Starting phenix.real_space_refine on Wed Mar 4 19:43:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ljf_23392/03_2026/7ljf_23392_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ljf_23392/03_2026/7ljf_23392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ljf_23392/03_2026/7ljf_23392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ljf_23392/03_2026/7ljf_23392.map" model { file = "/net/cci-nas-00/data/ceres_data/7ljf_23392/03_2026/7ljf_23392_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ljf_23392/03_2026/7ljf_23392_neut.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 7 5.49 5 Mg 3 5.21 5 S 48 5.16 5 C 9926 2.51 5 N 2713 2.21 5 O 3045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15742 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3551 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 22, 'TRANS': 431} Chain breaks: 5 Chain: "B" Number of atoms: 3551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3551 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 22, 'TRANS': 431} Chain breaks: 5 Chain: "C" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3346 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 20, 'TRANS': 406} Chain breaks: 5 Chain: "D" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 934 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 6, 'TRANS': 116} Chain breaks: 1 Chain: "E" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 934 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 6, 'TRANS': 116} Chain breaks: 1 Chain: "F" Number of atoms: 3338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3338 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 20, 'TRANS': 405} Chain breaks: 5 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.18, per 1000 atoms: 0.20 Number of scatterers: 15742 At special positions: 0 Unit cell: (133.812, 156.94, 128.856, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 48 16.00 P 7 15.00 Mg 3 11.99 O 3045 8.00 N 2713 7.00 C 9926 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 643.7 milliseconds 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3742 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 18 sheets defined 37.5% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 257 through 268 Processing helix chain 'A' and resid 268 through 274 removed outlier: 4.491A pdb=" N PHE A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 273 " --> pdb=" O GLU A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 282 removed outlier: 3.865A pdb=" N ARG A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 313 removed outlier: 3.775A pdb=" N ALA A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS A 304 " --> pdb=" O THR A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 removed outlier: 3.520A pdb=" N LEU A 337 " --> pdb=" O GLY A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 361 Processing helix chain 'A' and resid 372 through 376 Processing helix chain 'A' and resid 393 through 404 removed outlier: 3.790A pdb=" N LEU A 397 " --> pdb=" O VAL A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 426 Processing helix chain 'A' and resid 441 through 451 Processing helix chain 'A' and resid 460 through 466 removed outlier: 3.706A pdb=" N GLU A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 488 Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 511 through 513 No H-bonds generated for 'chain 'A' and resid 511 through 513' Processing helix chain 'A' and resid 516 through 538 removed outlier: 3.801A pdb=" N GLN A 520 " --> pdb=" O GLY A 516 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG A 525 " --> pdb=" O ASN A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 558 removed outlier: 3.941A pdb=" N LEU A 547 " --> pdb=" O ARG A 543 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 565 Proline residue: A 562 - end of helix Processing helix chain 'A' and resid 566 through 578 removed outlier: 3.595A pdb=" N TRP A 570 " --> pdb=" O ASN A 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 193 Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 257 through 274 removed outlier: 4.315A pdb=" N LEU B 270 " --> pdb=" O ASP B 266 " (cutoff:3.500A) Proline residue: B 271 - end of helix Processing helix chain 'B' and resid 274 through 282 Processing helix chain 'B' and resid 298 through 313 removed outlier: 4.492A pdb=" N ALA B 307 " --> pdb=" O ALA B 303 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASN B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 362 removed outlier: 4.189A pdb=" N ILE B 349 " --> pdb=" O THR B 345 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG B 350 " --> pdb=" O GLU B 346 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU B 351 " --> pdb=" O ARG B 347 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU B 362 " --> pdb=" O GLU B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 376 Processing helix chain 'B' and resid 393 through 403 Processing helix chain 'B' and resid 404 through 406 No H-bonds generated for 'chain 'B' and resid 404 through 406' Processing helix chain 'B' and resid 422 through 427 removed outlier: 3.839A pdb=" N LEU B 426 " --> pdb=" O ASP B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 453 removed outlier: 4.001A pdb=" N GLN B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 451 " --> pdb=" O ASP B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 467 removed outlier: 3.560A pdb=" N PHE B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 488 Processing helix chain 'B' and resid 511 through 513 No H-bonds generated for 'chain 'B' and resid 511 through 513' Processing helix chain 'B' and resid 515 through 538 Processing helix chain 'B' and resid 543 through 561 removed outlier: 3.874A pdb=" N LEU B 547 " --> pdb=" O ARG B 543 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 552 " --> pdb=" O LEU B 548 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE B 555 " --> pdb=" O ILE B 551 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ALA B 556 " --> pdb=" O VAL B 552 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 576 removed outlier: 4.128A pdb=" N LYS B 576 " --> pdb=" O ARG B 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 254 removed outlier: 3.722A pdb=" N ASP C 253 " --> pdb=" O SER C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 268 Processing helix chain 'C' and resid 268 through 274 removed outlier: 4.182A pdb=" N PHE C 272 " --> pdb=" O VAL C 268 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C 273 " --> pdb=" O GLU C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 282 removed outlier: 3.615A pdb=" N TYR C 278 " --> pdb=" O HIS C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 311 removed outlier: 3.711A pdb=" N ALA C 303 " --> pdb=" O LYS C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 339 Processing helix chain 'C' and resid 344 through 362 removed outlier: 3.914A pdb=" N HIS C 348 " --> pdb=" O GLU C 344 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU C 362 " --> pdb=" O GLU C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 405 removed outlier: 3.975A pdb=" N GLY C 405 " --> pdb=" O ASP C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 427 Processing helix chain 'C' and resid 441 through 453 Processing helix chain 'C' and resid 460 through 468 removed outlier: 4.332A pdb=" N ALA C 465 " --> pdb=" O ALA C 461 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLU C 466 " --> pdb=" O ASP C 462 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE C 467 " --> pdb=" O ASP C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 488 Processing helix chain 'C' and resid 490 through 492 No H-bonds generated for 'chain 'C' and resid 490 through 492' Processing helix chain 'C' and resid 511 through 513 No H-bonds generated for 'chain 'C' and resid 511 through 513' Processing helix chain 'C' and resid 515 through 538 Processing helix chain 'C' and resid 543 through 554 removed outlier: 3.656A pdb=" N LEU C 547 " --> pdb=" O ARG C 543 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL C 552 " --> pdb=" O LEU C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 557 No H-bonds generated for 'chain 'C' and resid 555 through 557' Processing helix chain 'E' and resid 189 through 193 Processing helix chain 'F' and resid 190 through 193 Processing helix chain 'F' and resid 250 through 254 Processing helix chain 'F' and resid 257 through 274 removed outlier: 3.621A pdb=" N GLN F 263 " --> pdb=" O ARG F 259 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU F 270 " --> pdb=" O ASP F 266 " (cutoff:3.500A) Proline residue: F 271 - end of helix Processing helix chain 'F' and resid 274 through 281 removed outlier: 3.725A pdb=" N TYR F 281 " --> pdb=" O LEU F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 313 Processing helix chain 'F' and resid 334 through 339 removed outlier: 3.829A pdb=" N LEU F 338 " --> pdb=" O GLY F 334 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASN F 339 " --> pdb=" O PRO F 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 334 through 339' Processing helix chain 'F' and resid 344 through 361 removed outlier: 3.585A pdb=" N PHE F 353 " --> pdb=" O ILE F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 376 Processing helix chain 'F' and resid 393 through 404 Processing helix chain 'F' and resid 422 through 427 Processing helix chain 'F' and resid 441 through 453 Processing helix chain 'F' and resid 460 through 467 removed outlier: 3.794A pdb=" N ALA F 465 " --> pdb=" O ALA F 461 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU F 466 " --> pdb=" O ASP F 462 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE F 467 " --> pdb=" O ASP F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 470 through 488 removed outlier: 4.269A pdb=" N LYS F 476 " --> pdb=" O SER F 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 492 No H-bonds generated for 'chain 'F' and resid 490 through 492' Processing helix chain 'F' and resid 511 through 514 removed outlier: 3.520A pdb=" N ASN F 514 " --> pdb=" O LYS F 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 511 through 514' Processing helix chain 'F' and resid 515 through 538 Processing helix chain 'F' and resid 543 through 557 removed outlier: 4.124A pdb=" N LEU F 547 " --> pdb=" O ARG F 543 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 151 through 152 removed outlier: 4.338A pdb=" N GLU A 151 " --> pdb=" O ARG A 142 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ASP A 114 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS A 121 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR B 101 " --> pdb=" O LYS A 121 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU B 104 " --> pdb=" O PHE B 116 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N PHE B 116 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 151 through 152 removed outlier: 4.338A pdb=" N GLU A 151 " --> pdb=" O ARG A 142 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ASP A 114 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS A 121 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR B 101 " --> pdb=" O LYS A 121 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLN B 139 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N THR B 140 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU B 151 " --> pdb=" O ARG B 142 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 219 through 222 removed outlier: 8.062A pdb=" N ALA F 229 " --> pdb=" O VAL F 185 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N TRP F 187 " --> pdb=" O ALA F 229 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N GLU F 231 " --> pdb=" O TRP F 187 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR F 228 " --> pdb=" O ASP F 223 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP F 223 " --> pdb=" O TYR F 228 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU F 221 " --> pdb=" O PHE F 230 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ARG F 232 " --> pdb=" O SER F 219 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N SER F 219 " --> pdb=" O ARG F 232 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY F 159 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL E 185 " --> pdb=" O GLY F 159 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N GLU E 183 " --> pdb=" O ILE F 161 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ALA E 229 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TRP E 187 " --> pdb=" O ALA E 229 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N GLU E 231 " --> pdb=" O TRP E 187 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU E 221 " --> pdb=" O PHE E 230 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ARG E 232 " --> pdb=" O SER E 219 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N SER E 219 " --> pdb=" O ARG E 232 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLU D 183 " --> pdb=" O ILE E 161 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N VAL D 177 " --> pdb=" O LEU D 164 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N LEU D 164 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N SER D 219 " --> pdb=" O ARG D 232 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ARG D 232 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU D 221 " --> pdb=" O PHE D 230 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR D 228 " --> pdb=" O ASP D 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 228 through 232 removed outlier: 3.599A pdb=" N TYR D 228 " --> pdb=" O ASP D 223 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU D 221 " --> pdb=" O PHE D 230 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ARG D 232 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N SER D 219 " --> pdb=" O ARG D 232 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY D 159 " --> pdb=" O VAL C 185 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 185 " --> pdb=" O GLY D 159 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N GLU C 183 " --> pdb=" O ILE D 161 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ALA C 229 " --> pdb=" O VAL C 185 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TRP C 187 " --> pdb=" O ALA C 229 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N GLU C 231 " --> pdb=" O TRP C 187 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR C 228 " --> pdb=" O ASP C 223 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP C 223 " --> pdb=" O TYR C 228 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU C 221 " --> pdb=" O PHE C 230 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ARG C 232 " --> pdb=" O SER C 219 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N SER C 219 " --> pdb=" O ARG C 232 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY C 159 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE C 161 " --> pdb=" O GLU B 183 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLU B 183 " --> pdb=" O ILE C 161 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL B 177 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU B 164 " --> pdb=" O VAL B 177 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY B 159 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A 185 " --> pdb=" O GLY B 159 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ARG A 173 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ILE A 167 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU A 175 " --> pdb=" O ARG A 165 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 219 through 222 removed outlier: 3.902A pdb=" N VAL F 186 " --> pdb=" O ALA F 174 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ARG F 173 " --> pdb=" O ILE F 167 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ILE F 167 " --> pdb=" O ARG F 173 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU F 175 " --> pdb=" O ARG F 165 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY F 159 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL E 185 " --> pdb=" O GLY F 159 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N GLU E 183 " --> pdb=" O ILE F 161 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N VAL E 177 " --> pdb=" O LEU E 164 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N LEU E 164 " --> pdb=" O VAL E 177 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLU D 183 " --> pdb=" O ILE E 161 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N VAL D 177 " --> pdb=" O LEU D 164 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N LEU D 164 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N SER D 219 " --> pdb=" O ARG D 232 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ARG D 232 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU D 221 " --> pdb=" O PHE D 230 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR D 228 " --> pdb=" O ASP D 223 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 228 through 232 removed outlier: 3.599A pdb=" N TYR D 228 " --> pdb=" O ASP D 223 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU D 221 " --> pdb=" O PHE D 230 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ARG D 232 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N SER D 219 " --> pdb=" O ARG D 232 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY D 159 " --> pdb=" O VAL C 185 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 185 " --> pdb=" O GLY D 159 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N GLU C 183 " --> pdb=" O ILE D 161 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL C 177 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU C 164 " --> pdb=" O VAL C 177 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY C 159 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE C 161 " --> pdb=" O GLU B 183 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLU B 183 " --> pdb=" O ILE C 161 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ALA B 229 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TRP B 187 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N GLU B 231 " --> pdb=" O TRP B 187 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU B 221 " --> pdb=" O PHE B 230 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARG B 232 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N SER B 219 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY B 159 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A 185 " --> pdb=" O GLY B 159 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ARG A 173 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ILE A 167 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU A 175 " --> pdb=" O ARG A 165 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 330 through 332 removed outlier: 6.248A pdb=" N LEU A 330 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 291 " --> pdb=" O GLY A 413 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLY A 288 " --> pdb=" O ASP A 432 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LYS A 434 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU A 290 " --> pdb=" O LYS A 434 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LYS A 436 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TYR A 292 " --> pdb=" O LYS A 436 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 505 through 509 removed outlier: 6.036A pdb=" N GLU A 506 " --> pdb=" O GLU A 497 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU A 497 " --> pdb=" O GLU A 506 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N MET A 508 " --> pdb=" O PHE A 495 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 329 through 333 removed outlier: 6.695A pdb=" N LEU B 330 " --> pdb=" O PHE B 369 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ASP B 371 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE B 332 " --> pdb=" O ASP B 371 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE B 410 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL B 289 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE B 435 " --> pdb=" O LEU B 290 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 507 through 509 removed outlier: 3.874A pdb=" N ARG B 585 " --> pdb=" O GLU B 497 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR B 499 " --> pdb=" O TYR B 583 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TYR B 583 " --> pdb=" O THR B 499 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 120 through 125 removed outlier: 7.303A pdb=" N THR C 112 " --> pdb=" O THR C 107 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N THR C 107 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASP C 114 " --> pdb=" O LEU C 105 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 328 through 332 removed outlier: 6.076A pdb=" N TYR C 328 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N PHE C 369 " --> pdb=" O TYR C 328 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU C 330 " --> pdb=" O PHE C 369 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ASP C 371 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE C 332 " --> pdb=" O ASP C 371 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL C 366 " --> pdb=" O ILE C 410 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N ILE C 412 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL C 368 " --> pdb=" O ILE C 412 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ALA C 414 " --> pdb=" O VAL C 368 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N PHE C 370 " --> pdb=" O ALA C 414 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL C 289 " --> pdb=" O VAL C 411 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY C 413 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLY C 288 " --> pdb=" O LEU C 431 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR C 292 " --> pdb=" O ILE C 435 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 505 through 509 Processing sheet with id=AB5, first strand: chain 'D' and resid 120 through 125 removed outlier: 3.654A pdb=" N ALA D 106 " --> pdb=" O ASP D 114 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N PHE D 116 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N LEU D 104 " --> pdb=" O PHE D 116 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU D 151 " --> pdb=" O ARG D 142 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 148 through 149 removed outlier: 8.305A pdb=" N VAL E 149 " --> pdb=" O ARG E 123 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR E 125 " --> pdb=" O VAL E 149 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N THR E 112 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N THR E 107 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ASP E 114 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU E 151 " --> pdb=" O ARG E 142 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 120 through 124 removed outlier: 6.668A pdb=" N ASP F 114 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 328 through 333 removed outlier: 6.054A pdb=" N TYR F 328 " --> pdb=" O ILE F 367 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N PHE F 369 " --> pdb=" O TYR F 328 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU F 330 " --> pdb=" O PHE F 369 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ASP F 371 " --> pdb=" O LEU F 330 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE F 332 " --> pdb=" O ASP F 371 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL F 366 " --> pdb=" O ILE F 410 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE F 412 " --> pdb=" O VAL F 366 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL F 368 " --> pdb=" O ILE F 412 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ALA F 414 " --> pdb=" O VAL F 368 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE F 370 " --> pdb=" O ALA F 414 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER F 415 " --> pdb=" O LEU F 291 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLY F 288 " --> pdb=" O VAL F 433 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ILE F 435 " --> pdb=" O GLY F 288 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU F 290 " --> pdb=" O ILE F 435 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 505 through 509 removed outlier: 3.780A pdb=" N TYR F 583 " --> pdb=" O THR F 499 " (cutoff:3.500A) 684 hydrogen bonds defined for protein. 1902 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.59 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5083 1.34 - 1.45: 1784 1.45 - 1.57: 9031 1.57 - 1.69: 11 1.69 - 1.81: 82 Bond restraints: 15991 Sorted by residual: bond pdb=" N VAL B 582 " pdb=" CA VAL B 582 " ideal model delta sigma weight residual 1.460 1.495 -0.035 8.60e-03 1.35e+04 1.68e+01 bond pdb=" N VAL A 393 " pdb=" CA VAL A 393 " ideal model delta sigma weight residual 1.461 1.497 -0.035 1.23e-02 6.61e+03 8.26e+00 bond pdb=" N TYR F 228 " pdb=" CA TYR F 228 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.19e-02 7.06e+03 6.93e+00 bond pdb=" N TYR E 228 " pdb=" CA TYR E 228 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.24e-02 6.50e+03 6.35e+00 bond pdb=" N TYR B 228 " pdb=" CA TYR B 228 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.24e-02 6.50e+03 6.03e+00 ... (remaining 15986 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 21115 1.75 - 3.51: 416 3.51 - 5.26: 79 5.26 - 7.02: 16 7.02 - 8.77: 3 Bond angle restraints: 21629 Sorted by residual: angle pdb=" N VAL B 582 " pdb=" CA VAL B 582 " pdb=" C VAL B 582 " ideal model delta sigma weight residual 113.71 108.22 5.49 9.50e-01 1.11e+00 3.34e+01 angle pdb=" CA ALA C 229 " pdb=" C ALA C 229 " pdb=" O ALA C 229 " ideal model delta sigma weight residual 121.47 117.07 4.40 1.15e+00 7.56e-01 1.46e+01 angle pdb=" CA ALA D 229 " pdb=" C ALA D 229 " pdb=" O ALA D 229 " ideal model delta sigma weight residual 121.81 117.34 4.47 1.18e+00 7.18e-01 1.43e+01 angle pdb=" N PRO A 394 " pdb=" CA PRO A 394 " pdb=" C PRO A 394 " ideal model delta sigma weight residual 112.47 120.21 -7.74 2.06e+00 2.36e-01 1.41e+01 angle pdb=" CA ALA F 229 " pdb=" C ALA F 229 " pdb=" O ALA F 229 " ideal model delta sigma weight residual 121.16 117.29 3.87 1.12e+00 7.97e-01 1.19e+01 ... (remaining 21624 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.77: 9352 25.77 - 51.54: 435 51.54 - 77.31: 23 77.31 - 103.08: 10 103.08 - 128.85: 3 Dihedral angle restraints: 9823 sinusoidal: 4046 harmonic: 5777 Sorted by residual: dihedral pdb=" O1B ADP B 701 " pdb=" O3A ADP B 701 " pdb=" PB ADP B 701 " pdb=" PA ADP B 701 " ideal model delta sinusoidal sigma weight residual -60.00 68.84 -128.85 1 2.00e+01 2.50e-03 3.91e+01 dihedral pdb=" O2A ADP C 701 " pdb=" O3A ADP C 701 " pdb=" PA ADP C 701 " pdb=" PB ADP C 701 " ideal model delta sinusoidal sigma weight residual -60.00 -176.46 116.46 1 2.00e+01 2.50e-03 3.47e+01 dihedral pdb=" O2A ADP B 701 " pdb=" O3A ADP B 701 " pdb=" PA ADP B 701 " pdb=" PB ADP B 701 " ideal model delta sinusoidal sigma weight residual -60.00 52.73 -112.73 1 2.00e+01 2.50e-03 3.33e+01 ... (remaining 9820 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1727 0.038 - 0.077: 479 0.077 - 0.115: 239 0.115 - 0.153: 37 0.153 - 0.191: 1 Chirality restraints: 2483 Sorted by residual: chirality pdb=" CA VAL B 582 " pdb=" N VAL B 582 " pdb=" C VAL B 582 " pdb=" CB VAL B 582 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.16e-01 chirality pdb=" CA VAL A 392 " pdb=" N VAL A 392 " pdb=" C VAL A 392 " pdb=" CB VAL A 392 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.85e-01 chirality pdb=" CA PRO A 394 " pdb=" N PRO A 394 " pdb=" C PRO A 394 " pdb=" CB PRO A 394 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.50e-01 ... (remaining 2480 not shown) Planarity restraints: 2801 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY F 334 " 0.031 5.00e-02 4.00e+02 4.70e-02 3.54e+00 pdb=" N PRO F 335 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO F 335 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO F 335 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 570 " 0.012 2.00e-02 2.50e+03 1.12e-02 3.13e+00 pdb=" CG TRP A 570 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP A 570 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 570 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 570 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 570 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 570 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 570 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 570 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 570 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 334 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO C 335 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO C 335 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 335 " 0.024 5.00e-02 4.00e+02 ... (remaining 2798 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 254 2.57 - 3.15: 13340 3.15 - 3.73: 25933 3.73 - 4.32: 33264 4.32 - 4.90: 53348 Nonbonded interactions: 126139 Sorted by model distance: nonbonded pdb="MG MG A 701 " pdb=" O1A ATP A 702 " model vdw 1.987 2.170 nonbonded pdb=" O1B ADP B 701 " pdb="MG MG B 702 " model vdw 1.987 2.170 nonbonded pdb="MG MG A 701 " pdb=" O3B ATP A 702 " model vdw 2.016 2.170 nonbonded pdb=" OG1 THR A 300 " pdb="MG MG A 701 " model vdw 2.049 2.170 nonbonded pdb=" O1A ADP B 701 " pdb="MG MG B 702 " model vdw 2.059 2.170 ... (remaining 126134 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 97 through 557 or resid 580 through 587)) selection = (chain 'B' and (resid 97 through 557 or resid 580 through 587)) selection = (chain 'C' and (resid 97 through 557 or resid 580 through 587)) selection = (chain 'F' and (resid 97 through 557 or resid 580 through 587)) } ncs_group { reference = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 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: 0.420 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 13.890 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 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 0.037 15991 Z= 0.155 Angle : 0.619 8.775 21629 Z= 0.324 Chirality : 0.044 0.191 2483 Planarity : 0.004 0.047 2801 Dihedral : 13.984 128.847 6081 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.41 % Allowed : 0.18 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.20), residues: 1951 helix: 0.57 (0.22), residues: 573 sheet: -0.93 (0.24), residues: 450 loop : 0.35 (0.22), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 123 TYR 0.020 0.001 TYR F 583 PHE 0.018 0.001 PHE A 370 TRP 0.030 0.002 TRP A 570 HIS 0.003 0.001 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00281 (15991) covalent geometry : angle 0.61934 (21629) hydrogen bonds : bond 0.17311 ( 619) hydrogen bonds : angle 7.58380 ( 1902) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 219 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 372 GLU cc_start: 0.6715 (mp0) cc_final: 0.6512 (mp0) REVERT: B 508 MET cc_start: 0.6751 (mpp) cc_final: 0.6525 (mpp) REVERT: C 328 TYR cc_start: 0.6577 (m-10) cc_final: 0.5987 (m-10) REVERT: E 131 ASP cc_start: 0.9109 (t70) cc_final: 0.8834 (t70) REVERT: F 448 ILE cc_start: 0.8281 (mm) cc_final: 0.8046 (mm) outliers start: 7 outliers final: 2 residues processed: 226 average time/residue: 0.0905 time to fit residues: 33.2289 Evaluate side-chains 164 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 162 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain B residue 582 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.4980 overall best weight: 7.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 ASN ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 HIS B 520 GLN C 354 GLN ** C 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 GLN F 529 ASN ** F 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.084163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.064024 restraints weight = 65839.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.066081 restraints weight = 42757.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.066136 restraints weight = 26538.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.066197 restraints weight = 23295.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.066245 restraints weight = 22527.228| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 15991 Z= 0.327 Angle : 0.757 10.865 21629 Z= 0.390 Chirality : 0.047 0.206 2483 Planarity : 0.006 0.056 2801 Dihedral : 8.225 125.338 2227 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.71 % Allowed : 13.25 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.19), residues: 1951 helix: 0.03 (0.21), residues: 592 sheet: -1.27 (0.22), residues: 489 loop : 0.05 (0.23), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG D 173 TYR 0.020 0.002 TYR F 487 PHE 0.026 0.002 PHE A 272 TRP 0.037 0.003 TRP A 570 HIS 0.010 0.002 HIS C 179 Details of bonding type rmsd covalent geometry : bond 0.00706 (15991) covalent geometry : angle 0.75707 (21629) hydrogen bonds : bond 0.04652 ( 619) hydrogen bonds : angle 5.96148 ( 1902) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 174 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 LEU cc_start: 0.8583 (mt) cc_final: 0.8359 (mt) REVERT: C 328 TYR cc_start: 0.6415 (m-10) cc_final: 0.5788 (m-10) REVERT: D 110 ASP cc_start: 0.8450 (t0) cc_final: 0.8227 (t0) REVERT: E 131 ASP cc_start: 0.8957 (t70) cc_final: 0.8716 (t70) REVERT: F 506 GLU cc_start: 0.7746 (tt0) cc_final: 0.7329 (mt-10) REVERT: F 529 ASN cc_start: 0.9184 (m-40) cc_final: 0.8756 (p0) outliers start: 29 outliers final: 23 residues processed: 193 average time/residue: 0.0951 time to fit residues: 29.5188 Evaluate side-chains 174 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 570 TRP Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 409 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 71 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 182 optimal weight: 6.9990 chunk 136 optimal weight: 0.0970 chunk 33 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.085972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.065590 restraints weight = 64779.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.067316 restraints weight = 40660.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.067470 restraints weight = 28926.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.067599 restraints weight = 24354.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.067752 restraints weight = 22315.428| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15991 Z= 0.165 Angle : 0.642 9.593 21629 Z= 0.324 Chirality : 0.044 0.184 2483 Planarity : 0.004 0.058 2801 Dihedral : 7.901 124.729 2225 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.60 % Allowed : 16.14 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.19), residues: 1951 helix: 0.31 (0.21), residues: 584 sheet: -1.08 (0.24), residues: 449 loop : 0.06 (0.22), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 173 TYR 0.011 0.001 TYR B 583 PHE 0.020 0.001 PHE A 272 TRP 0.032 0.002 TRP A 570 HIS 0.005 0.001 HIS C 179 Details of bonding type rmsd covalent geometry : bond 0.00362 (15991) covalent geometry : angle 0.64223 (21629) hydrogen bonds : bond 0.03869 ( 619) hydrogen bonds : angle 5.45941 ( 1902) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 181 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.8523 (tp30) cc_final: 0.8151 (tp30) REVERT: A 480 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8728 (mp0) REVERT: B 557 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8503 (mm-30) REVERT: C 183 GLU cc_start: 0.8376 (mp0) cc_final: 0.8063 (mp0) REVERT: C 328 TYR cc_start: 0.6369 (m-10) cc_final: 0.5749 (m-10) REVERT: D 110 ASP cc_start: 0.8516 (t0) cc_final: 0.8232 (t0) REVERT: E 104 LEU cc_start: 0.9209 (tp) cc_final: 0.8989 (tp) REVERT: E 131 ASP cc_start: 0.8899 (t70) cc_final: 0.8653 (t70) REVERT: E 151 GLU cc_start: 0.7473 (tm-30) cc_final: 0.7174 (tm-30) REVERT: E 182 GLU cc_start: 0.8091 (pm20) cc_final: 0.7691 (pm20) REVERT: F 448 ILE cc_start: 0.8140 (mm) cc_final: 0.7845 (mm) REVERT: F 529 ASN cc_start: 0.9144 (m-40) cc_final: 0.8890 (m-40) outliers start: 27 outliers final: 18 residues processed: 202 average time/residue: 0.0929 time to fit residues: 30.6938 Evaluate side-chains 176 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 570 TRP Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 228 TYR Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 280 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 60 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 13 optimal weight: 0.0040 chunk 105 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 149 optimal weight: 5.9990 chunk 154 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 overall best weight: 1.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 GLN F 263 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.087490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.067367 restraints weight = 64833.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.068892 restraints weight = 42021.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.069431 restraints weight = 27166.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.069604 restraints weight = 23683.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.069707 restraints weight = 22800.114| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15991 Z= 0.124 Angle : 0.618 9.494 21629 Z= 0.307 Chirality : 0.043 0.150 2483 Planarity : 0.004 0.056 2801 Dihedral : 7.679 122.127 2225 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.48 % Allowed : 16.62 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.20), residues: 1951 helix: 0.45 (0.21), residues: 586 sheet: -0.98 (0.24), residues: 455 loop : 0.15 (0.22), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 173 TYR 0.018 0.001 TYR F 583 PHE 0.021 0.001 PHE F 369 TRP 0.031 0.002 TRP A 570 HIS 0.007 0.001 HIS F 546 Details of bonding type rmsd covalent geometry : bond 0.00277 (15991) covalent geometry : angle 0.61796 (21629) hydrogen bonds : bond 0.03362 ( 619) hydrogen bonds : angle 5.09327 ( 1902) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 190 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.8116 (tp30) cc_final: 0.7852 (tm-30) REVERT: A 161 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.7920 (tt) REVERT: A 262 GLU cc_start: 0.8557 (tp30) cc_final: 0.8173 (tp30) REVERT: B 470 ASP cc_start: 0.9012 (t0) cc_final: 0.8413 (p0) REVERT: B 557 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8487 (mm-30) REVERT: C 328 TYR cc_start: 0.6282 (m-10) cc_final: 0.5775 (m-10) REVERT: C 529 ASN cc_start: 0.9054 (m-40) cc_final: 0.8489 (m110) REVERT: C 545 GLN cc_start: 0.9018 (tp40) cc_final: 0.8717 (tp-100) REVERT: D 137 LYS cc_start: 0.9139 (tmmt) cc_final: 0.8758 (tmmt) REVERT: D 139 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7787 (mp10) REVERT: E 104 LEU cc_start: 0.9166 (tp) cc_final: 0.8951 (tp) REVERT: E 131 ASP cc_start: 0.8768 (t70) cc_final: 0.8503 (t70) REVERT: F 448 ILE cc_start: 0.8095 (mm) cc_final: 0.7786 (mm) REVERT: F 528 LYS cc_start: 0.9030 (pttm) cc_final: 0.8750 (pttm) REVERT: F 529 ASN cc_start: 0.9103 (m-40) cc_final: 0.8768 (m-40) outliers start: 42 outliers final: 24 residues processed: 223 average time/residue: 0.0954 time to fit residues: 34.1573 Evaluate side-chains 189 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 570 TRP Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 228 TYR Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 139 GLN Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 409 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 153 optimal weight: 10.0000 chunk 117 optimal weight: 40.0000 chunk 86 optimal weight: 1.9990 chunk 193 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 94 optimal weight: 20.0000 chunk 99 optimal weight: 6.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.086696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.066389 restraints weight = 65086.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.068115 restraints weight = 41758.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.068242 restraints weight = 29149.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.068467 restraints weight = 24901.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.068524 restraints weight = 23626.553| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15991 Z= 0.162 Angle : 0.627 9.277 21629 Z= 0.314 Chirality : 0.043 0.190 2483 Planarity : 0.004 0.056 2801 Dihedral : 7.681 120.886 2225 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.78 % Allowed : 18.51 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.20), residues: 1951 helix: 0.50 (0.21), residues: 586 sheet: -1.05 (0.23), residues: 480 loop : 0.19 (0.23), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 123 TYR 0.012 0.001 TYR F 228 PHE 0.016 0.001 PHE A 272 TRP 0.030 0.002 TRP A 570 HIS 0.006 0.001 HIS F 546 Details of bonding type rmsd covalent geometry : bond 0.00359 (15991) covalent geometry : angle 0.62677 (21629) hydrogen bonds : bond 0.03375 ( 619) hydrogen bonds : angle 5.04972 ( 1902) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 166 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.8091 (tp30) cc_final: 0.7835 (tm-30) REVERT: A 161 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.7964 (tt) REVERT: A 262 GLU cc_start: 0.8558 (tp30) cc_final: 0.8192 (tp30) REVERT: A 406 LEU cc_start: 0.8526 (mt) cc_final: 0.8281 (mt) REVERT: B 470 ASP cc_start: 0.9017 (t0) cc_final: 0.8463 (p0) REVERT: B 557 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8486 (mm-30) REVERT: C 328 TYR cc_start: 0.6271 (m-10) cc_final: 0.5763 (m-10) REVERT: C 529 ASN cc_start: 0.9067 (m-40) cc_final: 0.8494 (m110) REVERT: D 183 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7068 (pt0) REVERT: E 104 LEU cc_start: 0.9194 (tp) cc_final: 0.8989 (tp) REVERT: E 131 ASP cc_start: 0.8835 (t70) cc_final: 0.8554 (t70) REVERT: F 269 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7698 (pm20) REVERT: F 448 ILE cc_start: 0.8083 (mm) cc_final: 0.7778 (mm) REVERT: F 529 ASN cc_start: 0.9136 (m-40) cc_final: 0.8829 (m-40) outliers start: 47 outliers final: 34 residues processed: 206 average time/residue: 0.0875 time to fit residues: 29.8027 Evaluate side-chains 195 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 570 TRP Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 228 TYR Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 409 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 24 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 139 optimal weight: 8.9990 chunk 156 optimal weight: 20.0000 chunk 31 optimal weight: 8.9990 chunk 166 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 104 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 7 optimal weight: 1.9990 chunk 122 optimal weight: 0.0270 overall best weight: 1.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 545 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.087961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.067699 restraints weight = 64470.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.068610 restraints weight = 38222.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.069775 restraints weight = 26943.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.069705 restraints weight = 23335.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.070007 restraints weight = 21195.939| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15991 Z= 0.116 Angle : 0.629 10.671 21629 Z= 0.310 Chirality : 0.044 0.321 2483 Planarity : 0.004 0.056 2801 Dihedral : 7.444 119.278 2225 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.01 % Allowed : 20.28 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.20), residues: 1951 helix: 0.55 (0.21), residues: 587 sheet: -1.00 (0.23), residues: 482 loop : 0.24 (0.23), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 123 TYR 0.018 0.001 TYR F 583 PHE 0.013 0.001 PHE A 272 TRP 0.031 0.002 TRP A 570 HIS 0.006 0.001 HIS F 348 Details of bonding type rmsd covalent geometry : bond 0.00259 (15991) covalent geometry : angle 0.62917 (21629) hydrogen bonds : bond 0.03199 ( 619) hydrogen bonds : angle 4.85367 ( 1902) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.8070 (tp30) cc_final: 0.7790 (tm-30) REVERT: A 161 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8008 (tt) REVERT: A 262 GLU cc_start: 0.8522 (tp30) cc_final: 0.8130 (tp30) REVERT: A 327 SER cc_start: 0.8168 (m) cc_final: 0.7967 (p) REVERT: A 406 LEU cc_start: 0.8440 (mt) cc_final: 0.8173 (mt) REVERT: B 358 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8479 (tm-30) REVERT: B 372 GLU cc_start: 0.7015 (mp0) cc_final: 0.6679 (mp0) REVERT: B 470 ASP cc_start: 0.8973 (t0) cc_final: 0.8496 (p0) REVERT: B 557 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8505 (mm-30) REVERT: C 328 TYR cc_start: 0.6237 (m-10) cc_final: 0.5755 (m-10) REVERT: C 529 ASN cc_start: 0.9068 (m-40) cc_final: 0.8482 (m110) REVERT: E 131 ASP cc_start: 0.8725 (t70) cc_final: 0.8441 (t70) REVERT: F 269 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7534 (pm20) REVERT: F 369 PHE cc_start: 0.8344 (t80) cc_final: 0.8107 (t80) REVERT: F 448 ILE cc_start: 0.7901 (mm) cc_final: 0.7598 (mm) REVERT: F 529 ASN cc_start: 0.9124 (m-40) cc_final: 0.8818 (m-40) outliers start: 34 outliers final: 22 residues processed: 209 average time/residue: 0.0956 time to fit residues: 32.4850 Evaluate side-chains 191 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 570 TRP Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 228 TYR Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain F residue 280 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 70 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 chunk 119 optimal weight: 20.0000 chunk 80 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 138 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 133 optimal weight: 9.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 546 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.085391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.065099 restraints weight = 64159.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.066789 restraints weight = 38280.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.067010 restraints weight = 26857.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.067068 restraints weight = 22157.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.067209 restraints weight = 21519.947| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15991 Z= 0.230 Angle : 0.675 8.962 21629 Z= 0.342 Chirality : 0.044 0.220 2483 Planarity : 0.004 0.058 2801 Dihedral : 7.664 118.228 2225 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.72 % Allowed : 21.64 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.20), residues: 1951 helix: 0.45 (0.21), residues: 591 sheet: -1.08 (0.23), residues: 478 loop : 0.11 (0.23), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 123 TYR 0.012 0.001 TYR B 328 PHE 0.019 0.002 PHE A 272 TRP 0.029 0.002 TRP A 570 HIS 0.004 0.001 HIS C 172 Details of bonding type rmsd covalent geometry : bond 0.00502 (15991) covalent geometry : angle 0.67458 (21629) hydrogen bonds : bond 0.03532 ( 619) hydrogen bonds : angle 5.06939 ( 1902) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 159 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.8117 (tp30) cc_final: 0.7802 (tm-30) REVERT: A 161 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8058 (tt) REVERT: A 262 GLU cc_start: 0.8622 (tp30) cc_final: 0.8259 (tp30) REVERT: A 406 LEU cc_start: 0.8588 (mt) cc_final: 0.8384 (mt) REVERT: B 470 ASP cc_start: 0.9036 (t0) cc_final: 0.8507 (p0) REVERT: B 557 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8519 (mm-30) REVERT: C 151 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7942 (pm20) REVERT: C 328 TYR cc_start: 0.6255 (m-10) cc_final: 0.5767 (m-10) REVERT: C 529 ASN cc_start: 0.9127 (m-40) cc_final: 0.8544 (m110) REVERT: D 183 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7114 (pt0) REVERT: E 131 ASP cc_start: 0.8918 (t70) cc_final: 0.8621 (t70) REVERT: F 448 ILE cc_start: 0.7956 (mm) cc_final: 0.7662 (mm) REVERT: F 529 ASN cc_start: 0.9147 (m-40) cc_final: 0.8863 (m-40) outliers start: 46 outliers final: 35 residues processed: 194 average time/residue: 0.0901 time to fit residues: 28.5273 Evaluate side-chains 193 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 154 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 570 TRP Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 228 TYR Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 409 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 146 optimal weight: 0.9980 chunk 185 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 164 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 151 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 178 optimal weight: 7.9990 chunk 184 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.086994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.066672 restraints weight = 64695.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.068511 restraints weight = 38526.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.068838 restraints weight = 25483.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.068903 restraints weight = 21537.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.068980 restraints weight = 20787.534| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15991 Z= 0.138 Angle : 0.658 10.903 21629 Z= 0.325 Chirality : 0.043 0.251 2483 Planarity : 0.004 0.058 2801 Dihedral : 7.489 118.152 2225 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.90 % Allowed : 21.64 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.20), residues: 1951 helix: 0.55 (0.22), residues: 588 sheet: -1.03 (0.23), residues: 479 loop : 0.14 (0.23), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 123 TYR 0.014 0.001 TYR B 583 PHE 0.016 0.001 PHE A 272 TRP 0.030 0.002 TRP A 570 HIS 0.006 0.001 HIS F 348 Details of bonding type rmsd covalent geometry : bond 0.00308 (15991) covalent geometry : angle 0.65806 (21629) hydrogen bonds : bond 0.03253 ( 619) hydrogen bonds : angle 4.89513 ( 1902) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 172 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.8073 (tp30) cc_final: 0.7766 (tm-30) REVERT: A 161 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8042 (tt) REVERT: A 262 GLU cc_start: 0.8549 (tp30) cc_final: 0.8172 (tp30) REVERT: A 327 SER cc_start: 0.8147 (m) cc_final: 0.7921 (p) REVERT: A 406 LEU cc_start: 0.8505 (mt) cc_final: 0.8275 (mt) REVERT: B 372 GLU cc_start: 0.7093 (mp0) cc_final: 0.6783 (mp0) REVERT: B 470 ASP cc_start: 0.9003 (t0) cc_final: 0.8541 (p0) REVERT: B 557 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8534 (mm-30) REVERT: C 328 TYR cc_start: 0.6220 (m-10) cc_final: 0.5739 (m-10) REVERT: D 123 ARG cc_start: 0.6826 (ptt-90) cc_final: 0.6589 (ptt90) REVERT: D 137 LYS cc_start: 0.9149 (tmmt) cc_final: 0.8604 (ttmt) REVERT: D 183 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7017 (pt0) REVERT: E 131 ASP cc_start: 0.8786 (t70) cc_final: 0.8489 (t70) REVERT: F 269 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7448 (pm20) REVERT: F 529 ASN cc_start: 0.9160 (m-40) cc_final: 0.8856 (m-40) outliers start: 49 outliers final: 36 residues processed: 211 average time/residue: 0.0921 time to fit residues: 31.8808 Evaluate side-chains 198 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 570 TRP Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 373 MET Chi-restraints excluded: chain F residue 409 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 180 optimal weight: 0.7980 chunk 36 optimal weight: 0.2980 chunk 45 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 164 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 chunk 133 optimal weight: 8.9990 chunk 24 optimal weight: 0.1980 chunk 169 optimal weight: 4.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.087129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.066809 restraints weight = 64764.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.068439 restraints weight = 38712.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.068687 restraints weight = 28496.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.068795 restraints weight = 23430.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.068934 restraints weight = 22808.740| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15991 Z= 0.142 Angle : 0.670 12.509 21629 Z= 0.331 Chirality : 0.044 0.338 2483 Planarity : 0.004 0.057 2801 Dihedral : 7.423 118.297 2225 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.02 % Allowed : 21.88 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.20), residues: 1951 helix: 0.42 (0.21), residues: 603 sheet: -1.00 (0.24), residues: 477 loop : 0.17 (0.23), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 123 TYR 0.020 0.001 TYR F 583 PHE 0.021 0.001 PHE F 369 TRP 0.029 0.002 TRP A 570 HIS 0.006 0.001 HIS F 348 Details of bonding type rmsd covalent geometry : bond 0.00319 (15991) covalent geometry : angle 0.66993 (21629) hydrogen bonds : bond 0.03215 ( 619) hydrogen bonds : angle 4.86132 ( 1902) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 162 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.8070 (tp30) cc_final: 0.7768 (tm-30) REVERT: A 161 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8053 (tt) REVERT: A 262 GLU cc_start: 0.8598 (tp30) cc_final: 0.8227 (tp30) REVERT: A 406 LEU cc_start: 0.8579 (mt) cc_final: 0.8368 (mt) REVERT: A 531 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.9026 (tp) REVERT: B 372 GLU cc_start: 0.7093 (mp0) cc_final: 0.6760 (mp0) REVERT: B 470 ASP cc_start: 0.9055 (t0) cc_final: 0.8583 (p0) REVERT: B 557 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8528 (mm-30) REVERT: C 328 TYR cc_start: 0.6193 (m-10) cc_final: 0.5722 (m-10) REVERT: D 183 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7058 (pt0) REVERT: D 190 ASP cc_start: 0.8503 (m-30) cc_final: 0.8003 (m-30) REVERT: E 131 ASP cc_start: 0.8830 (t70) cc_final: 0.8532 (t70) REVERT: F 529 ASN cc_start: 0.9134 (m-40) cc_final: 0.8837 (m-40) outliers start: 51 outliers final: 40 residues processed: 200 average time/residue: 0.0915 time to fit residues: 30.0730 Evaluate side-chains 197 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 153 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 570 TRP Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 373 MET Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 409 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 117 optimal weight: 9.9990 chunk 161 optimal weight: 1.9990 chunk 149 optimal weight: 0.0670 chunk 184 optimal weight: 8.9990 chunk 178 optimal weight: 8.9990 chunk 176 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 overall best weight: 2.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.086692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.066202 restraints weight = 64317.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.068089 restraints weight = 37547.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.068341 restraints weight = 25168.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.068424 restraints weight = 21808.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.068500 restraints weight = 20970.727| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15991 Z= 0.156 Angle : 0.693 13.053 21629 Z= 0.341 Chirality : 0.044 0.368 2483 Planarity : 0.004 0.056 2801 Dihedral : 7.424 118.469 2225 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.66 % Allowed : 22.29 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.20), residues: 1951 helix: 0.40 (0.21), residues: 599 sheet: -1.00 (0.24), residues: 477 loop : 0.15 (0.23), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 123 TYR 0.009 0.001 TYR B 328 PHE 0.027 0.001 PHE F 369 TRP 0.029 0.002 TRP A 570 HIS 0.006 0.001 HIS F 348 Details of bonding type rmsd covalent geometry : bond 0.00349 (15991) covalent geometry : angle 0.69286 (21629) hydrogen bonds : bond 0.03254 ( 619) hydrogen bonds : angle 4.86664 ( 1902) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 159 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.8049 (tp30) cc_final: 0.7754 (tm-30) REVERT: A 161 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8072 (tt) REVERT: A 262 GLU cc_start: 0.8586 (tp30) cc_final: 0.8217 (tp30) REVERT: A 406 LEU cc_start: 0.8559 (mt) cc_final: 0.8342 (mt) REVERT: A 531 ILE cc_start: 0.9320 (OUTLIER) cc_final: 0.9061 (tp) REVERT: B 372 GLU cc_start: 0.7096 (mp0) cc_final: 0.6756 (mp0) REVERT: B 470 ASP cc_start: 0.9018 (t0) cc_final: 0.8567 (p0) REVERT: B 557 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8508 (mm-30) REVERT: C 301 LEU cc_start: 0.8982 (mp) cc_final: 0.8577 (pp) REVERT: C 328 TYR cc_start: 0.6136 (m-10) cc_final: 0.5668 (m-10) REVERT: D 123 ARG cc_start: 0.6843 (ptt-90) cc_final: 0.6422 (ptt90) REVERT: D 137 LYS cc_start: 0.9081 (tmmt) cc_final: 0.8526 (ttmt) REVERT: D 183 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7028 (pt0) REVERT: E 131 ASP cc_start: 0.8830 (t70) cc_final: 0.8527 (t70) REVERT: F 529 ASN cc_start: 0.9133 (m-40) cc_final: 0.8840 (m-40) outliers start: 45 outliers final: 39 residues processed: 192 average time/residue: 0.0938 time to fit residues: 29.4952 Evaluate side-chains 197 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 570 TRP Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 373 MET Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 409 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 190 optimal weight: 20.0000 chunk 97 optimal weight: 9.9990 chunk 123 optimal weight: 30.0000 chunk 156 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 103 optimal weight: 20.0000 chunk 71 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.085027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.065507 restraints weight = 64858.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.066698 restraints weight = 46259.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.067676 restraints weight = 30203.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.067850 restraints weight = 25766.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.067811 restraints weight = 24300.384| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15991 Z= 0.231 Angle : 0.721 10.852 21629 Z= 0.361 Chirality : 0.045 0.355 2483 Planarity : 0.004 0.056 2801 Dihedral : 7.669 118.707 2225 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.66 % Allowed : 22.41 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.20), residues: 1951 helix: 0.26 (0.21), residues: 604 sheet: -1.13 (0.23), residues: 481 loop : 0.04 (0.23), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 123 TYR 0.023 0.002 TYR F 583 PHE 0.032 0.002 PHE A 495 TRP 0.028 0.002 TRP A 570 HIS 0.005 0.001 HIS F 179 Details of bonding type rmsd covalent geometry : bond 0.00503 (15991) covalent geometry : angle 0.72147 (21629) hydrogen bonds : bond 0.03543 ( 619) hydrogen bonds : angle 5.05377 ( 1902) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2252.54 seconds wall clock time: 39 minutes 52.89 seconds (2392.89 seconds total)