Starting phenix.real_space_refine on Thu Mar 5 04:25:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ut4_20865/03_2026/6ut4_20865.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ut4_20865/03_2026/6ut4_20865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ut4_20865/03_2026/6ut4_20865.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ut4_20865/03_2026/6ut4_20865.map" model { file = "/net/cci-nas-00/data/ceres_data/6ut4_20865/03_2026/6ut4_20865.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ut4_20865/03_2026/6ut4_20865.cif" } resolution = 3.1 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= 0.006 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 18 5.49 5 Mg 6 5.21 5 S 24 5.16 5 C 12412 2.51 5 N 3224 2.21 5 O 3442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.02s 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: 19126 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3164 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 16, 'TRANS': 370} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 3152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3152 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 16, 'TRANS': 368} Chain breaks: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 3144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3144 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 16, 'TRANS': 367} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "D" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3109 Classifications: {'peptide': 383} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 16, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 2, 'PHE:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 65 Chain: "E" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3164 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 16, 'TRANS': 369} Chain breaks: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "F" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3183 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 16, 'TRANS': 373} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 58 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.92, per 1000 atoms: 0.26 Number of scatterers: 19126 At special positions: 0 Unit cell: (136.25, 123.75, 88.75, 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 24 16.00 P 18 15.00 Mg 6 11.99 O 3442 8.00 N 3224 7.00 C 12412 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: 1.32 Conformation dependent library (CDL) restraints added in 793.7 milliseconds 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4330 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 24 sheets defined 51.4% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 199 through 204 removed outlier: 3.915A pdb=" N MET A 203 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 231 removed outlier: 3.625A pdb=" N VAL A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 277 through 290 removed outlier: 3.609A pdb=" N GLY A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 312 Processing helix chain 'A' and resid 318 through 336 removed outlier: 4.140A pdb=" N GLU A 324 " --> pdb=" O THR A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'A' and resid 420 through 424 removed outlier: 3.559A pdb=" N ARG A 424 " --> pdb=" O VAL A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 439 Processing helix chain 'A' and resid 440 through 451 removed outlier: 3.613A pdb=" N LYS A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 469 removed outlier: 3.842A pdb=" N ARG A 459 " --> pdb=" O GLU A 455 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN A 461 " --> pdb=" O ARG A 457 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 491 removed outlier: 3.750A pdb=" N VAL A 491 " --> pdb=" O VAL A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 498 removed outlier: 4.052A pdb=" N HIS A 497 " --> pdb=" O ASP A 494 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG A 498 " --> pdb=" O ARG A 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 494 through 498' Processing helix chain 'A' and resid 500 through 504 removed outlier: 3.990A pdb=" N TYR A 503 " --> pdb=" O GLY A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 519 removed outlier: 3.581A pdb=" N LEU A 513 " --> pdb=" O THR A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 529 Processing helix chain 'A' and resid 532 through 540 removed outlier: 3.821A pdb=" N LEU A 540 " --> pdb=" O ILE A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.530A pdb=" N ILE A 577 " --> pdb=" O GLY A 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 208 removed outlier: 3.507A pdb=" N LYS B 208 " --> pdb=" O LEU B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 234 Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 277 through 294 removed outlier: 4.083A pdb=" N LEU B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 311 Processing helix chain 'B' and resid 318 through 336 removed outlier: 4.609A pdb=" N GLU B 323 " --> pdb=" O PRO B 319 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU B 324 " --> pdb=" O THR B 320 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU B 328 " --> pdb=" O GLU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 339 No H-bonds generated for 'chain 'B' and resid 337 through 339' Processing helix chain 'B' and resid 362 through 367 Processing helix chain 'B' and resid 369 through 374 removed outlier: 3.808A pdb=" N THR B 372 " --> pdb=" O GLU B 369 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 425 removed outlier: 3.670A pdb=" N ARG B 424 " --> pdb=" O ASP B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 439 Processing helix chain 'B' and resid 440 through 447 Processing helix chain 'B' and resid 454 through 456 No H-bonds generated for 'chain 'B' and resid 454 through 456' Processing helix chain 'B' and resid 457 through 470 removed outlier: 3.697A pdb=" N GLU B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS B 463 " --> pdb=" O ARG B 459 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS B 470 " --> pdb=" O GLU B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 491 Processing helix chain 'B' and resid 500 through 504 removed outlier: 4.057A pdb=" N TYR B 503 " --> pdb=" O GLY B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 521 removed outlier: 3.693A pdb=" N VAL B 521 " --> pdb=" O TRP B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 529 Processing helix chain 'B' and resid 532 through 540 removed outlier: 3.527A pdb=" N ILE B 536 " --> pdb=" O ASP B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 582 removed outlier: 3.607A pdb=" N ILE B 577 " --> pdb=" O GLY B 573 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG B 582 " --> pdb=" O GLY B 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 209 removed outlier: 3.590A pdb=" N ASN C 206 " --> pdb=" O ASP C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 233 Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 277 through 294 removed outlier: 3.744A pdb=" N GLU C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 313 Processing helix chain 'C' and resid 318 through 336 removed outlier: 3.936A pdb=" N GLU C 323 " --> pdb=" O PRO C 319 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU C 324 " --> pdb=" O THR C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 346 removed outlier: 4.223A pdb=" N ASN C 346 " --> pdb=" O ASP C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 361 removed outlier: 3.701A pdb=" N GLY C 361 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 367 Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'C' and resid 420 through 425 Processing helix chain 'C' and resid 435 through 439 Processing helix chain 'C' and resid 440 through 449 Processing helix chain 'C' and resid 454 through 460 Processing helix chain 'C' and resid 462 through 471 removed outlier: 3.511A pdb=" N SER C 469 " --> pdb=" O ASN C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 491 removed outlier: 3.612A pdb=" N VAL C 491 " --> pdb=" O VAL C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 521 Processing helix chain 'C' and resid 521 through 529 Processing helix chain 'C' and resid 532 through 540 Processing helix chain 'C' and resid 573 through 584 removed outlier: 3.788A pdb=" N ILE C 583 " --> pdb=" O ALA C 579 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE C 584 " --> pdb=" O LEU C 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 208 removed outlier: 3.677A pdb=" N ASN D 206 " --> pdb=" O ASP D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 234 Processing helix chain 'D' and resid 252 through 257 Processing helix chain 'D' and resid 277 through 294 removed outlier: 4.136A pdb=" N GLU D 293 " --> pdb=" O LYS D 289 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU D 294 " --> pdb=" O GLY D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 312 Processing helix chain 'D' and resid 318 through 336 removed outlier: 3.852A pdb=" N GLU D 323 " --> pdb=" O PRO D 319 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 345 Processing helix chain 'D' and resid 357 through 361 removed outlier: 3.815A pdb=" N GLY D 361 " --> pdb=" O ILE D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 367 Processing helix chain 'D' and resid 369 through 374 removed outlier: 3.586A pdb=" N LEU D 374 " --> pdb=" O LEU D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 379 removed outlier: 3.654A pdb=" N ARG D 379 " --> pdb=" O LYS D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 440 removed outlier: 3.597A pdb=" N GLU D 440 " --> pdb=" O GLU D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 449 Processing helix chain 'D' and resid 456 through 471 removed outlier: 3.665A pdb=" N LYS D 463 " --> pdb=" O ARG D 459 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS D 470 " --> pdb=" O GLU D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 493 Processing helix chain 'D' and resid 494 through 498 removed outlier: 3.577A pdb=" N HIS D 497 " --> pdb=" O ASP D 494 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG D 498 " --> pdb=" O ARG D 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 494 through 498' Processing helix chain 'D' and resid 509 through 520 Processing helix chain 'D' and resid 521 through 529 Processing helix chain 'D' and resid 532 through 540 Processing helix chain 'D' and resid 573 through 584 removed outlier: 3.779A pdb=" N ILE D 583 " --> pdb=" O ALA D 579 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE D 584 " --> pdb=" O LEU D 580 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 209 Processing helix chain 'E' and resid 220 through 233 Processing helix chain 'E' and resid 277 through 291 removed outlier: 3.616A pdb=" N LEU E 287 " --> pdb=" O ALA E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 312 removed outlier: 3.652A pdb=" N ARG E 306 " --> pdb=" O ASP E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 337 removed outlier: 3.589A pdb=" N GLY E 337 " --> pdb=" O TRP E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 361 removed outlier: 3.633A pdb=" N GLY E 361 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 367 Processing helix chain 'E' and resid 369 through 374 removed outlier: 3.562A pdb=" N LEU E 374 " --> pdb=" O LEU E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 426 removed outlier: 3.597A pdb=" N ARG E 425 " --> pdb=" O ALA E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 439 Processing helix chain 'E' and resid 440 through 452 removed outlier: 3.804A pdb=" N LYS E 450 " --> pdb=" O LYS E 446 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LYS E 451 " --> pdb=" O ILE E 447 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU E 452 " --> pdb=" O ARG E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 472 removed outlier: 4.463A pdb=" N GLU E 462 " --> pdb=" O LYS E 458 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU E 467 " --> pdb=" O LYS E 463 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER E 469 " --> pdb=" O ASN E 465 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 493 removed outlier: 4.415A pdb=" N ARG E 488 " --> pdb=" O LYS E 484 " (cutoff:3.500A) Processing helix chain 'E' and resid 500 through 504 removed outlier: 3.651A pdb=" N TYR E 503 " --> pdb=" O GLY E 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 520 Processing helix chain 'E' and resid 521 through 529 Processing helix chain 'E' and resid 532 through 540 removed outlier: 3.725A pdb=" N TRP E 538 " --> pdb=" O GLU E 534 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 584 removed outlier: 4.089A pdb=" N ILE E 577 " --> pdb=" O GLY E 573 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE E 583 " --> pdb=" O ALA E 579 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE E 584 " --> pdb=" O LEU E 580 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 209 Processing helix chain 'F' and resid 220 through 233 Processing helix chain 'F' and resid 277 through 293 removed outlier: 4.026A pdb=" N GLU F 293 " --> pdb=" O LYS F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 313 removed outlier: 3.838A pdb=" N ARG F 306 " --> pdb=" O ASP F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 336 removed outlier: 3.827A pdb=" N GLU F 323 " --> pdb=" O PRO F 319 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLU F 324 " --> pdb=" O THR F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 345 removed outlier: 3.664A pdb=" N LEU F 344 " --> pdb=" O PRO F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 361 removed outlier: 3.883A pdb=" N GLY F 361 " --> pdb=" O ILE F 358 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 368 Processing helix chain 'F' and resid 369 through 374 Processing helix chain 'F' and resid 420 through 427 removed outlier: 3.652A pdb=" N ARG F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE F 427 " --> pdb=" O LEU F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 439 Processing helix chain 'F' and resid 440 through 450 Processing helix chain 'F' and resid 455 through 469 removed outlier: 4.074A pdb=" N ARG F 459 " --> pdb=" O GLU F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 493 removed outlier: 3.937A pdb=" N VAL F 492 " --> pdb=" O ARG F 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 498 removed outlier: 3.515A pdb=" N HIS F 497 " --> pdb=" O ASP F 494 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG F 498 " --> pdb=" O ARG F 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 494 through 498' Processing helix chain 'F' and resid 500 through 504 removed outlier: 4.015A pdb=" N TYR F 503 " --> pdb=" O GLY F 500 " (cutoff:3.500A) Processing helix chain 'F' and resid 509 through 521 removed outlier: 3.777A pdb=" N VAL F 521 " --> pdb=" O TRP F 517 " (cutoff:3.500A) Processing helix chain 'F' and resid 521 through 529 Processing helix chain 'F' and resid 532 through 540 removed outlier: 3.539A pdb=" N LEU F 540 " --> pdb=" O ILE F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 582 removed outlier: 3.624A pdb=" N ILE F 577 " --> pdb=" O GLY F 573 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 242 through 246 removed outlier: 6.348A pdb=" N GLU A 243 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ASP A 356 " --> pdb=" O GLU A 243 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE A 245 " --> pdb=" O ASP A 356 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLN A 210 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ILE A 430 " --> pdb=" O GLN A 210 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE A 212 " --> pdb=" O ILE A 430 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 264 Processing sheet with id=AA3, first strand: chain 'A' and resid 388 through 389 Processing sheet with id=AA4, first strand: chain 'A' and resid 552 through 554 Processing sheet with id=AA5, first strand: chain 'B' and resid 242 through 246 removed outlier: 6.173A pdb=" N GLU B 243 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ASP B 356 " --> pdb=" O GLU B 243 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE B 245 " --> pdb=" O ASP B 356 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N PHE B 351 " --> pdb=" O TYR B 404 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE B 406 " --> pdb=" O PHE B 351 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU B 353 " --> pdb=" O ILE B 406 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N THR B 408 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE B 355 " --> pdb=" O THR B 408 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL B 211 " --> pdb=" O GLY B 407 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE B 212 " --> pdb=" O ILE B 430 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 258 through 262 Processing sheet with id=AA7, first strand: chain 'B' and resid 388 through 389 Processing sheet with id=AA8, first strand: chain 'B' and resid 552 through 554 Processing sheet with id=AA9, first strand: chain 'C' and resid 242 through 246 removed outlier: 6.483A pdb=" N PHE C 351 " --> pdb=" O TYR C 404 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ILE C 406 " --> pdb=" O PHE C 351 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU C 353 " --> pdb=" O ILE C 406 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N THR C 408 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE C 355 " --> pdb=" O THR C 408 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N ASN C 410 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY C 215 " --> pdb=" O MET C 409 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLN C 210 " --> pdb=" O ALA C 428 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE C 430 " --> pdb=" O GLN C 210 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE C 212 " --> pdb=" O ILE C 430 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 258 through 262 Processing sheet with id=AB2, first strand: chain 'C' and resid 388 through 389 Processing sheet with id=AB3, first strand: chain 'C' and resid 552 through 554 Processing sheet with id=AB4, first strand: chain 'D' and resid 242 through 246 removed outlier: 6.397A pdb=" N PHE D 351 " --> pdb=" O TYR D 404 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ILE D 406 " --> pdb=" O PHE D 351 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU D 353 " --> pdb=" O ILE D 406 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N THR D 408 " --> pdb=" O LEU D 353 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE D 355 " --> pdb=" O THR D 408 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N ASN D 410 " --> pdb=" O ILE D 355 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL D 211 " --> pdb=" O GLY D 407 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N MET D 409 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU D 213 " --> pdb=" O MET D 409 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 258 through 262 Processing sheet with id=AB6, first strand: chain 'D' and resid 388 through 389 Processing sheet with id=AB7, first strand: chain 'D' and resid 552 through 554 Processing sheet with id=AB8, first strand: chain 'E' and resid 242 through 246 removed outlier: 6.719A pdb=" N GLU E 243 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ASP E 356 " --> pdb=" O GLU E 243 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE E 245 " --> pdb=" O ASP E 356 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE E 351 " --> pdb=" O TYR E 404 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ILE E 406 " --> pdb=" O PHE E 351 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU E 353 " --> pdb=" O ILE E 406 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N THR E 408 " --> pdb=" O LEU E 353 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ILE E 355 " --> pdb=" O THR E 408 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N ASN E 410 " --> pdb=" O ILE E 355 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL E 211 " --> pdb=" O GLY E 407 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N MET E 409 " --> pdb=" O VAL E 211 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU E 213 " --> pdb=" O MET E 409 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N GLN E 210 " --> pdb=" O ALA E 428 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ILE E 430 " --> pdb=" O GLN E 210 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE E 212 " --> pdb=" O ILE E 430 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 258 through 263 Processing sheet with id=AC1, first strand: chain 'E' and resid 388 through 389 Processing sheet with id=AC2, first strand: chain 'E' and resid 552 through 554 Processing sheet with id=AC3, first strand: chain 'F' and resid 242 through 246 removed outlier: 6.508A pdb=" N GLU F 243 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ASP F 356 " --> pdb=" O GLU F 243 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE F 245 " --> pdb=" O ASP F 356 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE F 351 " --> pdb=" O TYR F 404 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE F 406 " --> pdb=" O PHE F 351 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU F 353 " --> pdb=" O ILE F 406 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N THR F 408 " --> pdb=" O LEU F 353 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE F 355 " --> pdb=" O THR F 408 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N ASN F 410 " --> pdb=" O ILE F 355 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLN F 210 " --> pdb=" O ALA F 428 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N ILE F 430 " --> pdb=" O GLN F 210 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE F 212 " --> pdb=" O ILE F 430 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 258 through 265 removed outlier: 3.773A pdb=" N LYS F 269 " --> pdb=" O ASP F 265 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 388 through 389 Processing sheet with id=AC6, first strand: chain 'F' and resid 552 through 554 741 hydrogen bonds defined for protein. 2115 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: 3.26 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: 5906 1.34 - 1.46: 3854 1.46 - 1.58: 9724 1.58 - 1.70: 34 1.70 - 1.82: 38 Bond restraints: 19556 Sorted by residual: bond pdb=" C THR C 348 " pdb=" N PRO C 349 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.52e+00 bond pdb=" C THR F 348 " pdb=" N PRO F 349 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.38e+00 bond pdb=" C THR D 348 " pdb=" N PRO D 349 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.24e+00 bond pdb=" C THR E 348 " pdb=" N PRO E 349 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.07e+00 bond pdb=" C THR B 237 " pdb=" N PRO B 238 " ideal model delta sigma weight residual 1.330 1.349 -0.019 1.25e-02 6.40e+03 2.42e+00 ... (remaining 19551 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 25978 2.31 - 4.62: 432 4.62 - 6.94: 50 6.94 - 9.25: 13 9.25 - 11.56: 1 Bond angle restraints: 26474 Sorted by residual: angle pdb=" C LEU D 540 " pdb=" N ASN D 541 " pdb=" CA ASN D 541 " ideal model delta sigma weight residual 122.46 128.54 -6.08 1.41e+00 5.03e-01 1.86e+01 angle pdb=" C LEU A 540 " pdb=" N ASN A 541 " pdb=" CA ASN A 541 " ideal model delta sigma weight residual 121.54 129.61 -8.07 1.91e+00 2.74e-01 1.78e+01 angle pdb=" C LEU B 540 " pdb=" N ASN B 541 " pdb=" CA ASN B 541 " ideal model delta sigma weight residual 122.46 128.31 -5.85 1.41e+00 5.03e-01 1.72e+01 angle pdb=" C LEU C 540 " pdb=" N ASN C 541 " pdb=" CA ASN C 541 " ideal model delta sigma weight residual 121.54 129.45 -7.91 1.91e+00 2.74e-01 1.71e+01 angle pdb=" C LEU E 540 " pdb=" N ASN E 541 " pdb=" CA ASN E 541 " ideal model delta sigma weight residual 122.46 128.13 -5.67 1.41e+00 5.03e-01 1.62e+01 ... (remaining 26469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 10467 17.90 - 35.79: 1016 35.79 - 53.69: 161 53.69 - 71.59: 31 71.59 - 89.48: 16 Dihedral angle restraints: 11691 sinusoidal: 4938 harmonic: 6753 Sorted by residual: dihedral pdb=" CA PHE C 427 " pdb=" C PHE C 427 " pdb=" N ALA C 428 " pdb=" CA ALA C 428 " ideal model delta harmonic sigma weight residual 180.00 157.27 22.73 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA PHE E 427 " pdb=" C PHE E 427 " pdb=" N ALA E 428 " pdb=" CA ALA E 428 " ideal model delta harmonic sigma weight residual 180.00 157.27 22.73 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" N GLU A 268 " pdb=" C GLU A 268 " pdb=" CA GLU A 268 " pdb=" CB GLU A 268 " ideal model delta harmonic sigma weight residual 122.80 133.54 -10.74 0 2.50e+00 1.60e-01 1.85e+01 ... (remaining 11688 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2609 0.081 - 0.162: 261 0.162 - 0.243: 18 0.243 - 0.324: 1 0.324 - 0.404: 2 Chirality restraints: 2891 Sorted by residual: chirality pdb=" CA GLU A 268 " pdb=" N GLU A 268 " pdb=" C GLU A 268 " pdb=" CB GLU A 268 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" CB ILE F 416 " pdb=" CA ILE F 416 " pdb=" CG1 ILE F 416 " pdb=" CG2 ILE F 416 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" CB ILE B 354 " pdb=" CA ILE B 354 " pdb=" CG1 ILE B 354 " pdb=" CG2 ILE B 354 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 2888 not shown) Planarity restraints: 3311 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 251 " 0.012 2.00e-02 2.50e+03 1.74e-02 6.08e+00 pdb=" CG TYR E 251 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR E 251 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR E 251 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR E 251 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR E 251 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR E 251 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 251 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU F 395 " -0.039 5.00e-02 4.00e+02 5.94e-02 5.64e+00 pdb=" N PRO F 396 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO F 396 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO F 396 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 395 " -0.038 5.00e-02 4.00e+02 5.79e-02 5.37e+00 pdb=" N PRO B 396 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 396 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 396 " -0.032 5.00e-02 4.00e+02 ... (remaining 3308 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 344 2.67 - 3.23: 16826 3.23 - 3.78: 31148 3.78 - 4.34: 44581 4.34 - 4.90: 71895 Nonbonded interactions: 164794 Sorted by model distance: nonbonded pdb="MG MG C 702 " pdb=" O HOH C 801 " model vdw 2.109 2.170 nonbonded pdb=" OG1 THR F 222 " pdb="MG MG F 702 " model vdw 2.112 2.170 nonbonded pdb="MG MG B 702 " pdb=" O HOH C 802 " model vdw 2.115 2.170 nonbonded pdb=" O2B GSP D 701 " pdb="MG MG D 702 " model vdw 2.122 2.170 nonbonded pdb=" O2G GSP F 701 " pdb="MG MG F 702 " model vdw 2.122 2.170 ... (remaining 164789 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 198 through 199 and (name N or name CA or name C or name \ O or name CB )) or resid 200 through 230 or (resid 231 and (name N or name CA or \ name C or name O or name CB )) or resid 232 through 263 or (resid 270 through 2 \ 71 and (name N or name CA or name C or name O or name CB )) or resid 272 through \ 295 or (resid 296 through 298 and (name N or name CA or name C or name O or nam \ e CB )) or resid 299 through 301 or (resid 302 and (name N or name CA or name C \ or name O or name CB )) or resid 303 through 314 or (resid 315 and (name N or na \ me CA or name C or name O or name CB )) or resid 316 through 317 or (resid 318 a \ nd (name N or name CA or name C or name O or name CB )) or resid 319 or (resid 3 \ 20 through 321 and (name N or name CA or name C or name O or name CB )) or resid \ 322 through 394 or (resid 395 and (name N or name CA or name C or name O or nam \ e CB )) or resid 396 through 404 or (resid 405 and (name N or name CA or name C \ or name O or name CB )) or resid 406 through 439 or (resid 440 through 441 and ( \ name N or name CA or name C or name O or name CB )) or resid 442 through 444 or \ (resid 445 through 446 and (name N or name CA or name C or name O or name CB )) \ or resid 447 or (resid 448 through 459 and (name N or name CA or name C or name \ O or name CB )) or resid 460 through 493 or (resid 494 and (name N or name CA or \ name C or name O or name CB )) or resid 495 through 544 or (resid 545 through 5 \ 47 and (name N or name CA or name C or name O or name CB )) or resid 548 or (res \ id 549 and (name N or name CA or name C or name O or name CB )) or resid 550 thr \ ough 552 or (resid 553 and (name N or name CA or name C or name O or name CB )) \ or resid 554 through 555 or (resid 556 and (name N or name CA or name C or name \ O or name CB )) or resid 557 through 560 or (resid 561 and (name N or name CA or \ name C or name O or name CB )) or resid 562 through 571 or (resid 572 and (name \ N or name CA or name C or name O or name CB )) or resid 573 through 702)) selection = (chain 'B' and ((resid 198 through 199 and (name N or name CA or name C or name \ O or name CB )) or resid 200 through 230 or (resid 231 and (name N or name CA or \ name C or name O or name CB )) or resid 232 through 242 or (resid 243 and (name \ N or name CA or name C or name O or name CB )) or resid 244 through 263 or resi \ d 270 through 292 or (resid 293 and (name N or name CA or name C or name O or na \ me CB )) or resid 294 through 300 or (resid 301 through 302 and (name N or name \ CA or name C or name O or name CB )) or resid 303 through 368 or (resid 369 and \ (name N or name CA or name C or name O or name CB )) or resid 370 through 394 or \ (resid 395 and (name N or name CA or name C or name O or name CB )) or resid 39 \ 6 through 404 or (resid 405 and (name N or name CA or name C or name O or name C \ B )) or resid 406 through 417 or (resid 418 and (name N or name CA or name C or \ name O or name CB )) or resid 419 through 439 or (resid 440 through 441 and (nam \ e N or name CA or name C or name O or name CB )) or resid 442 through 444 or (re \ sid 445 through 446 and (name N or name CA or name C or name O or name CB )) or \ resid 447 or (resid 448 through 459 and (name N or name CA or name C or name O o \ r name CB )) or resid 460 through 493 or (resid 494 and (name N or name CA or na \ me C or name O or name CB )) or resid 495 through 545 or (resid 546 through 547 \ and (name N or name CA or name C or name O or name CB )) or resid 548 or (resid \ 549 and (name N or name CA or name C or name O or name CB )) or resid 550 throug \ h 552 or (resid 553 and (name N or name CA or name C or name O or name CB )) or \ resid 554 through 555 or (resid 556 and (name N or name CA or name C or name O o \ r name CB )) or resid 557 through 560 or (resid 561 and (name N or name CA or na \ me C or name O or name CB )) or resid 562 through 571 or (resid 572 and (name N \ or name CA or name C or name O or name CB )) or resid 573 through 702)) selection = (chain 'C' and ((resid 198 through 199 and (name N or name CA or name C or name \ O or name CB )) or resid 200 through 242 or (resid 243 and (name N or name CA or \ name C or name O or name CB )) or resid 244 through 292 or (resid 293 and (name \ N or name CA or name C or name O or name CB )) or resid 294 through 295 or (res \ id 296 through 298 and (name N or name CA or name C or name O or name CB )) or r \ esid 299 through 300 or (resid 301 through 302 and (name N or name CA or name C \ or name O or name CB )) or resid 303 through 314 or (resid 315 and (name N or na \ me CA or name C or name O or name CB )) or resid 316 through 317 or (resid 318 a \ nd (name N or name CA or name C or name O or name CB )) or resid 319 or (resid 3 \ 20 through 321 and (name N or name CA or name C or name O or name CB )) or resid \ 322 through 368 or (resid 369 and (name N or name CA or name C or name O or nam \ e CB )) or resid 370 through 394 or (resid 395 and (name N or name CA or name C \ or name O or name CB )) or resid 396 through 404 or (resid 405 and (name N or na \ me CA or name C or name O or name CB )) or resid 406 through 417 or (resid 418 a \ nd (name N or name CA or name C or name O or name CB )) or resid 419 through 439 \ or (resid 440 through 441 and (name N or name CA or name C or name O or name CB \ )) or resid 442 through 444 or (resid 445 through 446 and (name N or name CA or \ name C or name O or name CB )) or resid 447 or (resid 448 through 459 and (name \ N or name CA or name C or name O or name CB )) or resid 460 through 493 or (res \ id 494 and (name N or name CA or name C or name O or name CB )) or resid 495 thr \ ough 544 or (resid 545 through 547 and (name N or name CA or name C or name O or \ name CB )) or resid 548 or (resid 549 and (name N or name CA or name C or name \ O or name CB )) or resid 550 through 555 or (resid 556 and (name N or name CA or \ name C or name O or name CB )) or resid 557 through 560 or (resid 561 and (name \ N or name CA or name C or name O or name CB )) or resid 562 through 571 or (res \ id 572 and (name N or name CA or name C or name O or name CB )) or resid 573 thr \ ough 702)) selection = (chain 'D' and ((resid 198 through 199 and (name N or name CA or name C or name \ O or name CB )) or resid 200 through 242 or (resid 243 and (name N or name CA or \ name C or name O or name CB )) or resid 244 through 270 or (resid 271 and (name \ N or name CA or name C or name O or name CB )) or resid 272 through 292 or (res \ id 293 and (name N or name CA or name C or name O or name CB )) or resid 294 thr \ ough 295 or (resid 296 through 298 and (name N or name CA or name C or name O or \ name CB )) or resid 299 through 300 or (resid 301 through 302 and (name N or na \ me CA or name C or name O or name CB )) or resid 303 through 314 or (resid 315 a \ nd (name N or name CA or name C or name O or name CB )) or resid 316 through 317 \ or (resid 318 and (name N or name CA or name C or name O or name CB )) or resid \ 319 or (resid 320 through 321 and (name N or name CA or name C or name O or nam \ e CB )) or resid 322 through 368 or (resid 369 and (name N or name CA or name C \ or name O or name CB )) or resid 370 through 404 or (resid 405 and (name N or na \ me CA or name C or name O or name CB )) or resid 406 through 417 or (resid 418 a \ nd (name N or name CA or name C or name O or name CB )) or resid 419 through 452 \ or (resid 453 through 459 and (name N or name CA or name C or name O or name CB \ )) or resid 460 through 555 or (resid 556 and (name N or name CA or name C or n \ ame O or name CB )) or resid 557 through 702)) selection = (chain 'E' and ((resid 198 through 199 and (name N or name CA or name C or name \ O or name CB )) or resid 200 through 242 or (resid 243 and (name N or name CA or \ name C or name O or name CB )) or resid 244 through 263 or (resid 270 through 2 \ 71 and (name N or name CA or name C or name O or name CB )) or resid 272 through \ 292 or (resid 293 and (name N or name CA or name C or name O or name CB )) or r \ esid 294 through 295 or (resid 296 through 298 and (name N or name CA or name C \ or name O or name CB )) or resid 299 through 300 or (resid 301 through 302 and ( \ name N or name CA or name C or name O or name CB )) or resid 303 through 314 or \ (resid 315 and (name N or name CA or name C or name O or name CB )) or resid 316 \ through 317 or (resid 318 and (name N or name CA or name C or name O or name CB \ )) or resid 319 or (resid 320 through 321 and (name N or name CA or name C or n \ ame O or name CB )) or resid 322 through 368 or (resid 369 and (name N or name C \ A or name C or name O or name CB )) or resid 370 through 394 or (resid 395 and ( \ name N or name CA or name C or name O or name CB )) or resid 396 through 417 or \ (resid 418 and (name N or name CA or name C or name O or name CB )) or resid 419 \ through 439 or (resid 440 through 441 and (name N or name CA or name C or name \ O or name CB )) or resid 442 through 445 or (resid 446 and (name N or name CA or \ name C or name O or name CB )) or resid 447 or (resid 448 through 459 and (name \ N or name CA or name C or name O or name CB )) or resid 460 through 493 or (res \ id 494 and (name N or name CA or name C or name O or name CB )) or resid 495 thr \ ough 546 or (resid 547 and (name N or name CA or name C or name O or name CB )) \ or resid 548 or (resid 549 and (name N or name CA or name C or name O or name CB \ )) or resid 550 through 552 or (resid 553 and (name N or name CA or name C or n \ ame O or name CB )) or resid 554 through 560 or (resid 561 and (name N or name C \ A or name C or name O or name CB )) or resid 562 through 702)) selection = (chain 'F' and ((resid 198 through 199 and (name N or name CA or name C or name \ O or name CB )) or resid 200 through 242 or (resid 243 and (name N or name CA or \ name C or name O or name CB )) or resid 244 through 262 or (resid 263 and (name \ N or name CA or name C or name O or name CB )) or (resid 270 through 271 and (n \ ame N or name CA or name C or name O or name CB )) or resid 272 through 292 or ( \ resid 293 and (name N or name CA or name C or name O or name CB )) or resid 294 \ through 295 or (resid 296 through 298 and (name N or name CA or name C or name O \ or name CB )) or resid 299 through 300 or (resid 301 through 302 and (name N or \ name CA or name C or name O or name CB )) or resid 303 through 314 or (resid 31 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 316 through \ 317 or (resid 318 and (name N or name CA or name C or name O or name CB )) or re \ sid 319 or (resid 320 through 321 and (name N or name CA or name C or name O or \ name CB )) or resid 322 through 368 or (resid 369 and (name N or name CA or name \ C or name O or name CB )) or resid 370 through 394 or (resid 395 and (name N or \ name CA or name C or name O or name CB )) or resid 396 through 404 or (resid 40 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 406 through \ 417 or (resid 418 and (name N or name CA or name C or name O or name CB )) or re \ sid 419 through 439 or (resid 440 through 441 and (name N or name CA or name C o \ r name O or name CB )) or resid 442 through 444 or (resid 445 through 446 and (n \ ame N or name CA or name C or name O or name CB )) or resid 447 through 452 or ( \ resid 453 through 459 and (name N or name CA or name C or name O or name CB )) o \ r resid 460 through 493 or (resid 494 and (name N or name CA or name C or name O \ or name CB )) or resid 495 through 544 or (resid 545 through 547 and (name N or \ name CA or name C or name O or name CB )) or resid 548 or (resid 549 and (name \ N or name CA or name C or name O or name CB )) or resid 550 through 552 or (resi \ d 553 and (name N or name CA or name C or name O or name CB )) or resid 554 thro \ ugh 555 or (resid 556 and (name N or name CA or name C or name O or name CB )) o \ r resid 557 through 702)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 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: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.270 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19556 Z= 0.190 Angle : 0.751 11.562 26474 Z= 0.411 Chirality : 0.050 0.404 2891 Planarity : 0.006 0.059 3311 Dihedral : 14.347 89.483 7361 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.15 % Allowed : 5.52 % Favored : 94.33 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.72 (0.14), residues: 2295 helix: -3.30 (0.10), residues: 1025 sheet: -2.40 (0.26), residues: 284 loop : -1.24 (0.18), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 488 TYR 0.041 0.002 TYR E 251 PHE 0.018 0.002 PHE B 247 TRP 0.016 0.002 TRP D 242 HIS 0.009 0.001 HIS E 248 Details of bonding type rmsd covalent geometry : bond 0.00434 (19556) covalent geometry : angle 0.75064 (26474) hydrogen bonds : bond 0.18006 ( 741) hydrogen bonds : angle 7.90400 ( 2115) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 308 time to evaluate : 0.837 Fit side-chains revert: symmetry clash REVERT: A 519 TYR cc_start: 0.8319 (m-80) cc_final: 0.7991 (m-10) REVERT: B 409 MET cc_start: 0.8136 (ttt) cc_final: 0.7846 (tmm) REVERT: B 435 ARG cc_start: 0.8006 (mmm-85) cc_final: 0.7455 (mtt180) REVERT: B 515 HIS cc_start: 0.8465 (m170) cc_final: 0.8058 (m90) REVERT: B 542 GLU cc_start: 0.8256 (pt0) cc_final: 0.7943 (pt0) REVERT: C 261 ARG cc_start: 0.7578 (mtt180) cc_final: 0.7377 (mmm160) REVERT: C 305 HIS cc_start: 0.7562 (t70) cc_final: 0.7342 (t-90) REVERT: C 415 SER cc_start: 0.9072 (p) cc_final: 0.8815 (p) REVERT: C 446 LYS cc_start: 0.8608 (tmmt) cc_final: 0.8235 (ttmt) REVERT: C 577 ILE cc_start: 0.9153 (mm) cc_final: 0.8898 (mm) REVERT: D 253 TYR cc_start: 0.8738 (t80) cc_final: 0.8401 (t80) REVERT: D 255 GLU cc_start: 0.8060 (mp0) cc_final: 0.7328 (mp0) REVERT: F 518 TYR cc_start: 0.8538 (m-80) cc_final: 0.8297 (m-80) outliers start: 3 outliers final: 2 residues processed: 310 average time/residue: 0.1965 time to fit residues: 85.9684 Evaluate side-chains 195 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 193 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 418 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.1980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.2980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS A 346 ASN A 506 ASN A 515 HIS A 541 ASN B 248 HIS B 384 ASN B 465 ASN B 473 ASN B 501 HIS B 515 HIS B 561 ASN C 248 HIS C 249 GLN C 384 ASN ** C 497 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 HIS C 531 ASN C 541 ASN D 248 HIS D 305 HIS ** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 384 ASN ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 248 HIS F 384 ASN F 385 GLN F 461 ASN F 541 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.127135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.102687 restraints weight = 26679.734| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.75 r_work: 0.3026 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 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 : 0.003 0.026 19556 Z= 0.120 Angle : 0.526 7.902 26474 Z= 0.267 Chirality : 0.041 0.156 2891 Planarity : 0.004 0.050 3311 Dihedral : 5.984 58.826 2647 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.21 % Allowed : 10.27 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.16), residues: 2295 helix: -1.49 (0.14), residues: 1067 sheet: -2.30 (0.26), residues: 290 loop : -0.59 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 426 TYR 0.016 0.001 TYR E 251 PHE 0.019 0.001 PHE A 477 TRP 0.012 0.001 TRP A 333 HIS 0.004 0.001 HIS A 515 Details of bonding type rmsd covalent geometry : bond 0.00273 (19556) covalent geometry : angle 0.52634 (26474) hydrogen bonds : bond 0.03018 ( 741) hydrogen bonds : angle 4.86548 ( 2115) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 223 time to evaluate : 0.813 Fit side-chains revert: symmetry clash REVERT: A 227 LYS cc_start: 0.8158 (tttm) cc_final: 0.7844 (tttm) REVERT: A 409 MET cc_start: 0.8680 (ttp) cc_final: 0.8478 (ttp) REVERT: B 348 THR cc_start: 0.7537 (OUTLIER) cc_final: 0.7264 (m) REVERT: B 409 MET cc_start: 0.8573 (ttt) cc_final: 0.8198 (tmm) REVERT: B 542 GLU cc_start: 0.8553 (pt0) cc_final: 0.8220 (pt0) REVERT: C 261 ARG cc_start: 0.7428 (mtt180) cc_final: 0.6974 (mmm160) REVERT: C 305 HIS cc_start: 0.7933 (t70) cc_final: 0.7698 (t-90) REVERT: C 488 ARG cc_start: 0.8611 (mtt-85) cc_final: 0.8334 (mtp85) REVERT: C 549 ASN cc_start: 0.8656 (m-40) cc_final: 0.8077 (p0) REVERT: D 253 TYR cc_start: 0.8981 (t80) cc_final: 0.8699 (t80) REVERT: D 255 GLU cc_start: 0.8515 (mp0) cc_final: 0.7971 (mp0) REVERT: D 458 LYS cc_start: 0.7954 (tptt) cc_final: 0.7638 (pttp) REVERT: E 466 GLU cc_start: 0.8110 (tp30) cc_final: 0.7862 (tp30) REVERT: F 210 GLN cc_start: 0.9143 (pm20) cc_final: 0.8845 (pm20) REVERT: F 305 HIS cc_start: 0.7825 (t70) cc_final: 0.7611 (t70) REVERT: F 526 MET cc_start: 0.8934 (mtp) cc_final: 0.8690 (mtm) outliers start: 24 outliers final: 13 residues processed: 234 average time/residue: 0.1704 time to fit residues: 58.8478 Evaluate side-chains 201 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 187 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 305 HIS Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain F residue 292 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 214 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 178 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 10 optimal weight: 0.0370 chunk 112 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 192 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 overall best weight: 1.1862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN C 497 HIS ** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.124368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.101147 restraints weight = 26984.061| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.63 r_work: 0.2997 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19556 Z= 0.147 Angle : 0.526 8.155 26474 Z= 0.265 Chirality : 0.041 0.158 2891 Planarity : 0.004 0.041 3311 Dihedral : 5.738 55.102 2646 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.21 % Allowed : 11.94 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.17), residues: 2295 helix: -0.73 (0.15), residues: 1077 sheet: -2.17 (0.26), residues: 292 loop : -0.15 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 426 TYR 0.016 0.001 TYR E 251 PHE 0.016 0.001 PHE D 279 TRP 0.010 0.001 TRP D 242 HIS 0.015 0.001 HIS D 305 Details of bonding type rmsd covalent geometry : bond 0.00345 (19556) covalent geometry : angle 0.52596 (26474) hydrogen bonds : bond 0.02834 ( 741) hydrogen bonds : angle 4.52032 ( 2115) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 0.772 Fit side-chains revert: symmetry clash REVERT: A 227 LYS cc_start: 0.8169 (tttm) cc_final: 0.7803 (tttm) REVERT: A 460 LEU cc_start: 0.7409 (mt) cc_final: 0.7184 (mm) REVERT: A 520 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7950 (mt-10) REVERT: B 249 GLN cc_start: 0.8793 (mm-40) cc_final: 0.8524 (mm110) REVERT: B 348 THR cc_start: 0.7562 (OUTLIER) cc_final: 0.7278 (m) REVERT: B 409 MET cc_start: 0.8542 (ttt) cc_final: 0.8159 (tmm) REVERT: B 425 ARG cc_start: 0.6881 (tpt170) cc_final: 0.6612 (tpt170) REVERT: B 542 GLU cc_start: 0.8591 (pt0) cc_final: 0.8277 (pt0) REVERT: C 261 ARG cc_start: 0.7439 (mtt180) cc_final: 0.6937 (mmm160) REVERT: C 435 ARG cc_start: 0.8494 (mtm-85) cc_final: 0.8281 (mtm-85) REVERT: C 488 ARG cc_start: 0.8649 (mtt-85) cc_final: 0.8352 (mtp85) REVERT: C 532 ASP cc_start: 0.8730 (t0) cc_final: 0.8528 (t0) REVERT: C 549 ASN cc_start: 0.8757 (m-40) cc_final: 0.8337 (p0) REVERT: D 253 TYR cc_start: 0.9026 (t80) cc_final: 0.8764 (t80) REVERT: D 255 GLU cc_start: 0.8455 (mp0) cc_final: 0.7901 (mp0) REVERT: D 470 LYS cc_start: 0.8566 (mtpp) cc_final: 0.8232 (mttt) REVERT: E 466 GLU cc_start: 0.8042 (tp30) cc_final: 0.7684 (tp30) REVERT: F 526 MET cc_start: 0.8990 (mtp) cc_final: 0.8752 (mtm) outliers start: 24 outliers final: 16 residues processed: 216 average time/residue: 0.1737 time to fit residues: 55.5798 Evaluate side-chains 205 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 188 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 385 GLN Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 494 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 36 optimal weight: 7.9990 chunk 213 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 27 optimal weight: 9.9990 chunk 214 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 184 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 123 optimal weight: 0.0070 overall best weight: 1.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN C 206 ASN ** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.122080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.098782 restraints weight = 26837.947| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.64 r_work: 0.2964 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19556 Z= 0.175 Angle : 0.542 7.633 26474 Z= 0.273 Chirality : 0.042 0.168 2891 Planarity : 0.004 0.039 3311 Dihedral : 5.746 57.200 2646 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.67 % Allowed : 13.01 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.17), residues: 2295 helix: -0.28 (0.16), residues: 1072 sheet: -2.07 (0.26), residues: 300 loop : 0.03 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 426 TYR 0.020 0.001 TYR E 251 PHE 0.016 0.001 PHE D 279 TRP 0.012 0.001 TRP D 242 HIS 0.007 0.001 HIS D 305 Details of bonding type rmsd covalent geometry : bond 0.00415 (19556) covalent geometry : angle 0.54196 (26474) hydrogen bonds : bond 0.02835 ( 741) hydrogen bonds : angle 4.42327 ( 2115) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 207 time to evaluate : 0.798 Fit side-chains revert: symmetry clash REVERT: A 227 LYS cc_start: 0.8247 (tttm) cc_final: 0.7987 (tttm) REVERT: A 520 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7933 (mt-10) REVERT: B 198 TYR cc_start: 0.7408 (m-10) cc_final: 0.7139 (m-10) REVERT: B 348 THR cc_start: 0.7510 (OUTLIER) cc_final: 0.7229 (m) REVERT: B 542 GLU cc_start: 0.8605 (pt0) cc_final: 0.8287 (pt0) REVERT: C 261 ARG cc_start: 0.7501 (mtt180) cc_final: 0.6884 (mmm160) REVERT: C 435 ARG cc_start: 0.8563 (mtm-85) cc_final: 0.8292 (mtm-85) REVERT: C 532 ASP cc_start: 0.8770 (t0) cc_final: 0.8542 (t0) REVERT: C 549 ASN cc_start: 0.8709 (m-40) cc_final: 0.8274 (p0) REVERT: D 253 TYR cc_start: 0.9126 (t80) cc_final: 0.8913 (t80) REVERT: D 255 GLU cc_start: 0.8502 (mp0) cc_final: 0.7884 (mp0) REVERT: E 323 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7118 (pm20) REVERT: E 466 GLU cc_start: 0.8112 (tp30) cc_final: 0.7846 (tp30) REVERT: F 243 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8419 (mm-30) REVERT: F 511 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7947 (mp0) outliers start: 33 outliers final: 24 residues processed: 225 average time/residue: 0.1605 time to fit residues: 54.1164 Evaluate side-chains 201 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 305 HIS Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain E residue 323 GLU Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 385 GLN Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 370 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 86 optimal weight: 5.9990 chunk 22 optimal weight: 0.0970 chunk 42 optimal weight: 0.7980 chunk 148 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 173 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 133 optimal weight: 0.7980 chunk 198 optimal weight: 3.9990 chunk 149 optimal weight: 0.6980 chunk 130 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN ** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.126470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.102232 restraints weight = 26657.844| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.76 r_work: 0.2990 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19556 Z= 0.105 Angle : 0.494 6.800 26474 Z= 0.248 Chirality : 0.040 0.165 2891 Planarity : 0.003 0.037 3311 Dihedral : 5.281 56.844 2646 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.97 % Allowed : 13.82 % Favored : 84.21 % 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: -0.42 (0.18), residues: 2295 helix: 0.07 (0.16), residues: 1073 sheet: -2.02 (0.28), residues: 274 loop : 0.13 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 426 TYR 0.017 0.001 TYR E 322 PHE 0.015 0.001 PHE D 279 TRP 0.008 0.001 TRP F 242 HIS 0.004 0.001 HIS D 305 Details of bonding type rmsd covalent geometry : bond 0.00243 (19556) covalent geometry : angle 0.49375 (26474) hydrogen bonds : bond 0.02453 ( 741) hydrogen bonds : angle 4.15388 ( 2115) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 219 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: A 204 LEU cc_start: 0.9121 (mt) cc_final: 0.8796 (mt) REVERT: A 292 PHE cc_start: 0.6840 (OUTLIER) cc_final: 0.6547 (m-80) REVERT: A 395 GLU cc_start: 0.8465 (tt0) cc_final: 0.8251 (tt0) REVERT: B 198 TYR cc_start: 0.7276 (m-10) cc_final: 0.6937 (m-10) REVERT: B 249 GLN cc_start: 0.8903 (mm-40) cc_final: 0.8653 (mm110) REVERT: B 348 THR cc_start: 0.7536 (OUTLIER) cc_final: 0.7246 (m) REVERT: B 542 GLU cc_start: 0.8490 (pt0) cc_final: 0.8177 (pt0) REVERT: C 258 GLU cc_start: 0.8765 (pt0) cc_final: 0.8448 (pt0) REVERT: C 261 ARG cc_start: 0.7438 (mtt180) cc_final: 0.6899 (mmm160) REVERT: C 435 ARG cc_start: 0.8618 (mtm-85) cc_final: 0.8358 (mmm-85) REVERT: C 488 ARG cc_start: 0.8682 (mtt-85) cc_final: 0.8399 (mtp85) REVERT: C 532 ASP cc_start: 0.8817 (t0) cc_final: 0.8600 (t0) REVERT: C 549 ASN cc_start: 0.8647 (m-40) cc_final: 0.8338 (p0) REVERT: D 253 TYR cc_start: 0.9057 (t80) cc_final: 0.8834 (t80) REVERT: D 255 GLU cc_start: 0.8571 (mp0) cc_final: 0.8053 (mp0) REVERT: D 460 LEU cc_start: 0.8452 (tp) cc_final: 0.8116 (tt) REVERT: D 470 LYS cc_start: 0.8587 (mtpp) cc_final: 0.8280 (mttt) REVERT: E 323 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7208 (pm20) REVERT: E 466 GLU cc_start: 0.8145 (tp30) cc_final: 0.7885 (tp30) REVERT: F 243 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8392 (mm-30) REVERT: F 445 LYS cc_start: 0.8487 (ttmt) cc_final: 0.8243 (tttt) REVERT: F 511 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7992 (mp0) outliers start: 39 outliers final: 25 residues processed: 243 average time/residue: 0.1582 time to fit residues: 57.8381 Evaluate side-chains 219 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain E residue 323 GLU Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 420 ASP Chi-restraints excluded: chain F residue 550 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 0 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 171 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 185 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN D 515 HIS D 531 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.123139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.098236 restraints weight = 26643.461| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.82 r_work: 0.2930 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19556 Z= 0.172 Angle : 0.537 6.607 26474 Z= 0.270 Chirality : 0.042 0.166 2891 Planarity : 0.004 0.043 3311 Dihedral : 5.380 58.950 2646 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.13 % Allowed : 14.12 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.18), residues: 2295 helix: 0.12 (0.16), residues: 1080 sheet: -1.91 (0.28), residues: 298 loop : 0.22 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 426 TYR 0.018 0.001 TYR E 322 PHE 0.015 0.001 PHE D 279 TRP 0.013 0.001 TRP D 242 HIS 0.006 0.001 HIS D 305 Details of bonding type rmsd covalent geometry : bond 0.00412 (19556) covalent geometry : angle 0.53673 (26474) hydrogen bonds : bond 0.02725 ( 741) hydrogen bonds : angle 4.25598 ( 2115) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 191 time to evaluate : 0.707 Fit side-chains REVERT: A 292 PHE cc_start: 0.7205 (OUTLIER) cc_final: 0.6819 (m-80) REVERT: A 395 GLU cc_start: 0.8513 (tt0) cc_final: 0.8311 (tt0) REVERT: B 198 TYR cc_start: 0.7441 (m-10) cc_final: 0.7140 (m-10) REVERT: B 348 THR cc_start: 0.7562 (OUTLIER) cc_final: 0.7240 (m) REVERT: B 542 GLU cc_start: 0.8572 (pt0) cc_final: 0.8258 (pt0) REVERT: C 258 GLU cc_start: 0.8823 (pt0) cc_final: 0.8493 (pt0) REVERT: C 261 ARG cc_start: 0.7471 (mtt180) cc_final: 0.6851 (mmm160) REVERT: C 549 ASN cc_start: 0.8708 (m-40) cc_final: 0.8322 (p0) REVERT: C 566 TYR cc_start: 0.9410 (m-80) cc_final: 0.9147 (m-80) REVERT: D 255 GLU cc_start: 0.8648 (mp0) cc_final: 0.8073 (mp0) REVERT: E 294 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8738 (mp) REVERT: E 323 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7182 (pm20) REVERT: E 466 GLU cc_start: 0.8123 (tp30) cc_final: 0.7852 (tp30) REVERT: F 243 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8459 (mm-30) REVERT: F 292 PHE cc_start: 0.7537 (OUTLIER) cc_final: 0.7197 (m-10) REVERT: F 323 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7753 (mm-30) REVERT: F 511 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8001 (mp0) outliers start: 42 outliers final: 28 residues processed: 215 average time/residue: 0.1575 time to fit residues: 51.2240 Evaluate side-chains 214 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 181 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 547 HIS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain E residue 323 GLU Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 385 GLN Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 420 ASP Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain F residue 550 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 173 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 146 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 80 optimal weight: 0.3980 chunk 170 optimal weight: 0.6980 chunk 195 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN E 248 HIS ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.124087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.099283 restraints weight = 26777.763| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.81 r_work: 0.2955 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19556 Z= 0.140 Angle : 0.514 7.112 26474 Z= 0.258 Chirality : 0.041 0.166 2891 Planarity : 0.004 0.037 3311 Dihedral : 5.243 57.991 2646 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.97 % Allowed : 14.83 % Favored : 83.20 % 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 (0.18), residues: 2295 helix: 0.24 (0.16), residues: 1079 sheet: -1.87 (0.28), residues: 288 loop : 0.27 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 261 TYR 0.019 0.001 TYR E 322 PHE 0.015 0.001 PHE D 279 TRP 0.011 0.001 TRP D 242 HIS 0.006 0.001 HIS D 305 Details of bonding type rmsd covalent geometry : bond 0.00333 (19556) covalent geometry : angle 0.51421 (26474) hydrogen bonds : bond 0.02590 ( 741) hydrogen bonds : angle 4.18690 ( 2115) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 196 time to evaluate : 0.695 Fit side-chains REVERT: A 292 PHE cc_start: 0.7250 (OUTLIER) cc_final: 0.6878 (m-80) REVERT: A 395 GLU cc_start: 0.8508 (tt0) cc_final: 0.8210 (tt0) REVERT: B 198 TYR cc_start: 0.7407 (m-10) cc_final: 0.7105 (m-10) REVERT: B 348 THR cc_start: 0.7576 (OUTLIER) cc_final: 0.7276 (m) REVERT: B 542 GLU cc_start: 0.8537 (pt0) cc_final: 0.8213 (pt0) REVERT: C 258 GLU cc_start: 0.8820 (pt0) cc_final: 0.8470 (pt0) REVERT: C 261 ARG cc_start: 0.7432 (mtt180) cc_final: 0.6835 (mmm160) REVERT: C 488 ARG cc_start: 0.8728 (mtt-85) cc_final: 0.8458 (mtp85) REVERT: C 532 ASP cc_start: 0.8754 (t0) cc_final: 0.8538 (t0) REVERT: C 549 ASN cc_start: 0.8690 (m-40) cc_final: 0.8345 (p0) REVERT: C 566 TYR cc_start: 0.9377 (m-80) cc_final: 0.9094 (m-80) REVERT: D 255 GLU cc_start: 0.8640 (mp0) cc_final: 0.8058 (mp0) REVERT: D 460 LEU cc_start: 0.8446 (tp) cc_final: 0.8126 (tt) REVERT: E 210 GLN cc_start: 0.8673 (mp10) cc_final: 0.8384 (mp10) REVERT: E 294 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8694 (mp) REVERT: E 323 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7177 (pm20) REVERT: E 466 GLU cc_start: 0.8125 (tp30) cc_final: 0.7834 (tp30) REVERT: F 243 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8400 (mm-30) REVERT: F 445 LYS cc_start: 0.8712 (ttmt) cc_final: 0.8434 (tttt) REVERT: F 503 TYR cc_start: 0.8931 (m-80) cc_final: 0.8108 (m-80) REVERT: F 511 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7938 (mp0) outliers start: 39 outliers final: 30 residues processed: 218 average time/residue: 0.1622 time to fit residues: 53.2985 Evaluate side-chains 218 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 547 HIS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 563 GLU Chi-restraints excluded: chain C residue 572 GLU Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain E residue 323 GLU Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 385 GLN Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 420 ASP Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain F residue 550 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 170 optimal weight: 0.8980 chunk 216 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 90 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN D 305 HIS D 384 ASN ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.122071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.097223 restraints weight = 26914.922| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.80 r_work: 0.2921 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 19556 Z= 0.190 Angle : 0.554 7.992 26474 Z= 0.277 Chirality : 0.043 0.168 2891 Planarity : 0.004 0.037 3311 Dihedral : 5.414 59.188 2646 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.07 % Allowed : 15.18 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.18), residues: 2295 helix: 0.20 (0.16), residues: 1080 sheet: -1.86 (0.29), residues: 282 loop : 0.26 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 426 TYR 0.020 0.001 TYR E 322 PHE 0.015 0.001 PHE D 279 TRP 0.013 0.001 TRP D 242 HIS 0.007 0.001 HIS D 305 Details of bonding type rmsd covalent geometry : bond 0.00453 (19556) covalent geometry : angle 0.55364 (26474) hydrogen bonds : bond 0.02838 ( 741) hydrogen bonds : angle 4.31237 ( 2115) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 189 time to evaluate : 0.811 Fit side-chains REVERT: A 249 GLN cc_start: 0.7952 (mp10) cc_final: 0.7744 (mp10) REVERT: A 292 PHE cc_start: 0.7341 (OUTLIER) cc_final: 0.7040 (m-80) REVERT: A 520 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7759 (mt-10) REVERT: A 532 ASP cc_start: 0.8237 (t0) cc_final: 0.7888 (t0) REVERT: B 198 TYR cc_start: 0.7504 (m-10) cc_final: 0.7244 (m-10) REVERT: B 348 THR cc_start: 0.7572 (OUTLIER) cc_final: 0.7255 (m) REVERT: B 542 GLU cc_start: 0.8583 (pt0) cc_final: 0.8279 (pt0) REVERT: C 258 GLU cc_start: 0.8820 (pt0) cc_final: 0.8470 (pt0) REVERT: C 261 ARG cc_start: 0.7454 (mtt180) cc_final: 0.6854 (mmm160) REVERT: C 532 ASP cc_start: 0.8760 (t0) cc_final: 0.8463 (t0) REVERT: C 549 ASN cc_start: 0.8750 (m-40) cc_final: 0.8351 (p0) REVERT: D 255 GLU cc_start: 0.8633 (mp0) cc_final: 0.8009 (mp0) REVERT: D 470 LYS cc_start: 0.8630 (mtpp) cc_final: 0.8100 (mttt) REVERT: E 294 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8724 (mp) REVERT: E 323 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7203 (pm20) REVERT: E 466 GLU cc_start: 0.8130 (tp30) cc_final: 0.7852 (tp30) REVERT: F 243 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8427 (mm-30) REVERT: F 292 PHE cc_start: 0.7500 (OUTLIER) cc_final: 0.7139 (m-10) REVERT: F 323 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7742 (mm-30) REVERT: F 503 TYR cc_start: 0.8976 (m-80) cc_final: 0.8081 (m-80) REVERT: F 511 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7997 (mp0) outliers start: 41 outliers final: 28 residues processed: 215 average time/residue: 0.1604 time to fit residues: 52.0275 Evaluate side-chains 211 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 178 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 547 HIS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 305 HIS Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain E residue 323 GLU Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 385 GLN Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 420 ASP Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain F residue 550 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 159 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 78 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 161 optimal weight: 0.3980 chunk 50 optimal weight: 0.8980 chunk 156 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 120 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN D 305 HIS E 210 GLN ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.125023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.100854 restraints weight = 26649.306| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.73 r_work: 0.2972 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19556 Z= 0.117 Angle : 0.511 8.593 26474 Z= 0.255 Chirality : 0.041 0.164 2891 Planarity : 0.003 0.036 3311 Dihedral : 5.145 57.167 2646 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.97 % Allowed : 15.59 % Favored : 82.44 % 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: -0.06 (0.18), residues: 2295 helix: 0.35 (0.16), residues: 1079 sheet: -1.87 (0.29), residues: 277 loop : 0.35 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 306 TYR 0.020 0.001 TYR E 322 PHE 0.015 0.001 PHE D 279 TRP 0.014 0.001 TRP A 333 HIS 0.008 0.001 HIS D 305 Details of bonding type rmsd covalent geometry : bond 0.00275 (19556) covalent geometry : angle 0.51052 (26474) hydrogen bonds : bond 0.02493 ( 741) hydrogen bonds : angle 4.14219 ( 2115) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 201 time to evaluate : 0.796 Fit side-chains REVERT: A 292 PHE cc_start: 0.7339 (OUTLIER) cc_final: 0.7046 (m-80) REVERT: B 198 TYR cc_start: 0.7368 (m-10) cc_final: 0.7063 (m-10) REVERT: B 348 THR cc_start: 0.7535 (OUTLIER) cc_final: 0.7229 (m) REVERT: B 440 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7977 (mt-10) REVERT: B 542 GLU cc_start: 0.8510 (pt0) cc_final: 0.8195 (pt0) REVERT: C 258 GLU cc_start: 0.8784 (pt0) cc_final: 0.8475 (pt0) REVERT: C 488 ARG cc_start: 0.8682 (mtt-85) cc_final: 0.8409 (mtp85) REVERT: C 532 ASP cc_start: 0.8738 (t0) cc_final: 0.8466 (t0) REVERT: C 566 TYR cc_start: 0.9368 (m-80) cc_final: 0.9078 (m-80) REVERT: D 255 GLU cc_start: 0.8639 (mp0) cc_final: 0.8033 (mp0) REVERT: D 460 LEU cc_start: 0.8529 (tp) cc_final: 0.8244 (tt) REVERT: D 470 LYS cc_start: 0.8534 (mtpp) cc_final: 0.8194 (mttt) REVERT: E 210 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8374 (mp10) REVERT: E 294 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8818 (mp) REVERT: E 323 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7178 (pm20) REVERT: E 466 GLU cc_start: 0.8260 (tp30) cc_final: 0.7938 (tp30) REVERT: F 243 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8372 (mm-30) REVERT: F 292 PHE cc_start: 0.7329 (OUTLIER) cc_final: 0.7077 (m-10) REVERT: F 445 LYS cc_start: 0.8802 (ttmt) cc_final: 0.8588 (tttt) REVERT: F 457 ARG cc_start: 0.8250 (mtm180) cc_final: 0.7953 (mmm-85) REVERT: F 503 TYR cc_start: 0.8899 (m-80) cc_final: 0.8051 (m-80) REVERT: F 511 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7935 (mp0) outliers start: 39 outliers final: 30 residues processed: 224 average time/residue: 0.1572 time to fit residues: 53.6128 Evaluate side-chains 226 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 547 HIS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 563 GLU Chi-restraints excluded: chain C residue 572 GLU Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 305 HIS Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain E residue 323 GLU Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 385 GLN Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 420 ASP Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain F residue 550 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 218 optimal weight: 5.9990 chunk 210 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 162 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 199 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 228 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN E 210 GLN ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.124526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.100213 restraints weight = 26756.885| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.78 r_work: 0.2968 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19556 Z= 0.130 Angle : 0.522 8.445 26474 Z= 0.261 Chirality : 0.042 0.164 2891 Planarity : 0.003 0.035 3311 Dihedral : 5.133 57.487 2646 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.82 % Allowed : 15.94 % Favored : 82.24 % 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: -0.01 (0.18), residues: 2295 helix: 0.40 (0.16), residues: 1076 sheet: -1.84 (0.30), residues: 270 loop : 0.34 (0.21), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 261 TYR 0.024 0.001 TYR A 325 PHE 0.026 0.001 PHE A 477 TRP 0.022 0.001 TRP A 333 HIS 0.007 0.001 HIS C 515 Details of bonding type rmsd covalent geometry : bond 0.00310 (19556) covalent geometry : angle 0.52244 (26474) hydrogen bonds : bond 0.02536 ( 741) hydrogen bonds : angle 4.13680 ( 2115) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 192 time to evaluate : 0.751 Fit side-chains REVERT: A 292 PHE cc_start: 0.7327 (OUTLIER) cc_final: 0.7038 (m-80) REVERT: A 410 ASN cc_start: 0.9050 (t0) cc_final: 0.8838 (t0) REVERT: B 198 TYR cc_start: 0.7407 (m-10) cc_final: 0.7101 (m-10) REVERT: B 348 THR cc_start: 0.7543 (OUTLIER) cc_final: 0.7238 (m) REVERT: B 542 GLU cc_start: 0.8513 (pt0) cc_final: 0.8206 (pt0) REVERT: C 258 GLU cc_start: 0.8797 (pt0) cc_final: 0.8489 (pt0) REVERT: C 488 ARG cc_start: 0.8692 (mtt-85) cc_final: 0.8417 (mtp85) REVERT: C 532 ASP cc_start: 0.8747 (t0) cc_final: 0.8453 (t0) REVERT: C 566 TYR cc_start: 0.9374 (m-80) cc_final: 0.9081 (m-80) REVERT: D 255 GLU cc_start: 0.8711 (mp0) cc_final: 0.8114 (mp0) REVERT: D 460 LEU cc_start: 0.8528 (tp) cc_final: 0.8240 (tt) REVERT: D 470 LYS cc_start: 0.8546 (mtpp) cc_final: 0.8205 (mttt) REVERT: E 210 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8417 (mp10) REVERT: E 275 GLU cc_start: 0.8209 (pt0) cc_final: 0.7970 (pt0) REVERT: E 294 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8702 (mp) REVERT: E 323 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7179 (pm20) REVERT: E 466 GLU cc_start: 0.8256 (tp30) cc_final: 0.7926 (tp30) REVERT: F 243 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8374 (mm-30) REVERT: F 292 PHE cc_start: 0.7421 (OUTLIER) cc_final: 0.7185 (m-10) REVERT: F 445 LYS cc_start: 0.8803 (ttmt) cc_final: 0.8571 (tttt) REVERT: F 457 ARG cc_start: 0.8232 (mtm180) cc_final: 0.7921 (mmm-85) REVERT: F 503 TYR cc_start: 0.8908 (m-80) cc_final: 0.8045 (m-80) REVERT: F 511 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7942 (mp0) outliers start: 36 outliers final: 28 residues processed: 213 average time/residue: 0.1506 time to fit residues: 48.7888 Evaluate side-chains 219 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 185 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 547 HIS Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 572 GLU Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain E residue 323 GLU Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 385 GLN Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 420 ASP Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain F residue 550 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 31 optimal weight: 8.9990 chunk 211 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 147 optimal weight: 0.8980 chunk 141 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 50 optimal weight: 0.1980 chunk 157 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN D 305 HIS ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.125448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.101237 restraints weight = 26721.079| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.76 r_work: 0.2977 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19556 Z= 0.115 Angle : 0.511 8.459 26474 Z= 0.255 Chirality : 0.041 0.163 2891 Planarity : 0.003 0.035 3311 Dihedral : 5.033 56.432 2646 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.82 % Allowed : 16.04 % Favored : 82.14 % 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: 0.09 (0.18), residues: 2295 helix: 0.49 (0.16), residues: 1075 sheet: -1.82 (0.30), residues: 266 loop : 0.39 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 261 TYR 0.021 0.001 TYR A 325 PHE 0.017 0.001 PHE C 279 TRP 0.025 0.001 TRP A 333 HIS 0.005 0.001 HIS D 305 Details of bonding type rmsd covalent geometry : bond 0.00270 (19556) covalent geometry : angle 0.51089 (26474) hydrogen bonds : bond 0.02465 ( 741) hydrogen bonds : angle 4.08321 ( 2115) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4861.48 seconds wall clock time: 84 minutes 14.39 seconds (5054.39 seconds total)