR 0.012 0.001 TYR P 292 PHE 0.015 0.002 PHE Q 163 TRP 0.009 0.001 TRP P 387 HIS 0.007 0.002 HIS O 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (17916) covalent geometry : angle 0.63947 / 0.34 (24292) hydrogen bonds : bond 0.04023 / 2.69 ( 756) hydrogen bonds : angle 4.88253 / 3.40 ( 2172) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 461 time to evaluate : 1.000 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 revert: symmetry clash REVERT: F 103 LYS cc_start: 0.8073 (mtpp) cc_final: 0.7629 (mttp) REVERT: F 191 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8073 (mt-10) REVERT: F 232 MET cc_start: 0.7662 (mmm) cc_final: 0.7362 (tmm) REVERT: F 239 GLU cc_start: 0.7910 (pm20) cc_final: 0.7485 (tp30) REVERT: F 291 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7144 (mtp85) REVERT: F 294 ARG cc_start: 0.7212 (mtm110) cc_final: 0.6798 (ptp-170) REVERT: F 322 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8255 (mt-10) REVERT: F 333 GLU cc_start: 0.7843 (tt0) cc_final: 0.7440 (tm-30) REVERT: F 353 ARG cc_start: 0.6977 (mmm-85) cc_final: 0.6605 (mtm-85) REVERT: F 389 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.7027 (mtm110) REVERT: F 476 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8334 (mm-30) REVERT: F 477 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.8717 (mtt180) REVERT: F 535 LYS cc_start: 0.7969 (tttm) cc_final: 0.7657 (ttpt) REVERT: O 103 LYS cc_start: 0.8175 (mtpp) cc_final: 0.7755 (mttp) REVERT: O 231 SER cc_start: 0.9171 (m) cc_final: 0.8941 (p) REVERT: O 232 MET cc_start: 0.7702 (mmm) cc_final: 0.7332 (tmm) REVERT: O 286 LYS cc_start: 0.7903 (tptm) cc_final: 0.7692 (mmmt) REVERT: O 294 ARG cc_start: 0.7135 (mtm110) cc_final: 0.6649 (ptp-170) REVERT: O 322 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8228 (mt-10) REVERT: O 333 GLU cc_start: 0.7851 (tt0) cc_final: 0.7461 (tm-30) REVERT: O 387 TRP cc_start: 0.7739 (t-100) cc_final: 0.7514 (t-100) REVERT: O 389 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.6988 (mtm110) REVERT: O 391 GLN cc_start: 0.7527 (mp10) cc_final: 0.7008 (mp10) REVERT: O 476 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8441 (mm-30) REVERT: O 477 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8737 (mtt180) REVERT: O 502 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7599 (mt0) REVERT: O 535 LYS cc_start: 0.7969 (tttm) cc_final: 0.7625 (ttpt) REVERT: P 103 LYS cc_start: 0.8155 (mmmm) cc_final: 0.7842 (mttp) REVERT: P 191 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8101 (mt-10) REVERT: P 232 MET cc_start: 0.7674 (mmm) cc_final: 0.7358 (tmm) REVERT: P 239 GLU cc_start: 0.7858 (pm20) cc_final: 0.7456 (mm-30) REVERT: P 294 ARG cc_start: 0.6986 (mtp180) cc_final: 0.6481 (ptp-170) REVERT: P 322 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8270 (mt-10) REVERT: P 333 GLU cc_start: 0.7839 (tt0) cc_final: 0.7448 (tm-30) REVERT: P 353 ARG cc_start: 0.7063 (mmm-85) cc_final: 0.6725 (mtm-85) REVERT: P 387 TRP cc_start: 0.7746 (t-100) cc_final: 0.7534 (t-100) REVERT: P 391 GLN cc_start: 0.7447 (mp10) cc_final: 0.6964 (mp10) REVERT: P 476 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8512 (mm-30) REVERT: P 477 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8734 (mtt180) REVERT: P 502 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7485 (mt0) REVERT: P 535 LYS cc_start: 0.7973 (tttm) cc_final: 0.7649 (ttpt) REVERT: Q 79 ASP cc_start: 0.8001 (t0) cc_final: 0.7800 (t0) REVERT: Q 103 LYS cc_start: 0.8202 (mtpp) cc_final: 0.7748 (mttp) REVERT: Q 231 SER cc_start: 0.9133 (m) cc_final: 0.8919 (p) REVERT: Q 232 MET cc_start: 0.7706 (mmm) cc_final: 0.7328 (tmm) REVERT: Q 239 GLU cc_start: 0.7904 (pm20) cc_final: 0.7534 (tp30) REVERT: Q 286 LYS cc_start: 0.7916 (tptm) cc_final: 0.7690 (mmmt) REVERT: Q 288 MET cc_start: 0.8080 (mtm) cc_final: 0.7857 (mtp) REVERT: Q 291 ARG cc_start: 0.7618 (mtp85) cc_final: 0.7415 (mtp85) REVERT: Q 294 ARG cc_start: 0.7147 (mtp180) cc_final: 0.6604 (ptp-170) REVERT: Q 322 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8309 (mt-10) REVERT: Q 333 GLU cc_start: 0.7826 (tt0) cc_final: 0.7420 (tm-30) REVERT: Q 353 ARG cc_start: 0.6742 (tpp80) cc_final: 0.6518 (ttm-80) REVERT: Q 389 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.7057 (mtm110) REVERT: Q 391 GLN cc_start: 0.7691 (tp40) cc_final: 0.7290 (mp10) REVERT: Q 436 MET cc_start: 0.7798 (ttt) cc_final: 0.7547 (ttm) REVERT: Q 476 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8444 (mm-30) REVERT: Q 477 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8752 (mtt180) REVERT: Q 509 MET cc_start: 0.8335 (mmp) cc_final: 0.7924 (mmp) REVERT: Q 535 LYS cc_start: 0.7973 (tttm) cc_final: 0.7598 (ttpt) outliers start: 43 outliers final: 19 residues processed: 478 average time/residue: 1.2981 time to fit residues: 698.0530 Evaluate side-chains 473 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 442 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 191 GLU Chi-restraints excluded: chain F residue 243 CYS Chi-restraints excluded: chain F residue 291 ARG Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 389 ARG Chi-restraints excluded: chain F residue 477 ARG Chi-restraints excluded: chain F residue 503 ASP Chi-restraints excluded: chain O residue 243 CYS Chi-restraints excluded: chain O residue 367 VAL Chi-restraints excluded: chain O residue 389 ARG Chi-restraints excluded: chain O residue 458 GLN Chi-restraints excluded: chain O residue 477 ARG Chi-restraints excluded: chain O residue 502 GLN Chi-restraints excluded: chain O residue 503 ASP Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 191 GLU Chi-restraints excluded: chain P residue 243 CYS Chi-restraints excluded: chain P residue 326 LEU Chi-restraints excluded: chain P residue 367 VAL Chi-restraints excluded: chain P residue 389 ARG Chi-restraints excluded: chain P residue 458 GLN Chi-restraints excluded: chain P residue 477 ARG Chi-restraints excluded: chain P residue 502 GLN Chi-restraints excluded: chain P residue 503 ASP Chi-restraints excluded: chain Q residue 243 CYS Chi-restraints excluded: chain Q residue 367 VAL Chi-restraints excluded: chain Q residue 389 ARG Chi-restraints excluded: chain Q residue 477 ARG Chi-restraints excluded: chain Q residue 503 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 118 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 210 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 365 HIS ** O 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 365 HIS O 461 ASN P 365 HIS P 461 ASN Q 365 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.146445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.111040 restraints weight = 59212.759| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.99 r_work: 0.3024 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17916 Z= 0.227 Angle : 0.627 11.087 24292 Z= 0.326 Chirality : 0.072 1.469 2680 Planarity : 0.005 0.046 3104 Dihedral : 7.994 59.087 2632 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.91 % Allowed : 17.36 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.21 (0.18), residues: 2144 helix: 0.77 (0.17), residues: 932 sheet: -0.73 (0.25), residues: 380 loop : 0.07 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 481 TYR 0.013 0.002 TYR Q 42 PHE 0.015 0.002 PHE P 163 TRP 0.008 0.001 TRP Q 387 HIS 0.009 0.002 HIS O 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.23 (17916) covalent geometry : angle 0.62658 / 0.33 (24292) hydrogen bonds : bond 0.04093 / 2.74 ( 756) hydrogen bonds : angle 4.72128 / 3.29 ( 2172) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 435 time to evaluate : 1.156 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: F 103 LYS cc_start: 0.8177 (mtpp) cc_final: 0.7742 (mttp) REVERT: F 191 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8140 (mt-10) REVERT: F 232 MET cc_start: 0.7730 (mmm) cc_final: 0.7429 (tmm) REVERT: F 294 ARG cc_start: 0.7221 (mtm110) cc_final: 0.6793 (ptp-170) REVERT: F 322 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8308 (mt-10) REVERT: F 333 GLU cc_start: 0.7962 (tt0) cc_final: 0.7721 (tt0) REVERT: F 389 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.7088 (mtm110) REVERT: F 477 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8791 (mtt180) REVERT: F 535 LYS cc_start: 0.8069 (tttm) cc_final: 0.7762 (ttpt) REVERT: O 103 LYS cc_start: 0.8214 (mtpp) cc_final: 0.7784 (mttp) REVERT: O 191 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8079 (mt-10) REVERT: O 232 MET cc_start: 0.7771 (mmm) cc_final: 0.7397 (tmm) REVERT: O 239 GLU cc_start: 0.7929 (pm20) cc_final: 0.7495 (tp30) REVERT: O 294 ARG cc_start: 0.7217 (mtm110) cc_final: 0.6750 (ptp-170) REVERT: O 297 GLU cc_start: 0.7043 (pp20) cc_final: 0.6676 (pp20) REVERT: O 333 GLU cc_start: 0.8034 (tt0) cc_final: 0.7664 (tm-30) REVERT: O 387 TRP cc_start: 0.7932 (t-100) cc_final: 0.7662 (t-100) REVERT: O 436 MET cc_start: 0.7769 (ttt) cc_final: 0.7546 (ttm) REVERT: O 476 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8406 (mm-30) REVERT: O 477 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.8815 (mtt180) REVERT: O 502 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7721 (mt0) REVERT: O 507 GLU cc_start: 0.7356 (tm-30) cc_final: 0.7122 (tm-30) REVERT: O 535 LYS cc_start: 0.8082 (tttm) cc_final: 0.7742 (ttpt) REVERT: P 103 LYS cc_start: 0.8185 (mmmm) cc_final: 0.7866 (mttp) REVERT: P 191 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8151 (mt-10) REVERT: P 232 MET cc_start: 0.7755 (mmm) cc_final: 0.7415 (tmm) REVERT: P 294 ARG cc_start: 0.7000 (mtp180) cc_final: 0.6524 (ptp-170) REVERT: P 333 GLU cc_start: 0.7972 (tt0) cc_final: 0.7727 (tt0) REVERT: P 353 ARG cc_start: 0.7086 (mmm-85) cc_final: 0.6805 (mtm-85) REVERT: P 356 GLU cc_start: 0.7610 (tp30) cc_final: 0.7353 (mm-30) REVERT: P 387 TRP cc_start: 0.7913 (t-100) cc_final: 0.7650 (t-100) REVERT: P 389 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.7173 (mtm110) REVERT: P 476 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8498 (mm-30) REVERT: P 477 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8793 (mtt180) REVERT: P 502 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7534 (mt0) REVERT: P 535 LYS cc_start: 0.8100 (tttm) cc_final: 0.7777 (ttpt) REVERT: Q 103 LYS cc_start: 0.8240 (mtpp) cc_final: 0.7797 (mttp) REVERT: Q 191 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8122 (mt-10) REVERT: Q 232 MET cc_start: 0.7752 (mmm) cc_final: 0.7367 (tmm) REVERT: Q 286 LYS cc_start: 0.7978 (tptm) cc_final: 0.7767 (mmmt) REVERT: Q 288 MET cc_start: 0.8190 (mtm) cc_final: 0.7968 (mtp) REVERT: Q 294 ARG cc_start: 0.7185 (mtp180) cc_final: 0.6590 (ptp-170) REVERT: Q 333 GLU cc_start: 0.7996 (tt0) cc_final: 0.7746 (tt0) REVERT: Q 353 ARG cc_start: 0.6865 (tpp80) cc_final: 0.6643 (ttm-80) REVERT: Q 389 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.7124 (mtm110) REVERT: Q 391 GLN cc_start: 0.7730 (tp40) cc_final: 0.7272 (mp10) REVERT: Q 436 MET cc_start: 0.7778 (ttt) cc_final: 0.7547 (ttm) REVERT: Q 476 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8414 (mm-30) REVERT: Q 477 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8806 (mtt180) REVERT: Q 535 LYS cc_start: 0.8057 (tttm) cc_final: 0.7710 (ttpt) outliers start: 56 outliers final: 27 residues processed: 463 average time/residue: 1.3615 time to fit residues: 704.5107 Evaluate side-chains 450 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 410 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 191 GLU Chi-restraints excluded: chain F residue 243 CYS Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 389 ARG Chi-restraints excluded: chain F residue 477 ARG Chi-restraints excluded: chain F residue 503 ASP Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain O residue 138 LEU Chi-restraints excluded: chain O residue 191 GLU Chi-restraints excluded: chain O residue 243 CYS Chi-restraints excluded: chain O residue 367 VAL Chi-restraints excluded: chain O residue 458 GLN Chi-restraints excluded: chain O residue 477 ARG Chi-restraints excluded: chain O residue 502 GLN Chi-restraints excluded: chain O residue 503 ASP Chi-restraints excluded: chain O residue 547 SER Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 138 LEU Chi-restraints excluded: chain P residue 191 GLU Chi-restraints excluded: chain P residue 243 CYS Chi-restraints excluded: chain P residue 297 GLU Chi-restraints excluded: chain P residue 326 LEU Chi-restraints excluded: chain P residue 367 VAL Chi-restraints excluded: chain P residue 389 ARG Chi-restraints excluded: chain P residue 458 GLN Chi-restraints excluded: chain P residue 477 ARG Chi-restraints excluded: chain P residue 502 GLN Chi-restraints excluded: chain P residue 503 ASP Chi-restraints excluded: chain P residue 547 SER Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain Q residue 191 GLU Chi-restraints excluded: chain Q residue 243 CYS Chi-restraints excluded: chain Q residue 367 VAL Chi-restraints excluded: chain Q residue 389 ARG Chi-restraints excluded: chain Q residue 477 ARG Chi-restraints excluded: chain Q residue 503 ASP Chi-restraints excluded: chain Q residue 547 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 167 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 182 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 43 optimal weight: 0.3980 chunk 58 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 365 HIS F 461 ASN O 365 HIS O 461 ASN P 365 HIS P 461 ASN Q 365 HIS Q 461 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.146025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.110811 restraints weight = 59749.111| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.99 r_work: 0.3047 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.4783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17916 Z= 0.199 Angle : 0.610 11.165 24292 Z= 0.318 Chirality : 0.071 1.465 2680 Planarity : 0.005 0.053 3104 Dihedral : 7.923 59.267 2632 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.91 % Allowed : 18.76 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.37 (0.18), residues: 2144 helix: 0.92 (0.17), residues: 932 sheet: -0.80 (0.25), residues: 380 loop : 0.22 (0.23), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 353 TYR 0.013 0.002 TYR P 292 PHE 0.014 0.001 PHE P 482 TRP 0.007 0.001 TRP F 387 HIS 0.008 0.002 HIS O 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 (17916) covalent geometry : angle 0.61016 / 0.32 (24292) hydrogen bonds : bond 0.03866 / 2.59 ( 756) hydrogen bonds : angle 4.63344 / 3.23 ( 2172) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 423 time to evaluate : 0.986 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: F 103 LYS cc_start: 0.8197 (mtpp) cc_final: 0.7777 (mtmt) REVERT: F 156 SER cc_start: 0.9162 (OUTLIER) cc_final: 0.8860 (p) REVERT: F 191 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8057 (mt-10) REVERT: F 232 MET cc_start: 0.7754 (mmm) cc_final: 0.7443 (tmm) REVERT: F 291 ARG cc_start: 0.7704 (mtp85) cc_final: 0.7312 (mtp85) REVERT: F 294 ARG cc_start: 0.7263 (mtm110) cc_final: 0.6842 (ptp-170) REVERT: F 322 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8269 (mt-10) REVERT: F 333 GLU cc_start: 0.7845 (tt0) cc_final: 0.7627 (tt0) REVERT: F 353 ARG cc_start: 0.7068 (mmm-85) cc_final: 0.6661 (mtm-85) REVERT: F 389 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.7138 (mtm110) REVERT: F 391 GLN cc_start: 0.7720 (tp40) cc_final: 0.7197 (mp10) REVERT: F 477 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.8827 (mtt180) REVERT: F 535 LYS cc_start: 0.8069 (tttm) cc_final: 0.7727 (ttpt) REVERT: O 103 LYS cc_start: 0.8174 (mtpp) cc_final: 0.7763 (mtmt) REVERT: O 156 SER cc_start: 0.9166 (OUTLIER) cc_final: 0.8854 (p) REVERT: O 191 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7986 (mt-10) REVERT: O 232 MET cc_start: 0.7713 (mmm) cc_final: 0.7432 (tmm) REVERT: O 239 GLU cc_start: 0.8000 (pm20) cc_final: 0.7532 (mm-30) REVERT: O 294 ARG cc_start: 0.7233 (mtm110) cc_final: 0.6723 (ptp-170) REVERT: O 333 GLU cc_start: 0.8008 (tt0) cc_final: 0.7602 (tm-30) REVERT: O 389 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7262 (ttp-110) REVERT: O 436 MET cc_start: 0.7757 (ttt) cc_final: 0.7480 (ttm) REVERT: O 502 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7783 (mt0) REVERT: O 535 LYS cc_start: 0.8091 (tttm) cc_final: 0.7742 (ttpt) REVERT: P 103 LYS cc_start: 0.8182 (mmmm) cc_final: 0.7801 (mttp) REVERT: P 156 SER cc_start: 0.9161 (OUTLIER) cc_final: 0.8858 (p) REVERT: P 191 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8086 (mt-10) REVERT: P 232 MET cc_start: 0.7811 (mmm) cc_final: 0.7475 (tmm) REVERT: P 291 ARG cc_start: 0.7710 (mtp85) cc_final: 0.7449 (mtp85) REVERT: P 294 ARG cc_start: 0.6995 (mtp180) cc_final: 0.6436 (ptp-170) REVERT: P 333 GLU cc_start: 0.7861 (tt0) cc_final: 0.7436 (tm-30) REVERT: P 353 ARG cc_start: 0.7128 (mmm-85) cc_final: 0.6869 (mtm-85) REVERT: P 356 GLU cc_start: 0.7687 (tp30) cc_final: 0.7324 (mm-30) REVERT: P 387 TRP cc_start: 0.7788 (t-100) cc_final: 0.7582 (t-100) REVERT: P 476 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8403 (mm-30) REVERT: P 477 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8853 (mtt180) REVERT: P 502 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7543 (mt0) REVERT: P 535 LYS cc_start: 0.8116 (tttm) cc_final: 0.7762 (ttpt) REVERT: Q 103 LYS cc_start: 0.8188 (mtpp) cc_final: 0.7766 (mtmt) REVERT: Q 156 SER cc_start: 0.9173 (OUTLIER) cc_final: 0.8855 (p) REVERT: Q 191 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8087 (mt-10) REVERT: Q 232 MET cc_start: 0.7744 (mmm) cc_final: 0.7420 (tmm) REVERT: Q 286 LYS cc_start: 0.7965 (tptm) cc_final: 0.7742 (mmmt) REVERT: Q 287 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8134 (tm-30) REVERT: Q 288 MET cc_start: 0.8182 (mtm) cc_final: 0.7948 (mtp) REVERT: Q 291 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7440 (mtp85) REVERT: Q 294 ARG cc_start: 0.7190 (mtp180) cc_final: 0.6629 (ptp-170) REVERT: Q 333 GLU cc_start: 0.8021 (tt0) cc_final: 0.7761 (tt0) REVERT: Q 353 ARG cc_start: 0.6809 (tpp80) cc_final: 0.6580 (ttm-80) REVERT: Q 476 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8398 (mm-30) REVERT: Q 477 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8853 (mtt180) REVERT: Q 535 LYS cc_start: 0.8089 (tttm) cc_final: 0.7733 (ttpt) outliers start: 56 outliers final: 28 residues processed: 452 average time/residue: 1.4690 time to fit residues: 741.4922 Evaluate side-chains 450 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 406 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 156 SER Chi-restraints excluded: chain F residue 191 GLU Chi-restraints excluded: chain F residue 243 CYS Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 389 ARG Chi-restraints excluded: chain F residue 477 ARG Chi-restraints excluded: chain F residue 503 ASP Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain O residue 138 LEU Chi-restraints excluded: chain O residue 156 SER Chi-restraints excluded: chain O residue 191 GLU Chi-restraints excluded: chain O residue 243 CYS Chi-restraints excluded: chain O residue 367 VAL Chi-restraints excluded: chain O residue 389 ARG Chi-restraints excluded: chain O residue 458 GLN Chi-restraints excluded: chain O residue 502 GLN Chi-restraints excluded: chain O residue 503 ASP Chi-restraints excluded: chain O residue 547 SER Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 138 LEU Chi-restraints excluded: chain P residue 156 SER Chi-restraints excluded: chain P residue 191 GLU Chi-restraints excluded: chain P residue 243 CYS Chi-restraints excluded: chain P residue 326 LEU Chi-restraints excluded: chain P residue 367 VAL Chi-restraints excluded: chain P residue 458 GLN Chi-restraints excluded: chain P residue 477 ARG Chi-restraints excluded: chain P residue 502 GLN Chi-restraints excluded: chain P residue 503 ASP Chi-restraints excluded: chain P residue 547 SER Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain Q residue 156 SER Chi-restraints excluded: chain Q residue 191 GLU Chi-restraints excluded: chain Q residue 243 CYS Chi-restraints excluded: chain Q residue 291 ARG Chi-restraints excluded: chain Q residue 297 GLU Chi-restraints excluded: chain Q residue 367 VAL Chi-restraints excluded: chain Q residue 477 ARG Chi-restraints excluded: chain Q residue 503 ASP Chi-restraints excluded: chain Q residue 547 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 38 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 190 optimal weight: 0.6980 chunk 179 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 199 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 365 HIS F 461 ASN O 365 HIS O 391 GLN O 461 ASN P 365 HIS P 391 GLN P 461 ASN Q 365 HIS Q 461 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.147249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.112114 restraints weight = 59282.554| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.97 r_work: 0.3067 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17916 Z= 0.141 Angle : 0.579 11.162 24292 Z= 0.301 Chirality : 0.071 1.475 2680 Planarity : 0.005 0.054 3104 Dihedral : 7.655 55.697 2632 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.91 % Allowed : 19.02 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.61 (0.18), residues: 2144 helix: 1.15 (0.17), residues: 932 sheet: -0.83 (0.25), residues: 380 loop : 0.37 (0.23), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 353 TYR 0.013 0.001 TYR P 292 PHE 0.017 0.001 PHE O 482 TRP 0.018 0.001 TRP O 387 HIS 0.008 0.001 HIS F 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (17916) covalent geometry : angle 0.57933 / 0.30 (24292) hydrogen bonds : bond 0.03511 / 2.36 ( 756) hydrogen bonds : angle 4.49901 / 3.14 ( 2172) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 416 time to evaluate : 0.964 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: F 103 LYS cc_start: 0.8216 (mtpp) cc_final: 0.7763 (mtmt) REVERT: F 156 SER cc_start: 0.9090 (OUTLIER) cc_final: 0.8858 (p) REVERT: F 169 LYS cc_start: 0.7002 (OUTLIER) cc_final: 0.6241 (tttm) REVERT: F 191 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8157 (mt-10) REVERT: F 232 MET cc_start: 0.7737 (mmm) cc_final: 0.7509 (tmm) REVERT: F 294 ARG cc_start: 0.7252 (mtm110) cc_final: 0.6858 (ptp-170) REVERT: F 322 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8304 (mt-10) REVERT: F 333 GLU cc_start: 0.7961 (tt0) cc_final: 0.7717 (tt0) REVERT: F 353 ARG cc_start: 0.7103 (mmm-85) cc_final: 0.6583 (mtm-85) REVERT: F 391 GLN cc_start: 0.7685 (tp40) cc_final: 0.7195 (mp10) REVERT: F 535 LYS cc_start: 0.8029 (tttm) cc_final: 0.7696 (ttpt) REVERT: O 103 LYS cc_start: 0.8211 (mtpp) cc_final: 0.7828 (mtmt) REVERT: O 156 SER cc_start: 0.9120 (OUTLIER) cc_final: 0.8877 (p) REVERT: O 191 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8081 (mt-10) REVERT: O 232 MET cc_start: 0.7726 (mmm) cc_final: 0.7464 (tmm) REVERT: O 239 GLU cc_start: 0.7954 (pm20) cc_final: 0.7537 (mm-30) REVERT: O 291 ARG cc_start: 0.7755 (mtp85) cc_final: 0.7498 (mtp85) REVERT: O 294 ARG cc_start: 0.7190 (mtm110) cc_final: 0.6693 (ptp-170) REVERT: O 333 GLU cc_start: 0.8176 (tt0) cc_final: 0.7935 (tt0) REVERT: O 391 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7655 (mp10) REVERT: O 502 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7932 (mt0) REVERT: O 535 LYS cc_start: 0.8052 (tttm) cc_final: 0.7707 (ttpt) REVERT: P 103 LYS cc_start: 0.8189 (mmmm) cc_final: 0.7820 (mttp) REVERT: P 156 SER cc_start: 0.9091 (OUTLIER) cc_final: 0.8862 (p) REVERT: P 191 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8158 (mt-10) REVERT: P 232 MET cc_start: 0.7777 (mmm) cc_final: 0.7508 (tmm) REVERT: P 239 GLU cc_start: 0.7937 (pm20) cc_final: 0.7480 (tp30) REVERT: P 291 ARG cc_start: 0.7796 (mtp85) cc_final: 0.7538 (mtp85) REVERT: P 294 ARG cc_start: 0.6973 (mtp180) cc_final: 0.6399 (ptp-170) REVERT: P 333 GLU cc_start: 0.8000 (tt0) cc_final: 0.7766 (tt0) REVERT: P 356 GLU cc_start: 0.7561 (tp30) cc_final: 0.7214 (mm-30) REVERT: P 387 TRP cc_start: 0.7834 (t-100) cc_final: 0.7592 (t-100) REVERT: P 502 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7513 (mt0) REVERT: P 535 LYS cc_start: 0.8055 (tttm) cc_final: 0.7718 (ttpt) REVERT: Q 103 LYS cc_start: 0.8247 (mtpp) cc_final: 0.7835 (mtmt) REVERT: Q 156 SER cc_start: 0.9126 (OUTLIER) cc_final: 0.8871 (p) REVERT: Q 191 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8130 (mt-10) REVERT: Q 232 MET cc_start: 0.7733 (mmm) cc_final: 0.7434 (tmm) REVERT: Q 286 LYS cc_start: 0.7989 (tptm) cc_final: 0.7770 (mmmt) REVERT: Q 288 MET cc_start: 0.8206 (mtm) cc_final: 0.7958 (mtp) REVERT: Q 294 ARG cc_start: 0.7115 (mtp180) cc_final: 0.6549 (ptp-170) REVERT: Q 333 GLU cc_start: 0.8062 (tt0) cc_final: 0.7814 (tt0) REVERT: Q 389 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7200 (ttp-110) REVERT: Q 434 VAL cc_start: 0.7656 (m) cc_final: 0.7373 (p) REVERT: Q 502 GLN cc_start: 0.7979 (mt0) cc_final: 0.7768 (mm-40) REVERT: Q 535 LYS cc_start: 0.8070 (tttm) cc_final: 0.7705 (ttpt) outliers start: 56 outliers final: 26 residues processed: 444 average time/residue: 1.4384 time to fit residues: 715.8318 Evaluate side-chains 451 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 412 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 156 SER Chi-restraints excluded: chain F residue 169 LYS Chi-restraints excluded: chain F residue 191 GLU Chi-restraints excluded: chain F residue 243 CYS Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 503 ASP Chi-restraints excluded: chain O residue 138 LEU Chi-restraints excluded: chain O residue 156 SER Chi-restraints excluded: chain O residue 191 GLU Chi-restraints excluded: chain O residue 243 CYS Chi-restraints excluded: chain O residue 367 VAL Chi-restraints excluded: chain O residue 391 GLN Chi-restraints excluded: chain O residue 458 GLN Chi-restraints excluded: chain O residue 502 GLN Chi-restraints excluded: chain O residue 503 ASP Chi-restraints excluded: chain O residue 547 SER Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 138 LEU Chi-restraints excluded: chain P residue 156 SER Chi-restraints excluded: chain P residue 191 GLU Chi-restraints excluded: chain P residue 243 CYS Chi-restraints excluded: chain P residue 326 LEU Chi-restraints excluded: chain P residue 367 VAL Chi-restraints excluded: chain P residue 458 GLN Chi-restraints excluded: chain P residue 502 GLN Chi-restraints excluded: chain P residue 503 ASP Chi-restraints excluded: chain P residue 547 SER Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain Q residue 156 SER Chi-restraints excluded: chain Q residue 191 GLU Chi-restraints excluded: chain Q residue 243 CYS Chi-restraints excluded: chain Q residue 367 VAL Chi-restraints excluded: chain Q residue 389 ARG Chi-restraints excluded: chain Q residue 503 ASP Chi-restraints excluded: chain Q residue 547 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 11 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 6 optimal weight: 0.0670 chunk 193 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 365 HIS F 461 ASN O 365 HIS ** P 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 365 HIS P 461 ASN Q 220 ASN Q 365 HIS Q 461 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.148872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.113977 restraints weight = 59501.956| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.98 r_work: 0.3055 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17916 Z= 0.135 Angle : 0.573 11.150 24292 Z= 0.297 Chirality : 0.071 1.481 2680 Planarity : 0.005 0.065 3104 Dihedral : 7.507 53.697 2632 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.65 % Allowed : 19.39 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.73 (0.19), residues: 2144 helix: 1.31 (0.17), residues: 932 sheet: -1.01 (0.25), residues: 392 loop : 0.52 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG P 353 TYR 0.014 0.001 TYR P 292 PHE 0.011 0.001 PHE O 163 TRP 0.033 0.001 TRP O 387 HIS 0.008 0.001 HIS O 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (17916) covalent geometry : angle 0.57343 / 0.30 (24292) hydrogen bonds : bond 0.03403 / 2.29 ( 756) hydrogen bonds : angle 4.40573 / 3.08 ( 2172) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 423 time to evaluate : 0.912 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: F 103 LYS cc_start: 0.8225 (mtpp) cc_final: 0.7761 (mtmt) REVERT: F 156 SER cc_start: 0.9091 (OUTLIER) cc_final: 0.8882 (p) REVERT: F 191 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8141 (mt-10) REVERT: F 232 MET cc_start: 0.7728 (mmm) cc_final: 0.7509 (tmm) REVERT: F 291 ARG cc_start: 0.7790 (mtp85) cc_final: 0.7538 (mtp85) REVERT: F 294 ARG cc_start: 0.7259 (mtm110) cc_final: 0.6868 (ptp-170) REVERT: F 322 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8276 (mt-10) REVERT: F 333 GLU cc_start: 0.7969 (tt0) cc_final: 0.7723 (tt0) REVERT: F 353 ARG cc_start: 0.7080 (mmm-85) cc_final: 0.6589 (mtm-85) REVERT: F 391 GLN cc_start: 0.7676 (tp40) cc_final: 0.7177 (mp10) REVERT: F 402 MET cc_start: 0.8726 (ttp) cc_final: 0.8362 (ttp) REVERT: F 434 VAL cc_start: 0.7562 (m) cc_final: 0.7285 (p) REVERT: F 535 LYS cc_start: 0.8001 (tttm) cc_final: 0.7623 (ttpt) REVERT: O 103 LYS cc_start: 0.8222 (mtpp) cc_final: 0.7819 (mtmt) REVERT: O 156 SER cc_start: 0.9130 (OUTLIER) cc_final: 0.8905 (p) REVERT: O 191 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8082 (mt-10) REVERT: O 232 MET cc_start: 0.7648 (mmm) cc_final: 0.7428 (tmm) REVERT: O 291 ARG cc_start: 0.7831 (mtp85) cc_final: 0.7605 (mtp85) REVERT: O 294 ARG cc_start: 0.7192 (mtm110) cc_final: 0.6692 (ptp-170) REVERT: O 297 GLU cc_start: 0.6869 (pp20) cc_final: 0.6599 (pp20) REVERT: O 333 GLU cc_start: 0.8143 (tt0) cc_final: 0.7943 (tt0) REVERT: O 402 MET cc_start: 0.8740 (ttp) cc_final: 0.8385 (ttp) REVERT: O 502 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7882 (mt0) REVERT: O 535 LYS cc_start: 0.8045 (tttm) cc_final: 0.7666 (ttpt) REVERT: P 81 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7920 (tpt170) REVERT: P 103 LYS cc_start: 0.8185 (mmmm) cc_final: 0.7810 (mttp) REVERT: P 156 SER cc_start: 0.9089 (OUTLIER) cc_final: 0.8880 (p) REVERT: P 191 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8163 (mt-10) REVERT: P 232 MET cc_start: 0.7757 (mmm) cc_final: 0.7498 (tmm) REVERT: P 239 GLU cc_start: 0.8006 (pm20) cc_final: 0.7565 (mp0) REVERT: P 294 ARG cc_start: 0.6940 (mtp180) cc_final: 0.6358 (ptp-170) REVERT: P 333 GLU cc_start: 0.8000 (tt0) cc_final: 0.7737 (tt0) REVERT: P 353 ARG cc_start: 0.7197 (mmm-85) cc_final: 0.6863 (mtm-85) REVERT: P 356 GLU cc_start: 0.7572 (tp30) cc_final: 0.7237 (mm-30) REVERT: P 387 TRP cc_start: 0.7821 (t-100) cc_final: 0.7603 (t-100) REVERT: P 476 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8141 (mm-30) REVERT: P 502 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7491 (mt0) REVERT: P 535 LYS cc_start: 0.8039 (tttm) cc_final: 0.7670 (ttpt) REVERT: Q 103 LYS cc_start: 0.8268 (mtpp) cc_final: 0.7840 (mtmt) REVERT: Q 156 SER cc_start: 0.9137 (OUTLIER) cc_final: 0.8902 (p) REVERT: Q 232 MET cc_start: 0.7723 (mmm) cc_final: 0.7430 (tmm) REVERT: Q 235 HIS cc_start: 0.8042 (m90) cc_final: 0.7766 (m90) REVERT: Q 286 LYS cc_start: 0.7903 (tptm) cc_final: 0.7668 (mmmt) REVERT: Q 288 MET cc_start: 0.8208 (mtm) cc_final: 0.7964 (mtp) REVERT: Q 294 ARG cc_start: 0.7075 (mtp180) cc_final: 0.6466 (ptp-170) REVERT: Q 333 GLU cc_start: 0.8108 (tt0) cc_final: 0.7846 (tt0) REVERT: Q 353 ARG cc_start: 0.6914 (ttm-80) cc_final: 0.6380 (mtm-85) REVERT: Q 402 MET cc_start: 0.8743 (ttp) cc_final: 0.8372 (ttp) REVERT: Q 434 VAL cc_start: 0.7594 (m) cc_final: 0.7300 (p) REVERT: Q 535 LYS cc_start: 0.8118 (tttm) cc_final: 0.7758 (ttpt) REVERT: Q 603 GLN cc_start: 0.8326 (pt0) cc_final: 0.7529 (pt0) outliers start: 51 outliers final: 28 residues processed: 449 average time/residue: 1.4208 time to fit residues: 716.3858 Evaluate side-chains 429 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 391 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 156 SER Chi-restraints excluded: chain F residue 191 GLU Chi-restraints excluded: chain F residue 243 CYS Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 503 ASP Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain O residue 138 LEU Chi-restraints excluded: chain O residue 156 SER Chi-restraints excluded: chain O residue 191 GLU Chi-restraints excluded: chain O residue 243 CYS Chi-restraints excluded: chain O residue 367 VAL Chi-restraints excluded: chain O residue 458 GLN Chi-restraints excluded: chain O residue 502 GLN Chi-restraints excluded: chain O residue 503 ASP Chi-restraints excluded: chain O residue 547 SER Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 81 ARG Chi-restraints excluded: chain P residue 138 LEU Chi-restraints excluded: chain P residue 156 SER Chi-restraints excluded: chain P residue 191 GLU Chi-restraints excluded: chain P residue 243 CYS Chi-restraints excluded: chain P residue 326 LEU Chi-restraints excluded: chain P residue 367 VAL Chi-restraints excluded: chain P residue 458 GLN Chi-restraints excluded: chain P residue 502 GLN Chi-restraints excluded: chain P residue 503 ASP Chi-restraints excluded: chain P residue 547 SER Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain Q residue 156 SER Chi-restraints excluded: chain Q residue 243 CYS Chi-restraints excluded: chain Q residue 296 LEU Chi-restraints excluded: chain Q residue 367 VAL Chi-restraints excluded: chain Q residue 503 ASP Chi-restraints excluded: chain Q residue 547 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 94 optimal weight: 0.0170 chunk 53 optimal weight: 0.9990 chunk 174 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 201 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 220 ASN F 365 HIS F 461 ASN O 365 HIS P 365 HIS P 461 ASN Q 220 ASN Q 365 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.148773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.113507 restraints weight = 59134.243| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.99 r_work: 0.3074 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.5122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17916 Z= 0.135 Angle : 0.574 11.189 24292 Z= 0.296 Chirality : 0.071 1.492 2680 Planarity : 0.005 0.070 3104 Dihedral : 7.366 54.499 2632 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.29 % Allowed : 20.48 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.91 (0.19), residues: 2144 helix: 1.51 (0.17), residues: 932 sheet: -0.96 (0.25), residues: 392 loop : 0.58 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG P 353 TYR 0.014 0.001 TYR P 292 PHE 0.011 0.001 PHE P 163 TRP 0.030 0.001 TRP O 387 HIS 0.007 0.001 HIS F 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (17916) covalent geometry : angle 0.57382 / 0.30 (24292) hydrogen bonds : bond 0.03379 / 2.27 ( 756) hydrogen bonds : angle 4.31770 / 3.01 ( 2172) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 412 time to evaluate : 1.210 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: F 103 LYS cc_start: 0.8227 (mtpp) cc_final: 0.7757 (mtmt) REVERT: F 232 MET cc_start: 0.7792 (mmm) cc_final: 0.7558 (tmm) REVERT: F 291 ARG cc_start: 0.7809 (mtp85) cc_final: 0.7573 (mtp85) REVERT: F 294 ARG cc_start: 0.7229 (mtm110) cc_final: 0.6816 (ptp-170) REVERT: F 322 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8199 (mt-10) REVERT: F 333 GLU cc_start: 0.8081 (tt0) cc_final: 0.7854 (tt0) REVERT: F 353 ARG cc_start: 0.7076 (mmm-85) cc_final: 0.6612 (mtm-85) REVERT: F 402 MET cc_start: 0.8707 (ttp) cc_final: 0.8352 (ttp) REVERT: F 434 VAL cc_start: 0.7544 (m) cc_final: 0.7270 (p) REVERT: F 535 LYS cc_start: 0.8041 (tttm) cc_final: 0.7704 (ttpt) REVERT: O 103 LYS cc_start: 0.8226 (mtpp) cc_final: 0.7799 (mtmt) REVERT: O 191 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8126 (mt-10) REVERT: O 232 MET cc_start: 0.7652 (mmm) cc_final: 0.7443 (tmm) REVERT: O 291 ARG cc_start: 0.7829 (mtp85) cc_final: 0.7569 (mtp85) REVERT: O 294 ARG cc_start: 0.7189 (mtm110) cc_final: 0.6690 (ptp-170) REVERT: O 333 GLU cc_start: 0.8122 (tt0) cc_final: 0.7916 (tt0) REVERT: O 402 MET cc_start: 0.8713 (ttp) cc_final: 0.8349 (ttp) REVERT: O 411 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.6062 (mtt-85) REVERT: O 502 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7810 (mt0) REVERT: O 535 LYS cc_start: 0.8085 (tttm) cc_final: 0.7696 (ttpt) REVERT: P 81 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7945 (tpt170) REVERT: P 103 LYS cc_start: 0.8197 (mmmm) cc_final: 0.7811 (mttp) REVERT: P 232 MET cc_start: 0.7806 (mmm) cc_final: 0.7521 (tmm) REVERT: P 291 ARG cc_start: 0.7806 (mtp85) cc_final: 0.7538 (mtp85) REVERT: P 294 ARG cc_start: 0.6943 (mtp180) cc_final: 0.6342 (ptp-170) REVERT: P 333 GLU cc_start: 0.7964 (tt0) cc_final: 0.7673 (tt0) REVERT: P 353 ARG cc_start: 0.7153 (mmm-85) cc_final: 0.6773 (mtm-85) REVERT: P 356 GLU cc_start: 0.7590 (tp30) cc_final: 0.7258 (mm-30) REVERT: P 387 TRP cc_start: 0.7875 (t-100) cc_final: 0.7614 (t-100) REVERT: P 391 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7614 (mp10) REVERT: P 535 LYS cc_start: 0.8075 (tttm) cc_final: 0.7706 (ttpt) REVERT: Q 103 LYS cc_start: 0.8240 (mtpp) cc_final: 0.7756 (mtmt) REVERT: Q 156 SER cc_start: 0.9124 (OUTLIER) cc_final: 0.8910 (p) REVERT: Q 191 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8101 (mt-10) REVERT: Q 232 MET cc_start: 0.7712 (mmm) cc_final: 0.7408 (tmm) REVERT: Q 235 HIS cc_start: 0.8035 (m90) cc_final: 0.7773 (m90) REVERT: Q 286 LYS cc_start: 0.7890 (tptm) cc_final: 0.7647 (mmmt) REVERT: Q 288 MET cc_start: 0.8200 (mtm) cc_final: 0.7965 (mtp) REVERT: Q 294 ARG cc_start: 0.7058 (mtp180) cc_final: 0.6441 (ptp-170) REVERT: Q 322 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8173 (mt-10) REVERT: Q 333 GLU cc_start: 0.8000 (tt0) cc_final: 0.7768 (tt0) REVERT: Q 353 ARG cc_start: 0.6900 (ttm-80) cc_final: 0.6378 (mtm-85) REVERT: Q 391 GLN cc_start: 0.7662 (tp40) cc_final: 0.7117 (mp10) REVERT: Q 402 MET cc_start: 0.8737 (ttp) cc_final: 0.8361 (ttp) REVERT: Q 434 VAL cc_start: 0.7518 (m) cc_final: 0.7263 (p) REVERT: F 602 GLN cc_start: 0.8370 (pt0) cc_final: 0.7792 (pt0) outliers start: 44 outliers final: 22 residues processed: 434 average time/residue: 1.4291 time to fit residues: 695.7853 Evaluate side-chains 432 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 403 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 243 CYS Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 503 ASP Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain O residue 138 LEU Chi-restraints excluded: chain O residue 191 GLU Chi-restraints excluded: chain O residue 243 CYS Chi-restraints excluded: chain O residue 411 ARG Chi-restraints excluded: chain O residue 502 GLN Chi-restraints excluded: chain O residue 503 ASP Chi-restraints excluded: chain O residue 547 SER Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 81 ARG Chi-restraints excluded: chain P residue 138 LEU Chi-restraints excluded: chain P residue 243 CYS Chi-restraints excluded: chain P residue 326 LEU Chi-restraints excluded: chain P residue 391 GLN Chi-restraints excluded: chain P residue 502 GLN Chi-restraints excluded: chain P residue 503 ASP Chi-restraints excluded: chain P residue 547 SER Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain Q residue 156 SER Chi-restraints excluded: chain Q residue 191 GLU Chi-restraints excluded: chain Q residue 243 CYS Chi-restraints excluded: chain Q residue 503 ASP Chi-restraints excluded: chain Q residue 547 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 0 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 161 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 220 ASN F 365 HIS O 220 ASN ** O 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 365 HIS P 365 HIS P 461 ASN Q 220 ASN Q 365 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.148485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.113496 restraints weight = 59435.313| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.98 r_work: 0.3079 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17916 Z= 0.168 Angle : 0.584 11.153 24292 Z= 0.301 Chirality : 0.072 1.487 2680 Planarity : 0.005 0.065 3104 Dihedral : 7.468 59.941 2628 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.92 % Allowed : 21.15 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.91 (0.19), residues: 2144 helix: 1.52 (0.17), residues: 932 sheet: -0.97 (0.25), residues: 392 loop : 0.57 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG P 353 TYR 0.015 0.001 TYR P 292 PHE 0.013 0.001 PHE O 163 TRP 0.031 0.001 TRP O 387 HIS 0.007 0.001 HIS O 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (17916) covalent geometry : angle 0.58355 / 0.30 (24292) hydrogen bonds : bond 0.03545 / 2.38 ( 756) hydrogen bonds : angle 4.32549 / 3.02 ( 2172) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 417 time to evaluate : 0.913 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: F 103 LYS cc_start: 0.8210 (mtpp) cc_final: 0.7684 (mttp) REVERT: F 232 MET cc_start: 0.7802 (mmm) cc_final: 0.7544 (tmm) REVERT: F 282 LEU cc_start: 0.8668 (mm) cc_final: 0.8410 (mp) REVERT: F 294 ARG cc_start: 0.7294 (mtm110) cc_final: 0.6850 (ptp-170) REVERT: F 322 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8245 (mt-10) REVERT: F 333 GLU cc_start: 0.7948 (tt0) cc_final: 0.7701 (tt0) REVERT: F 353 ARG cc_start: 0.7098 (mmm-85) cc_final: 0.6642 (mtm-85) REVERT: F 391 GLN cc_start: 0.7642 (tp40) cc_final: 0.7355 (mm110) REVERT: F 436 MET cc_start: 0.8068 (ttt) cc_final: 0.7637 (ttm) REVERT: F 535 LYS cc_start: 0.8080 (tttm) cc_final: 0.7769 (ttpt) REVERT: O 101 GLU cc_start: 0.8800 (tm-30) cc_final: 0.7616 (tm-30) REVERT: O 103 LYS cc_start: 0.8198 (mtpp) cc_final: 0.7734 (mtmt) REVERT: O 291 ARG cc_start: 0.7782 (mtp85) cc_final: 0.7519 (mtp85) REVERT: O 294 ARG cc_start: 0.7201 (mtm110) cc_final: 0.6709 (ptp-170) REVERT: O 411 ARG cc_start: 0.6905 (OUTLIER) cc_final: 0.6065 (mtt-85) REVERT: O 436 MET cc_start: 0.8115 (ttm) cc_final: 0.7771 (ttp) REVERT: O 502 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7765 (mt0) REVERT: O 535 LYS cc_start: 0.8137 (tttm) cc_final: 0.7752 (ttpt) REVERT: P 81 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7948 (tpt170) REVERT: P 103 LYS cc_start: 0.8211 (mmmm) cc_final: 0.7847 (mttp) REVERT: P 232 MET cc_start: 0.7784 (mmm) cc_final: 0.7458 (tmm) REVERT: P 291 ARG cc_start: 0.7793 (mtp85) cc_final: 0.7542 (mtp85) REVERT: P 294 ARG cc_start: 0.6974 (mtp180) cc_final: 0.6359 (ptp-170) REVERT: P 333 GLU cc_start: 0.7949 (tt0) cc_final: 0.7691 (tt0) REVERT: P 353 ARG cc_start: 0.7168 (mmm-85) cc_final: 0.6843 (mtm-85) REVERT: P 356 GLU cc_start: 0.7674 (tp30) cc_final: 0.7349 (mm-30) REVERT: P 387 TRP cc_start: 0.8025 (t-100) cc_final: 0.7795 (t-100) REVERT: P 502 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7461 (mt0) REVERT: P 535 LYS cc_start: 0.8124 (tttm) cc_final: 0.7751 (ttpt) REVERT: Q 103 LYS cc_start: 0.8230 (mtpp) cc_final: 0.7698 (mttp) REVERT: Q 156 SER cc_start: 0.9156 (OUTLIER) cc_final: 0.8938 (p) REVERT: Q 232 MET cc_start: 0.7757 (mmm) cc_final: 0.7449 (tmm) REVERT: Q 235 HIS cc_start: 0.8095 (m90) cc_final: 0.7799 (m90) REVERT: Q 286 LYS cc_start: 0.7973 (tptm) cc_final: 0.7727 (mmmt) REVERT: Q 288 MET cc_start: 0.8179 (mtm) cc_final: 0.7940 (mtp) REVERT: Q 294 ARG cc_start: 0.7101 (mtp180) cc_final: 0.6476 (ptp-170) REVERT: Q 333 GLU cc_start: 0.7877 (tt0) cc_final: 0.7650 (tt0) REVERT: Q 353 ARG cc_start: 0.6942 (ttm-80) cc_final: 0.6427 (mtm-85) REVERT: Q 411 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.6113 (mtt-85) REVERT: Q 436 MET cc_start: 0.7812 (ttp) cc_final: 0.7477 (ttp) outliers start: 37 outliers final: 21 residues processed: 433 average time/residue: 1.4666 time to fit residues: 710.6252 Evaluate side-chains 427 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 400 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 243 CYS Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 503 ASP Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain O residue 138 LEU Chi-restraints excluded: chain O residue 243 CYS Chi-restraints excluded: chain O residue 411 ARG Chi-restraints excluded: chain O residue 502 GLN Chi-restraints excluded: chain O residue 503 ASP Chi-restraints excluded: chain O residue 547 SER Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 81 ARG Chi-restraints excluded: chain P residue 138 LEU Chi-restraints excluded: chain P residue 243 CYS Chi-restraints excluded: chain P residue 326 LEU Chi-restraints excluded: chain P residue 502 GLN Chi-restraints excluded: chain P residue 503 ASP Chi-restraints excluded: chain P residue 547 SER Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain Q residue 156 SER Chi-restraints excluded: chain Q residue 243 CYS Chi-restraints excluded: chain Q residue 367 VAL Chi-restraints excluded: chain Q residue 411 ARG Chi-restraints excluded: chain Q residue 503 ASP Chi-restraints excluded: chain Q residue 547 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 215 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 76 optimal weight: 0.3980 chunk 102 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 220 ASN ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 365 HIS O 220 ASN ** O 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 365 HIS P 365 HIS P 461 ASN Q 220 ASN Q 365 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.146891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.111381 restraints weight = 58949.887| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.02 r_work: 0.3061 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.5241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17916 Z= 0.147 Angle : 0.578 11.187 24292 Z= 0.297 Chirality : 0.072 1.493 2680 Planarity : 0.005 0.065 3104 Dihedral : 7.356 59.317 2628 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.82 % Allowed : 22.14 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.96 (0.19), residues: 2144 helix: 1.57 (0.17), residues: 936 sheet: -0.95 (0.25), residues: 392 loop : 0.58 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P 353 TYR 0.015 0.001 TYR P 292 PHE 0.012 0.001 PHE P 163 TRP 0.032 0.001 TRP O 387 HIS 0.007 0.001 HIS P 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (17916) covalent geometry : angle 0.57752 / 0.30 (24292) hydrogen bonds : bond 0.03422 / 2.30 ( 756) hydrogen bonds : angle 4.28023 / 2.99 ( 2172) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 415 time to evaluate : 0.999 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: F 103 LYS cc_start: 0.8204 (mtpp) cc_final: 0.7645 (mttp) REVERT: F 232 MET cc_start: 0.7758 (mmm) cc_final: 0.7426 (tmm) REVERT: F 291 ARG cc_start: 0.7743 (mtp85) cc_final: 0.7484 (mtp85) REVERT: F 294 ARG cc_start: 0.7219 (mtm110) cc_final: 0.6743 (ptp-170) REVERT: F 322 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8229 (mt-10) REVERT: F 333 GLU cc_start: 0.7952 (tt0) cc_final: 0.7651 (tt0) REVERT: F 353 ARG cc_start: 0.7023 (mmm-85) cc_final: 0.6574 (mtm-85) REVERT: F 436 MET cc_start: 0.8057 (ttt) cc_final: 0.7736 (ttm) REVERT: F 535 LYS cc_start: 0.8071 (tttm) cc_final: 0.7740 (ttpt) REVERT: O 103 LYS cc_start: 0.8206 (mtpp) cc_final: 0.7700 (mtmt) REVERT: O 191 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7911 (mt-10) REVERT: O 291 ARG cc_start: 0.7750 (mtp85) cc_final: 0.7511 (mtp85) REVERT: O 294 ARG cc_start: 0.7171 (mtm110) cc_final: 0.6675 (ptp-170) REVERT: O 411 ARG cc_start: 0.6832 (OUTLIER) cc_final: 0.5988 (mtt-85) REVERT: O 436 MET cc_start: 0.8128 (ttm) cc_final: 0.7737 (ttp) REVERT: O 502 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7851 (mt0) REVERT: O 535 LYS cc_start: 0.8141 (tttm) cc_final: 0.7736 (ttpt) REVERT: P 81 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7938 (tpt170) REVERT: P 103 LYS cc_start: 0.8200 (mmmm) cc_final: 0.7813 (mttp) REVERT: P 232 MET cc_start: 0.7751 (mmm) cc_final: 0.7443 (tmm) REVERT: P 294 ARG cc_start: 0.6953 (mtp180) cc_final: 0.6409 (ptp-170) REVERT: P 333 GLU cc_start: 0.7939 (tt0) cc_final: 0.7685 (tt0) REVERT: P 353 ARG cc_start: 0.7043 (mmm-85) cc_final: 0.6700 (mtm-85) REVERT: P 356 GLU cc_start: 0.7631 (tp30) cc_final: 0.7297 (mm-30) REVERT: P 436 MET cc_start: 0.8111 (ttm) cc_final: 0.7777 (ttp) REVERT: P 476 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8187 (mm-30) REVERT: P 535 LYS cc_start: 0.8092 (tttm) cc_final: 0.7688 (ttpt) REVERT: Q 103 LYS cc_start: 0.8219 (mtpp) cc_final: 0.7664 (mttp) REVERT: Q 156 SER cc_start: 0.9139 (OUTLIER) cc_final: 0.8925 (p) REVERT: Q 191 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7964 (mt-10) REVERT: Q 232 MET cc_start: 0.7704 (mmm) cc_final: 0.7434 (tmm) REVERT: Q 235 HIS cc_start: 0.8091 (m90) cc_final: 0.7783 (m90) REVERT: Q 287 GLU cc_start: 0.8279 (tt0) cc_final: 0.7626 (tm-30) REVERT: Q 288 MET cc_start: 0.8165 (mtm) cc_final: 0.7919 (mtp) REVERT: Q 294 ARG cc_start: 0.7052 (mtp180) cc_final: 0.6426 (ptp-170) REVERT: Q 322 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8097 (mt-10) REVERT: Q 333 GLU cc_start: 0.7827 (tt0) cc_final: 0.7560 (tt0) REVERT: Q 353 ARG cc_start: 0.6878 (ttm-80) cc_final: 0.6353 (mtm-85) REVERT: Q 391 GLN cc_start: 0.7690 (tp40) cc_final: 0.7145 (mp10) outliers start: 35 outliers final: 21 residues processed: 430 average time/residue: 1.4573 time to fit residues: 702.0028 Evaluate side-chains 429 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 402 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 243 CYS Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 503 ASP Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain O residue 138 LEU Chi-restraints excluded: chain O residue 191 GLU Chi-restraints excluded: chain O residue 243 CYS Chi-restraints excluded: chain O residue 411 ARG Chi-restraints excluded: chain O residue 502 GLN Chi-restraints excluded: chain O residue 503 ASP Chi-restraints excluded: chain O residue 547 SER Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 81 ARG Chi-restraints excluded: chain P residue 138 LEU Chi-restraints excluded: chain P residue 243 CYS Chi-restraints excluded: chain P residue 326 LEU Chi-restraints excluded: chain P residue 503 ASP Chi-restraints excluded: chain P residue 547 SER Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain Q residue 156 SER Chi-restraints excluded: chain Q residue 191 GLU Chi-restraints excluded: chain Q residue 243 CYS Chi-restraints excluded: chain Q residue 367 VAL Chi-restraints excluded: chain Q residue 503 ASP Chi-restraints excluded: chain Q residue 547 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 138 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 47 optimal weight: 0.0050 chunk 181 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 184 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 220 ASN F 365 HIS O 220 ASN ** O 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 365 HIS P 365 HIS P 461 ASN Q 220 ASN Q 365 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.147592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.112358 restraints weight = 59043.930| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.99 r_work: 0.3073 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.5306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17916 Z= 0.132 Angle : 0.571 11.182 24292 Z= 0.293 Chirality : 0.071 1.495 2680 Planarity : 0.005 0.064 3104 Dihedral : 7.130 55.987 2628 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.92 % Allowed : 22.14 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.03 (0.19), residues: 2144 helix: 1.65 (0.18), residues: 936 sheet: -0.91 (0.25), residues: 392 loop : 0.58 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P 481 TYR 0.015 0.001 TYR F 292 PHE 0.011 0.001 PHE P 163 TRP 0.033 0.001 TRP O 387 HIS 0.006 0.001 HIS P 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (17916) covalent geometry : angle 0.57067 / 0.29 (24292) hydrogen bonds : bond 0.03314 / 2.22 ( 756) hydrogen bonds : angle 4.22725 / 2.96 ( 2172) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14761.36 seconds wall clock time: 250 minutes 8.49 seconds (15008.49 seconds total)