Starting phenix.real_space_refine on Mon Apr 6 00:25:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y7x_72674/04_2026/9y7x_72674.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y7x_72674/04_2026/9y7x_72674.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9y7x_72674/04_2026/9y7x_72674.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y7x_72674/04_2026/9y7x_72674.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9y7x_72674/04_2026/9y7x_72674.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y7x_72674/04_2026/9y7x_72674.map" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 9205 2.51 5 N 2309 2.21 5 O 2595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14199 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2784 Classifications: {'peptide': 344} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 328} Chain breaks: 1 Chain: "B" Number of atoms: 2821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2821 Classifications: {'peptide': 348} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 332} Chain breaks: 1 Chain: "C" Number of atoms: 2804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2804 Classifications: {'peptide': 346} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 330} Chain breaks: 1 Chain: "D" Number of atoms: 2830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2830 Classifications: {'peptide': 349} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 333} Chain breaks: 1 Chain: "E" Number of atoms: 2795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2795 Classifications: {'peptide': 345} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 329} Chain breaks: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.43, per 1000 atoms: 0.24 Number of scatterers: 14199 At special positions: 0 Unit cell: (94.08, 91.56, 133.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 2595 8.00 N 2309 7.00 C 9205 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 186 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 243 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 243 " distance=2.03 Simple disulfide: pdb=" SG CYS C 172 " - pdb=" SG CYS C 186 " distance=2.03 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS C 243 " distance=2.03 Simple disulfide: pdb=" SG CYS D 172 " - pdb=" SG CYS D 186 " distance=2.03 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 243 " distance=2.03 Simple disulfide: pdb=" SG CYS E 172 " - pdb=" SG CYS E 186 " distance=2.03 Simple disulfide: pdb=" SG CYS E 232 " - pdb=" SG CYS E 243 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 592.3 milliseconds 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3324 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 13 sheets defined 40.9% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 43 through 52 removed outlier: 3.600A pdb=" N LEU A 51 " --> pdb=" O PHE A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 127 removed outlier: 4.021A pdb=" N ASP A 125 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A 127 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 259 removed outlier: 3.561A pdb=" N ILE A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 272 Processing helix chain 'A' and resid 273 through 277 Processing helix chain 'A' and resid 282 through 305 removed outlier: 3.666A pdb=" N THR A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THR A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR A 298 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 347 removed outlier: 3.506A pdb=" N ARG A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN A 344 " --> pdb=" O PHE A 340 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 450 Proline residue: A 427 - end of helix Processing helix chain 'B' and resid 43 through 53 removed outlier: 3.505A pdb=" N LEU B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 127 removed outlier: 3.676A pdb=" N MET B 123 " --> pdb=" O ASP B 120 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ASP B 125 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER B 126 " --> pdb=" O MET B 123 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE B 127 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 260 removed outlier: 3.810A pdb=" N ILE B 259 " --> pdb=" O GLY B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 278 removed outlier: 3.866A pdb=" N SER B 265 " --> pdb=" O MET B 261 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N PHE B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TRP B 277 " --> pdb=" O TRP B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 306 removed outlier: 3.746A pdb=" N ALA B 306 " --> pdb=" O SER B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 346 removed outlier: 3.576A pdb=" N GLN B 344 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N HIS B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS B 346 " --> pdb=" O SER B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 441 removed outlier: 3.871A pdb=" N LYS B 416 " --> pdb=" O VAL B 412 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP B 419 " --> pdb=" O ALA B 415 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B 424 " --> pdb=" O THR B 420 " (cutoff:3.500A) Proline residue: B 427 - end of helix removed outlier: 4.064A pdb=" N ILE B 439 " --> pdb=" O ILE B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 450 removed outlier: 3.626A pdb=" N HIS B 446 " --> pdb=" O LYS B 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 52 Processing helix chain 'C' and resid 53 through 57 removed outlier: 4.106A pdb=" N GLY C 57 " --> pdb=" O ARG C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 108 removed outlier: 3.541A pdb=" N ALA C 108 " --> pdb=" O SER C 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 105 through 108' Processing helix chain 'C' and resid 120 through 127 removed outlier: 3.502A pdb=" N MET C 123 " --> pdb=" O ASP C 120 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASP C 125 " --> pdb=" O SER C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 272 Processing helix chain 'C' and resid 273 through 278 removed outlier: 3.736A pdb=" N TRP C 277 " --> pdb=" O TRP C 273 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE C 278 " --> pdb=" O VAL C 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 273 through 278' Processing helix chain 'C' and resid 282 through 305 removed outlier: 3.745A pdb=" N THR C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR C 299 " --> pdb=" O LEU C 295 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG C 305 " --> pdb=" O SER C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 346 removed outlier: 3.887A pdb=" N LEU C 332 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS C 346 " --> pdb=" O SER C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 450 Proline residue: C 427 - end of helix removed outlier: 3.952A pdb=" N ARG C 445 " --> pdb=" O TYR C 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 52 Processing helix chain 'D' and resid 53 through 57 removed outlier: 3.587A pdb=" N SER D 56 " --> pdb=" O GLY D 53 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY D 57 " --> pdb=" O ARG D 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 53 through 57' Processing helix chain 'D' and resid 105 through 108 Processing helix chain 'D' and resid 120 through 127 removed outlier: 3.565A pdb=" N MET D 123 " --> pdb=" O ASP D 120 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU D 124 " --> pdb=" O PRO D 121 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ASP D 125 " --> pdb=" O SER D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 261 removed outlier: 3.675A pdb=" N ILE D 259 " --> pdb=" O GLY D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 279 removed outlier: 3.694A pdb=" N SER D 265 " --> pdb=" O MET D 261 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL D 274 " --> pdb=" O ILE D 270 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N PHE D 276 " --> pdb=" O SER D 272 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TRP D 277 " --> pdb=" O TRP D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 304 removed outlier: 3.574A pdb=" N LEU D 289 " --> pdb=" O ALA D 285 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY D 290 " --> pdb=" O ARG D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 344 Processing helix chain 'D' and resid 345 through 347 No H-bonds generated for 'chain 'D' and resid 345 through 347' Processing helix chain 'D' and resid 409 through 450 removed outlier: 3.882A pdb=" N ALA D 424 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE D 426 " --> pdb=" O SER D 422 " (cutoff:3.500A) Proline residue: D 427 - end of helix removed outlier: 3.535A pdb=" N ARG D 445 " --> pdb=" O TYR D 441 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL D 449 " --> pdb=" O ARG D 445 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N HIS D 450 " --> pdb=" O HIS D 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 52 Processing helix chain 'E' and resid 53 through 57 removed outlier: 3.527A pdb=" N SER E 56 " --> pdb=" O GLY E 53 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLY E 57 " --> pdb=" O ARG E 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 57' Processing helix chain 'E' and resid 105 through 108 Processing helix chain 'E' and resid 120 through 127 removed outlier: 3.505A pdb=" N MET E 123 " --> pdb=" O ASP E 120 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU E 124 " --> pdb=" O PRO E 121 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ASP E 125 " --> pdb=" O SER E 122 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE E 127 " --> pdb=" O LEU E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 261 removed outlier: 3.643A pdb=" N ILE E 259 " --> pdb=" O GLY E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 273 Processing helix chain 'E' and resid 282 through 305 removed outlier: 3.853A pdb=" N ARG E 305 " --> pdb=" O SER E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 343 removed outlier: 3.872A pdb=" N LEU E 332 " --> pdb=" O VAL E 328 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG E 343 " --> pdb=" O ASN E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 346 No H-bonds generated for 'chain 'E' and resid 344 through 346' Processing helix chain 'E' and resid 411 through 450 removed outlier: 3.700A pdb=" N ASP E 419 " --> pdb=" O ALA E 415 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR E 420 " --> pdb=" O LYS E 416 " (cutoff:3.500A) Proline residue: E 427 - end of helix removed outlier: 3.630A pdb=" N TYR E 441 " --> pdb=" O TYR E 437 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE E 444 " --> pdb=" O THR E 440 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG E 445 " --> pdb=" O TYR E 441 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 86 removed outlier: 6.852A pdb=" N ASN A 72 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASN A 103 " --> pdb=" O ASN A 72 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASN A 95 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N PHE A 82 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ARG A 93 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N SER A 84 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ASP A 91 " --> pdb=" O SER A 84 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 91 through 103 current: chain 'A' and resid 159 through 171 Processing sheet with id=AA2, first strand: chain 'A' and resid 132 through 134 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 132 through 134 current: chain 'A' and resid 239 through 252 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 86 removed outlier: 6.962A pdb=" N ASN B 72 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASN B 103 " --> pdb=" O ASN B 72 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASN B 95 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N PHE B 82 " --> pdb=" O ARG B 93 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ARG B 93 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N SER B 84 " --> pdb=" O ASP B 91 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ASP B 91 " --> pdb=" O SER B 84 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 91 through 103 current: chain 'B' and resid 159 through 171 Processing sheet with id=AA4, first strand: chain 'B' and resid 133 through 134 removed outlier: 7.081A pdb=" N CYS B 243 " --> pdb=" O GLY B 230 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLY B 230 " --> pdb=" O CYS B 243 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLU B 245 " --> pdb=" O GLU B 228 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLU B 228 " --> pdb=" O GLU B 245 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LYS B 247 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLU B 226 " --> pdb=" O LYS B 247 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N HIS B 249 " --> pdb=" O LYS B 224 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 234 through 236 removed outlier: 3.563A pdb=" N GLY B 239 " --> pdb=" O TYR B 236 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 71 through 86 removed outlier: 7.375A pdb=" N ASN C 72 " --> pdb=" O ASN C 103 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ASN C 103 " --> pdb=" O ASN C 72 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASN C 95 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N PHE C 82 " --> pdb=" O ARG C 93 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ARG C 93 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER C 84 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ASP C 91 " --> pdb=" O SER C 84 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 91 through 103 current: chain 'C' and resid 159 through 171 Processing sheet with id=AA7, first strand: chain 'C' and resid 132 through 134 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 183 through 192 current: chain 'C' and resid 243 through 252 Processing sheet with id=AA8, first strand: chain 'C' and resid 234 through 236 Processing sheet with id=AA9, first strand: chain 'D' and resid 71 through 86 removed outlier: 6.838A pdb=" N ASN D 72 " --> pdb=" O ASN D 103 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ASN D 103 " --> pdb=" O ASN D 72 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN D 95 " --> pdb=" O ASN D 80 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N PHE D 82 " --> pdb=" O ARG D 93 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ARG D 93 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N SER D 84 " --> pdb=" O ASP D 91 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP D 91 " --> pdb=" O SER D 84 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 91 through 103 current: chain 'D' and resid 159 through 171 Processing sheet with id=AB1, first strand: chain 'D' and resid 132 through 134 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 183 through 192 current: chain 'D' and resid 239 through 252 Processing sheet with id=AB2, first strand: chain 'E' and resid 71 through 86 removed outlier: 6.876A pdb=" N ASN E 72 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ASN E 103 " --> pdb=" O ASN E 72 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE E 78 " --> pdb=" O PHE E 97 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASN E 95 " --> pdb=" O ASN E 80 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N PHE E 82 " --> pdb=" O ARG E 93 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ARG E 93 " --> pdb=" O PHE E 82 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N SER E 84 " --> pdb=" O ASP E 91 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASP E 91 " --> pdb=" O SER E 84 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 91 through 103 current: chain 'E' and resid 159 through 171 Processing sheet with id=AB3, first strand: chain 'E' and resid 132 through 134 Processing sheet with id=AB4, first strand: chain 'E' and resid 234 through 236 524 hydrogen bonds defined for protein. 1509 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: 1.93 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4293 1.34 - 1.46: 3650 1.46 - 1.59: 6455 1.59 - 1.71: 0 1.71 - 1.84: 150 Bond restraints: 14548 Sorted by residual: bond pdb=" N ILE D 278 " pdb=" CA ILE D 278 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.51e+00 bond pdb=" N VAL D 274 " pdb=" CA VAL D 274 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.41e-02 5.03e+03 7.06e+00 bond pdb=" N ARG E 343 " pdb=" CA ARG E 343 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.35e-02 5.49e+03 6.81e+00 bond pdb=" N VAL D 338 " pdb=" CA VAL D 338 " ideal model delta sigma weight residual 1.461 1.491 -0.030 1.17e-02 7.31e+03 6.37e+00 bond pdb=" N GLU E 137 " pdb=" CA GLU E 137 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.27e-02 6.20e+03 6.22e+00 ... (remaining 14543 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 18987 1.31 - 2.63: 583 2.63 - 3.94: 124 3.94 - 5.26: 17 5.26 - 6.57: 20 Bond angle restraints: 19731 Sorted by residual: angle pdb=" CA THR D 238 " pdb=" CB THR D 238 " pdb=" OG1 THR D 238 " ideal model delta sigma weight residual 109.60 104.16 5.44 1.50e+00 4.44e-01 1.32e+01 angle pdb=" CA ALA D 282 " pdb=" C ALA D 282 " pdb=" O ALA D 282 " ideal model delta sigma weight residual 122.63 118.13 4.50 1.29e+00 6.01e-01 1.22e+01 angle pdb=" N VAL D 338 " pdb=" CA VAL D 338 " pdb=" C VAL D 338 " ideal model delta sigma weight residual 110.42 107.15 3.27 9.60e-01 1.09e+00 1.16e+01 angle pdb=" CA ASP D 281 " pdb=" C ASP D 281 " pdb=" O ASP D 281 " ideal model delta sigma weight residual 121.54 117.86 3.68 1.16e+00 7.43e-01 1.01e+01 angle pdb=" N LEU D 289 " pdb=" CA LEU D 289 " pdb=" C LEU D 289 " ideal model delta sigma weight residual 111.07 107.94 3.13 1.07e+00 8.73e-01 8.58e+00 ... (remaining 19726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.33: 8380 25.33 - 50.67: 381 50.67 - 76.00: 30 76.00 - 101.33: 6 101.33 - 126.66: 1 Dihedral angle restraints: 8798 sinusoidal: 3677 harmonic: 5121 Sorted by residual: dihedral pdb=" C2 NAG D 501 " pdb=" C1 NAG D 501 " pdb=" O5 NAG D 501 " pdb=" C5 NAG D 501 " ideal model delta sinusoidal sigma weight residual -62.96 63.70 -126.66 1 3.00e+01 1.11e-03 1.70e+01 dihedral pdb=" CA PRO E 209 " pdb=" C PRO E 209 " pdb=" N VAL E 210 " pdb=" CA VAL E 210 " ideal model delta harmonic sigma weight residual 180.00 -161.83 -18.17 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" C3 NAG D 501 " pdb=" C1 NAG D 501 " pdb=" C2 NAG D 501 " pdb=" O5 NAG D 501 " ideal model delta sinusoidal sigma weight residual -55.55 35.42 -90.97 1 3.00e+01 1.11e-03 1.08e+01 ... (remaining 8795 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1725 0.048 - 0.097: 423 0.097 - 0.145: 80 0.145 - 0.194: 4 0.194 - 0.242: 2 Chirality restraints: 2234 Sorted by residual: chirality pdb=" CB VAL E 274 " pdb=" CA VAL E 274 " pdb=" CG1 VAL E 274 " pdb=" CG2 VAL E 274 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA LEU A 271 " pdb=" N LEU A 271 " pdb=" C LEU A 271 " pdb=" CB LEU A 271 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA VAL D 338 " pdb=" N VAL D 338 " pdb=" C VAL D 338 " pdb=" CB VAL D 338 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.11e-01 ... (remaining 2231 not shown) Planarity restraints: 2455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 210 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.47e+00 pdb=" C VAL E 210 " 0.032 2.00e-02 2.50e+03 pdb=" O VAL E 210 " -0.012 2.00e-02 2.50e+03 pdb=" N GLN E 211 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 120 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO A 121 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 121 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 121 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 208 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO E 209 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO E 209 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 209 " 0.024 5.00e-02 4.00e+02 ... (remaining 2452 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2447 2.77 - 3.30: 13550 3.30 - 3.83: 23683 3.83 - 4.37: 27912 4.37 - 4.90: 47752 Nonbonded interactions: 115344 Sorted by model distance: nonbonded pdb=" OG1 THR B 196 " pdb=" OD1 ASN B 198 " model vdw 2.235 3.040 nonbonded pdb=" OD2 ASP E 120 " pdb=" OG SER E 122 " model vdw 2.254 3.040 nonbonded pdb=" OG SER B 155 " pdb=" OD1 ASN B 157 " model vdw 2.255 3.040 nonbonded pdb=" OH TYR C 58 " pdb=" OD2 ASP C 104 " model vdw 2.266 3.040 nonbonded pdb=" OD1 ASP B 120 " pdb=" OH TYR C 195 " model vdw 2.284 3.040 ... (remaining 115339 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 43 through 346 or resid 412 through 502)) selection = (chain 'B' and (resid 43 through 346 or resid 412 through 502)) selection = (chain 'C' and (resid 43 through 346 or resid 412 through 502)) selection = (chain 'D' and (resid 43 through 346 or resid 412 through 502)) selection = (chain 'E' and (resid 43 through 346 or resid 412 through 450 or resid 502 throu \ gh 503)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.130 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 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 : 0.003 0.069 14558 Z= 0.175 Angle : 0.586 6.569 19751 Z= 0.325 Chirality : 0.043 0.242 2234 Planarity : 0.004 0.047 2455 Dihedral : 13.575 126.665 5444 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.17 (0.20), residues: 1712 helix: 1.17 (0.21), residues: 603 sheet: -0.10 (0.29), residues: 355 loop : -0.57 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 423 TYR 0.018 0.001 TYR A 441 PHE 0.026 0.001 PHE C 433 TRP 0.010 0.001 TRP C 277 HIS 0.004 0.000 HIS B 450 Details of bonding type rmsd covalent geometry : bond 0.00319 (14548) covalent geometry : angle 0.58109 (19731) SS BOND : bond 0.00216 ( 10) SS BOND : angle 2.38705 ( 20) hydrogen bonds : bond 0.15964 ( 524) hydrogen bonds : angle 5.97609 ( 1509) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.7954 (tmtt) cc_final: 0.7655 (tmtt) REVERT: A 131 ASP cc_start: 0.8457 (p0) cc_final: 0.8211 (p0) REVERT: A 260 GLN cc_start: 0.8465 (tm-30) cc_final: 0.8161 (tm-30) REVERT: A 297 MET cc_start: 0.8194 (ppp) cc_final: 0.7927 (ppp) REVERT: A 313 TYR cc_start: 0.7212 (m-80) cc_final: 0.6934 (m-80) REVERT: A 317 ILE cc_start: 0.9304 (tp) cc_final: 0.8985 (tp) REVERT: A 324 CYS cc_start: 0.8888 (m) cc_final: 0.8615 (m) REVERT: A 446 HIS cc_start: 0.8078 (m90) cc_final: 0.7773 (m90) REVERT: B 54 ARG cc_start: 0.6888 (tpm170) cc_final: 0.6682 (tpm170) REVERT: B 87 GLU cc_start: 0.8840 (pm20) cc_final: 0.8488 (pm20) REVERT: B 253 GLN cc_start: 0.7864 (mp10) cc_final: 0.7575 (mp10) REVERT: B 271 LEU cc_start: 0.8946 (mp) cc_final: 0.8346 (mt) REVERT: B 300 GLN cc_start: 0.8250 (tm-30) cc_final: 0.7693 (tm-30) REVERT: B 345 HIS cc_start: 0.7243 (t-170) cc_final: 0.7002 (t70) REVERT: C 314 VAL cc_start: 0.8410 (p) cc_final: 0.8209 (p) REVERT: D 251 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7654 (mt-10) REVERT: E 80 ASN cc_start: 0.8424 (t0) cc_final: 0.8042 (t0) REVERT: E 86 THR cc_start: 0.9067 (m) cc_final: 0.8630 (p) REVERT: E 280 MET cc_start: 0.7837 (mtm) cc_final: 0.7370 (mtm) REVERT: E 308 LEU cc_start: 0.8733 (mt) cc_final: 0.8462 (mp) REVERT: E 321 MET cc_start: 0.8281 (mmm) cc_final: 0.8067 (mmm) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.1027 time to fit residues: 48.1876 Evaluate side-chains 243 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 GLN C 149 ASN D 100 GLN D 141 ASN E 95 ASN ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.107382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.079965 restraints weight = 31340.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.083042 restraints weight = 16114.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.084990 restraints weight = 10745.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.086144 restraints weight = 8366.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.086918 restraints weight = 7225.455| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 14558 Z= 0.290 Angle : 0.661 9.036 19751 Z= 0.337 Chirality : 0.044 0.161 2234 Planarity : 0.004 0.051 2455 Dihedral : 5.958 69.600 2092 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.41 % Allowed : 10.95 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 (0.20), residues: 1712 helix: 1.29 (0.21), residues: 618 sheet: -0.28 (0.28), residues: 360 loop : -0.69 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 286 TYR 0.033 0.002 TYR A 441 PHE 0.023 0.002 PHE C 433 TRP 0.015 0.002 TRP B 273 HIS 0.005 0.001 HIS D 143 Details of bonding type rmsd covalent geometry : bond 0.00652 (14548) covalent geometry : angle 0.65958 (19731) SS BOND : bond 0.00450 ( 10) SS BOND : angle 1.55117 ( 20) hydrogen bonds : bond 0.04885 ( 524) hydrogen bonds : angle 4.95019 ( 1509) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 242 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.7977 (tmtt) cc_final: 0.7704 (tmtt) REVERT: A 148 ASP cc_start: 0.8625 (OUTLIER) cc_final: 0.8277 (t0) REVERT: A 260 GLN cc_start: 0.8545 (tm-30) cc_final: 0.7941 (tm-30) REVERT: A 313 TYR cc_start: 0.7594 (m-80) cc_final: 0.7291 (m-80) REVERT: A 325 LEU cc_start: 0.9092 (tt) cc_final: 0.8806 (mp) REVERT: B 253 GLN cc_start: 0.8176 (mp10) cc_final: 0.7961 (mp10) REVERT: B 271 LEU cc_start: 0.8994 (mp) cc_final: 0.8556 (mt) REVERT: B 300 GLN cc_start: 0.8279 (tm-30) cc_final: 0.7658 (tm-30) REVERT: B 345 HIS cc_start: 0.7301 (t-170) cc_final: 0.6994 (t70) REVERT: C 321 MET cc_start: 0.8519 (mmm) cc_final: 0.8204 (mmm) REVERT: E 80 ASN cc_start: 0.8629 (t0) cc_final: 0.8285 (t0) REVERT: E 86 THR cc_start: 0.9102 (m) cc_final: 0.8722 (p) REVERT: E 191 GLU cc_start: 0.7993 (tt0) cc_final: 0.7715 (tt0) REVERT: E 280 MET cc_start: 0.7953 (mtm) cc_final: 0.7428 (mtm) outliers start: 22 outliers final: 15 residues processed: 249 average time/residue: 0.0991 time to fit residues: 38.9784 Evaluate side-chains 245 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 229 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 436 PHE Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 273 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 42 optimal weight: 3.9990 chunk 162 optimal weight: 0.0870 chunk 23 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 141 optimal weight: 0.7980 chunk 109 optimal weight: 9.9990 chunk 28 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN C 100 GLN C 149 ASN E 95 ASN E 211 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.109733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.082236 restraints weight = 31064.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.085459 restraints weight = 16067.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.087459 restraints weight = 10665.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.088737 restraints weight = 8266.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.089530 restraints weight = 7051.301| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14558 Z= 0.121 Angle : 0.541 11.244 19751 Z= 0.276 Chirality : 0.041 0.150 2234 Planarity : 0.003 0.053 2455 Dihedral : 4.845 52.122 2092 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.09 % Allowed : 13.44 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.40 (0.20), residues: 1712 helix: 1.47 (0.21), residues: 623 sheet: -0.14 (0.28), residues: 370 loop : -0.51 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 343 TYR 0.022 0.001 TYR D 231 PHE 0.025 0.001 PHE C 433 TRP 0.023 0.001 TRP D 273 HIS 0.007 0.001 HIS A 446 Details of bonding type rmsd covalent geometry : bond 0.00265 (14548) covalent geometry : angle 0.53903 (19731) SS BOND : bond 0.00272 ( 10) SS BOND : angle 1.51912 ( 20) hydrogen bonds : bond 0.04133 ( 524) hydrogen bonds : angle 4.60144 ( 1509) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 252 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.7903 (tmtt) cc_final: 0.7588 (tmtt) REVERT: A 101 GLN cc_start: 0.8725 (tt0) cc_final: 0.8265 (mt0) REVERT: A 148 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8316 (t0) REVERT: A 297 MET cc_start: 0.8096 (ppp) cc_final: 0.7518 (ppp) REVERT: A 313 TYR cc_start: 0.7561 (m-80) cc_final: 0.7134 (m-10) REVERT: B 271 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8573 (mt) REVERT: B 300 GLN cc_start: 0.8236 (tm-30) cc_final: 0.7618 (tm-30) REVERT: B 345 HIS cc_start: 0.7308 (t-170) cc_final: 0.7068 (t70) REVERT: D 225 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8419 (tp30) REVERT: D 327 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.7485 (t80) REVERT: E 80 ASN cc_start: 0.8587 (t0) cc_final: 0.8312 (t0) REVERT: E 86 THR cc_start: 0.9107 (m) cc_final: 0.8784 (p) REVERT: E 137 GLU cc_start: 0.7835 (pt0) cc_final: 0.7287 (pt0) REVERT: E 191 GLU cc_start: 0.7853 (tt0) cc_final: 0.7636 (tt0) REVERT: E 280 MET cc_start: 0.7944 (mtm) cc_final: 0.7466 (mtm) outliers start: 17 outliers final: 8 residues processed: 256 average time/residue: 0.0991 time to fit residues: 40.2015 Evaluate side-chains 241 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 230 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 436 PHE Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 327 PHE Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 211 GLN Chi-restraints excluded: chain E residue 273 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 100 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 138 optimal weight: 0.0370 chunk 94 optimal weight: 0.0470 chunk 58 optimal weight: 40.0000 chunk 38 optimal weight: 5.9990 chunk 75 optimal weight: 0.0030 chunk 1 optimal weight: 8.9990 chunk 83 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 overall best weight: 2.2170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 ASN C 149 ASN C 300 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.110445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.082524 restraints weight = 30592.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.085763 restraints weight = 15403.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.087819 restraints weight = 10164.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.089106 restraints weight = 7896.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.089920 restraints weight = 6734.683| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 14558 Z= 0.154 Angle : 0.547 9.176 19751 Z= 0.281 Chirality : 0.041 0.179 2234 Planarity : 0.003 0.043 2455 Dihedral : 4.663 49.827 2092 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.28 % Allowed : 15.17 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.39 (0.20), residues: 1712 helix: 1.50 (0.21), residues: 618 sheet: -0.12 (0.28), residues: 369 loop : -0.55 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 445 TYR 0.023 0.001 TYR A 441 PHE 0.024 0.001 PHE C 433 TRP 0.022 0.001 TRP D 273 HIS 0.003 0.001 HIS A 446 Details of bonding type rmsd covalent geometry : bond 0.00347 (14548) covalent geometry : angle 0.54558 (19731) SS BOND : bond 0.00398 ( 10) SS BOND : angle 1.21779 ( 20) hydrogen bonds : bond 0.04030 ( 524) hydrogen bonds : angle 4.56049 ( 1509) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 239 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.7881 (tmtt) cc_final: 0.7581 (tmtt) REVERT: A 101 GLN cc_start: 0.8750 (tt0) cc_final: 0.8373 (mt0) REVERT: A 148 ASP cc_start: 0.8630 (OUTLIER) cc_final: 0.8322 (t0) REVERT: A 260 GLN cc_start: 0.8506 (tm-30) cc_final: 0.7723 (tm-30) REVERT: A 313 TYR cc_start: 0.7675 (m-80) cc_final: 0.7430 (m-80) REVERT: B 300 GLN cc_start: 0.8246 (tm-30) cc_final: 0.7592 (tm-30) REVERT: B 345 HIS cc_start: 0.7323 (t-170) cc_final: 0.6923 (t70) REVERT: B 411 PHE cc_start: 0.5077 (m-10) cc_final: 0.4794 (m-80) REVERT: E 80 ASN cc_start: 0.8601 (t0) cc_final: 0.8284 (t0) REVERT: E 86 THR cc_start: 0.9108 (m) cc_final: 0.8755 (p) REVERT: E 191 GLU cc_start: 0.7926 (tt0) cc_final: 0.7701 (tt0) REVERT: E 280 MET cc_start: 0.7995 (mtm) cc_final: 0.7524 (mtm) REVERT: E 436 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.7358 (m-80) outliers start: 20 outliers final: 12 residues processed: 243 average time/residue: 0.0993 time to fit residues: 38.1372 Evaluate side-chains 241 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 227 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 436 PHE Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 273 TRP Chi-restraints excluded: chain E residue 436 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 125 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 134 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 161 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN C 149 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.110897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.082859 restraints weight = 30715.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.086187 restraints weight = 15480.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.088317 restraints weight = 10163.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.089576 restraints weight = 7832.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.090414 restraints weight = 6711.855| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14558 Z= 0.138 Angle : 0.548 10.268 19751 Z= 0.278 Chirality : 0.041 0.159 2234 Planarity : 0.003 0.041 2455 Dihedral : 4.469 47.853 2092 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.54 % Allowed : 16.26 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.44 (0.20), residues: 1712 helix: 1.56 (0.21), residues: 619 sheet: -0.07 (0.28), residues: 369 loop : -0.57 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 445 TYR 0.022 0.001 TYR A 441 PHE 0.024 0.001 PHE C 433 TRP 0.025 0.001 TRP D 273 HIS 0.004 0.001 HIS A 446 Details of bonding type rmsd covalent geometry : bond 0.00308 (14548) covalent geometry : angle 0.54701 (19731) SS BOND : bond 0.00284 ( 10) SS BOND : angle 1.01830 ( 20) hydrogen bonds : bond 0.03832 ( 524) hydrogen bonds : angle 4.45990 ( 1509) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 241 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.7820 (tmtt) cc_final: 0.7518 (tmtt) REVERT: A 101 GLN cc_start: 0.8727 (tt0) cc_final: 0.8412 (mt0) REVERT: A 148 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8312 (t0) REVERT: A 260 GLN cc_start: 0.8516 (tm-30) cc_final: 0.8263 (tm-30) REVERT: A 273 TRP cc_start: 0.8721 (m-10) cc_final: 0.8444 (m-10) REVERT: A 313 TYR cc_start: 0.7714 (m-80) cc_final: 0.7477 (m-80) REVERT: B 93 ARG cc_start: 0.8513 (ttm110) cc_final: 0.8102 (ttm110) REVERT: B 271 LEU cc_start: 0.8994 (mt) cc_final: 0.8623 (mm) REVERT: B 300 GLN cc_start: 0.8250 (tm-30) cc_final: 0.7573 (tm-30) REVERT: B 345 HIS cc_start: 0.7313 (t-170) cc_final: 0.6910 (t70) REVERT: B 411 PHE cc_start: 0.5161 (m-10) cc_final: 0.4875 (m-80) REVERT: C 123 MET cc_start: 0.8258 (mpp) cc_final: 0.7854 (mpp) REVERT: E 80 ASN cc_start: 0.8598 (t0) cc_final: 0.8283 (t0) REVERT: E 86 THR cc_start: 0.9099 (m) cc_final: 0.8780 (p) REVERT: E 191 GLU cc_start: 0.7896 (tt0) cc_final: 0.7674 (tt0) REVERT: E 280 MET cc_start: 0.7998 (mtm) cc_final: 0.7553 (mtm) REVERT: E 436 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.7284 (m-80) outliers start: 24 outliers final: 14 residues processed: 251 average time/residue: 0.1020 time to fit residues: 39.8945 Evaluate side-chains 245 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 229 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 436 PHE Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 273 TRP Chi-restraints excluded: chain E residue 436 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 25 optimal weight: 0.7980 chunk 162 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 166 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 155 optimal weight: 0.2980 chunk 32 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 115 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN C 300 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.110063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.082141 restraints weight = 30536.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.085377 restraints weight = 15437.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.087444 restraints weight = 10230.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.088675 restraints weight = 7907.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.089501 restraints weight = 6799.379| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14558 Z= 0.169 Angle : 0.568 8.529 19751 Z= 0.288 Chirality : 0.041 0.171 2234 Planarity : 0.003 0.041 2455 Dihedral : 4.461 46.480 2092 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.73 % Allowed : 17.09 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.36 (0.20), residues: 1712 helix: 1.52 (0.21), residues: 623 sheet: -0.12 (0.28), residues: 370 loop : -0.63 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 54 TYR 0.023 0.001 TYR A 441 PHE 0.025 0.001 PHE C 433 TRP 0.065 0.001 TRP D 273 HIS 0.005 0.001 HIS A 446 Details of bonding type rmsd covalent geometry : bond 0.00380 (14548) covalent geometry : angle 0.56735 (19731) SS BOND : bond 0.00310 ( 10) SS BOND : angle 0.92424 ( 20) hydrogen bonds : bond 0.03881 ( 524) hydrogen bonds : angle 4.45188 ( 1509) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 238 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.7821 (tmtt) cc_final: 0.7540 (tmtt) REVERT: A 101 GLN cc_start: 0.8743 (tt0) cc_final: 0.8433 (mt0) REVERT: A 131 ASP cc_start: 0.8676 (p0) cc_final: 0.8411 (p0) REVERT: A 148 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8299 (t0) REVERT: A 260 GLN cc_start: 0.8539 (tm-30) cc_final: 0.8270 (tm-30) REVERT: A 321 MET cc_start: 0.8515 (mpp) cc_final: 0.8167 (mpp) REVERT: B 93 ARG cc_start: 0.8504 (ttm110) cc_final: 0.8078 (ttm110) REVERT: B 300 GLN cc_start: 0.8259 (tm-30) cc_final: 0.7561 (tm-30) REVERT: B 345 HIS cc_start: 0.7369 (t-170) cc_final: 0.6919 (t70) REVERT: B 411 PHE cc_start: 0.5224 (m-10) cc_final: 0.4931 (m-80) REVERT: C 123 MET cc_start: 0.8287 (mpp) cc_final: 0.7875 (mpp) REVERT: C 321 MET cc_start: 0.8668 (mmm) cc_final: 0.8212 (mmm) REVERT: E 80 ASN cc_start: 0.8635 (t0) cc_final: 0.8393 (t0) REVERT: E 86 THR cc_start: 0.9049 (m) cc_final: 0.8764 (p) REVERT: E 191 GLU cc_start: 0.7933 (tt0) cc_final: 0.7715 (tt0) REVERT: E 280 MET cc_start: 0.8005 (mtm) cc_final: 0.7545 (mtm) REVERT: E 436 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7247 (m-80) outliers start: 27 outliers final: 17 residues processed: 249 average time/residue: 0.1048 time to fit residues: 40.8128 Evaluate side-chains 247 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 228 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 436 PHE Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 273 TRP Chi-restraints excluded: chain E residue 436 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 59 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 139 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 153 optimal weight: 0.3980 chunk 113 optimal weight: 10.0000 chunk 2 optimal weight: 0.0570 chunk 79 optimal weight: 8.9990 chunk 13 optimal weight: 0.1980 chunk 105 optimal weight: 1.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN B 339 ASN C 149 ASN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.111977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.084281 restraints weight = 30259.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.087566 restraints weight = 15117.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.089644 restraints weight = 9937.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.090935 restraints weight = 7698.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.091749 restraints weight = 6572.875| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14558 Z= 0.107 Angle : 0.570 12.811 19751 Z= 0.285 Chirality : 0.041 0.246 2234 Planarity : 0.003 0.041 2455 Dihedral : 4.174 44.945 2092 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.54 % Allowed : 17.73 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.42 (0.20), residues: 1712 helix: 1.45 (0.21), residues: 622 sheet: 0.03 (0.28), residues: 369 loop : -0.55 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 54 TYR 0.023 0.001 TYR D 231 PHE 0.025 0.001 PHE C 433 TRP 0.035 0.001 TRP A 273 HIS 0.004 0.000 HIS A 446 Details of bonding type rmsd covalent geometry : bond 0.00235 (14548) covalent geometry : angle 0.56866 (19731) SS BOND : bond 0.00287 ( 10) SS BOND : angle 1.46256 ( 20) hydrogen bonds : bond 0.03594 ( 524) hydrogen bonds : angle 4.35914 ( 1509) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 243 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.7702 (tmtt) cc_final: 0.7451 (tmtt) REVERT: A 101 GLN cc_start: 0.8646 (tt0) cc_final: 0.8433 (mt0) REVERT: A 131 ASP cc_start: 0.8548 (p0) cc_final: 0.8270 (p0) REVERT: A 148 ASP cc_start: 0.8615 (OUTLIER) cc_final: 0.8323 (t0) REVERT: A 260 GLN cc_start: 0.8556 (tm-30) cc_final: 0.8296 (tm-30) REVERT: A 313 TYR cc_start: 0.7723 (m-80) cc_final: 0.7453 (m-80) REVERT: A 321 MET cc_start: 0.8488 (mpp) cc_final: 0.8203 (mpp) REVERT: B 93 ARG cc_start: 0.8479 (ttm110) cc_final: 0.8081 (ttm110) REVERT: B 273 TRP cc_start: 0.7074 (m-10) cc_final: 0.6864 (m-10) REVERT: B 300 GLN cc_start: 0.8252 (tm-30) cc_final: 0.7552 (tm-30) REVERT: B 345 HIS cc_start: 0.7331 (t-170) cc_final: 0.6911 (t70) REVERT: B 411 PHE cc_start: 0.5220 (m-10) cc_final: 0.4931 (m-80) REVERT: C 123 MET cc_start: 0.8225 (mpp) cc_final: 0.7851 (mpp) REVERT: E 80 ASN cc_start: 0.8560 (t0) cc_final: 0.8259 (t0) REVERT: E 86 THR cc_start: 0.9027 (m) cc_final: 0.8756 (p) REVERT: E 191 GLU cc_start: 0.7870 (tt0) cc_final: 0.7657 (tt0) REVERT: E 280 MET cc_start: 0.7996 (mtm) cc_final: 0.7678 (mtm) REVERT: E 436 PHE cc_start: 0.8088 (OUTLIER) cc_final: 0.7244 (m-80) outliers start: 24 outliers final: 16 residues processed: 251 average time/residue: 0.1041 time to fit residues: 40.8245 Evaluate side-chains 253 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 235 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 436 PHE Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 273 TRP Chi-restraints excluded: chain E residue 436 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 3 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 73 optimal weight: 0.1980 chunk 142 optimal weight: 5.9990 chunk 115 optimal weight: 0.0470 chunk 113 optimal weight: 5.9990 chunk 35 optimal weight: 0.2980 chunk 22 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 132 optimal weight: 20.0000 overall best weight: 1.2680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN C 300 GLN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.111787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.084092 restraints weight = 30275.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.087367 restraints weight = 15233.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.089459 restraints weight = 10015.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.090729 restraints weight = 7727.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.091538 restraints weight = 6625.282| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14558 Z= 0.118 Angle : 0.581 12.238 19751 Z= 0.288 Chirality : 0.042 0.230 2234 Planarity : 0.003 0.040 2455 Dihedral : 4.087 43.133 2092 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.47 % Allowed : 17.67 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.40 (0.20), residues: 1712 helix: 1.46 (0.21), residues: 622 sheet: 0.03 (0.28), residues: 364 loop : -0.60 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 445 TYR 0.021 0.001 TYR A 335 PHE 0.025 0.001 PHE C 433 TRP 0.026 0.001 TRP D 273 HIS 0.004 0.000 HIS A 446 Details of bonding type rmsd covalent geometry : bond 0.00264 (14548) covalent geometry : angle 0.57959 (19731) SS BOND : bond 0.00249 ( 10) SS BOND : angle 1.53867 ( 20) hydrogen bonds : bond 0.03562 ( 524) hydrogen bonds : angle 4.36024 ( 1509) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 234 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 GLN cc_start: 0.8635 (tt0) cc_final: 0.8339 (mt0) REVERT: A 131 ASP cc_start: 0.8565 (p0) cc_final: 0.8257 (p0) REVERT: A 148 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8345 (t0) REVERT: A 260 GLN cc_start: 0.8574 (tm-30) cc_final: 0.8299 (tm-30) REVERT: A 313 TYR cc_start: 0.7814 (m-80) cc_final: 0.7607 (m-80) REVERT: A 321 MET cc_start: 0.8539 (mpp) cc_final: 0.8258 (mpp) REVERT: B 93 ARG cc_start: 0.8497 (ttm110) cc_final: 0.8096 (ttm110) REVERT: B 300 GLN cc_start: 0.8242 (tm-30) cc_final: 0.7550 (tm-30) REVERT: B 345 HIS cc_start: 0.7378 (t-170) cc_final: 0.6918 (t70) REVERT: B 411 PHE cc_start: 0.5242 (m-10) cc_final: 0.4943 (m-80) REVERT: C 123 MET cc_start: 0.8254 (mpp) cc_final: 0.7877 (mpp) REVERT: C 321 MET cc_start: 0.8665 (mmm) cc_final: 0.8285 (mmm) REVERT: E 80 ASN cc_start: 0.8585 (t0) cc_final: 0.8270 (t0) REVERT: E 86 THR cc_start: 0.9003 (m) cc_final: 0.8745 (p) REVERT: E 191 GLU cc_start: 0.7910 (tt0) cc_final: 0.7700 (tt0) REVERT: E 280 MET cc_start: 0.7959 (mtm) cc_final: 0.7673 (mtm) REVERT: E 436 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7291 (m-80) outliers start: 23 outliers final: 18 residues processed: 239 average time/residue: 0.0988 time to fit residues: 37.3546 Evaluate side-chains 247 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 227 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 436 PHE Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 273 TRP Chi-restraints excluded: chain E residue 436 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 92 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 77 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.111346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.083557 restraints weight = 30413.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.086853 restraints weight = 15426.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.088964 restraints weight = 10147.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.090284 restraints weight = 7809.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.091085 restraints weight = 6652.149| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14558 Z= 0.140 Angle : 0.595 12.314 19751 Z= 0.295 Chirality : 0.042 0.207 2234 Planarity : 0.003 0.044 2455 Dihedral : 4.105 42.440 2092 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.47 % Allowed : 18.05 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.36 (0.20), residues: 1712 helix: 1.49 (0.21), residues: 621 sheet: -0.01 (0.28), residues: 355 loop : -0.67 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 445 TYR 0.020 0.001 TYR A 441 PHE 0.025 0.001 PHE C 433 TRP 0.049 0.001 TRP B 273 HIS 0.004 0.001 HIS A 446 Details of bonding type rmsd covalent geometry : bond 0.00319 (14548) covalent geometry : angle 0.59336 (19731) SS BOND : bond 0.00237 ( 10) SS BOND : angle 1.54204 ( 20) hydrogen bonds : bond 0.03633 ( 524) hydrogen bonds : angle 4.40529 ( 1509) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 227 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLN cc_start: 0.8632 (tt0) cc_final: 0.8343 (mt0) REVERT: A 131 ASP cc_start: 0.8579 (p0) cc_final: 0.8263 (p0) REVERT: A 148 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8345 (t0) REVERT: A 260 GLN cc_start: 0.8591 (tm-30) cc_final: 0.8272 (tm-30) REVERT: A 321 MET cc_start: 0.8550 (mpp) cc_final: 0.8267 (mpp) REVERT: B 93 ARG cc_start: 0.8484 (ttm110) cc_final: 0.8093 (ttm110) REVERT: B 300 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7554 (tm-30) REVERT: B 345 HIS cc_start: 0.7384 (t-170) cc_final: 0.6928 (t70) REVERT: B 411 PHE cc_start: 0.5188 (m-10) cc_final: 0.4896 (m-80) REVERT: C 123 MET cc_start: 0.8292 (mpp) cc_final: 0.7951 (mpp) REVERT: E 80 ASN cc_start: 0.8623 (t0) cc_final: 0.8293 (t0) REVERT: E 191 GLU cc_start: 0.7915 (tt0) cc_final: 0.7706 (tt0) REVERT: E 280 MET cc_start: 0.8009 (mtm) cc_final: 0.7691 (mtm) REVERT: E 436 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.7205 (m-80) outliers start: 23 outliers final: 19 residues processed: 234 average time/residue: 0.0992 time to fit residues: 36.4546 Evaluate side-chains 247 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 226 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 436 PHE Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 273 TRP Chi-restraints excluded: chain E residue 436 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 120 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 113 optimal weight: 0.1980 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN C 149 ASN D 249 HIS ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.112926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.085202 restraints weight = 30329.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.088536 restraints weight = 15252.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.090658 restraints weight = 10001.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.091989 restraints weight = 7718.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.092801 restraints weight = 6545.113| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 14558 Z= 0.108 Angle : 0.587 10.948 19751 Z= 0.291 Chirality : 0.042 0.270 2234 Planarity : 0.003 0.040 2455 Dihedral : 3.942 41.131 2092 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.41 % Allowed : 18.37 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 (0.20), residues: 1712 helix: 1.47 (0.21), residues: 620 sheet: 0.14 (0.29), residues: 351 loop : -0.61 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 445 TYR 0.033 0.001 TYR A 335 PHE 0.026 0.001 PHE C 433 TRP 0.055 0.001 TRP B 273 HIS 0.005 0.000 HIS A 446 Details of bonding type rmsd covalent geometry : bond 0.00244 (14548) covalent geometry : angle 0.58523 (19731) SS BOND : bond 0.00239 ( 10) SS BOND : angle 1.44439 ( 20) hydrogen bonds : bond 0.03500 ( 524) hydrogen bonds : angle 4.35093 ( 1509) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 234 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLN cc_start: 0.8588 (tt0) cc_final: 0.8376 (mt0) REVERT: A 131 ASP cc_start: 0.8517 (p0) cc_final: 0.8206 (p0) REVERT: A 260 GLN cc_start: 0.8605 (tm-30) cc_final: 0.8288 (tm-30) REVERT: A 313 TYR cc_start: 0.7786 (m-80) cc_final: 0.7570 (m-80) REVERT: A 321 MET cc_start: 0.8554 (mpp) cc_final: 0.8267 (mpp) REVERT: A 445 ARG cc_start: 0.8242 (tpt90) cc_final: 0.7838 (tpt90) REVERT: B 54 ARG cc_start: 0.6745 (tpm170) cc_final: 0.6405 (tpm170) REVERT: B 93 ARG cc_start: 0.8463 (ttm110) cc_final: 0.8091 (ttm110) REVERT: B 300 GLN cc_start: 0.8247 (tm-30) cc_final: 0.7515 (tm-30) REVERT: B 345 HIS cc_start: 0.7379 (t-170) cc_final: 0.6930 (t70) REVERT: B 411 PHE cc_start: 0.5211 (m-10) cc_final: 0.4931 (m-80) REVERT: C 123 MET cc_start: 0.8209 (mpp) cc_final: 0.7885 (mpp) REVERT: C 253 GLN cc_start: 0.9007 (mt0) cc_final: 0.8513 (mp10) REVERT: C 334 GLU cc_start: 0.9001 (tm-30) cc_final: 0.8750 (tm-30) REVERT: E 80 ASN cc_start: 0.8589 (t0) cc_final: 0.8291 (t0) REVERT: E 191 GLU cc_start: 0.7901 (tt0) cc_final: 0.7685 (tt0) REVERT: E 280 MET cc_start: 0.7972 (mtm) cc_final: 0.7715 (mtm) REVERT: E 436 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7293 (m-80) outliers start: 22 outliers final: 18 residues processed: 241 average time/residue: 0.1002 time to fit residues: 37.8423 Evaluate side-chains 245 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 226 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 436 PHE Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 273 TRP Chi-restraints excluded: chain E residue 436 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 149 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 168 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 13 optimal weight: 0.4980 chunk 125 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 161 optimal weight: 10.0000 chunk 113 optimal weight: 0.9980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN D 220 GLN D 260 GLN ** E 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.112381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.084526 restraints weight = 30423.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.087804 restraints weight = 15306.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.089896 restraints weight = 10104.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.091190 restraints weight = 7808.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.091907 restraints weight = 6663.443| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 14558 Z= 0.127 Angle : 0.600 11.624 19751 Z= 0.297 Chirality : 0.042 0.220 2234 Planarity : 0.003 0.047 2455 Dihedral : 3.980 40.776 2092 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.47 % Allowed : 18.69 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.44 (0.20), residues: 1712 helix: 1.52 (0.21), residues: 619 sheet: 0.12 (0.29), residues: 351 loop : -0.63 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 445 TYR 0.019 0.001 TYR A 441 PHE 0.025 0.001 PHE C 433 TRP 0.058 0.001 TRP B 273 HIS 0.005 0.001 HIS A 446 Details of bonding type rmsd covalent geometry : bond 0.00293 (14548) covalent geometry : angle 0.59884 (19731) SS BOND : bond 0.00269 ( 10) SS BOND : angle 1.50323 ( 20) hydrogen bonds : bond 0.03531 ( 524) hydrogen bonds : angle 4.35294 ( 1509) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2327.44 seconds wall clock time: 41 minutes 4.61 seconds (2464.61 seconds total)