Starting phenix.real_space_refine on Sat Oct 11 13:01:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wy4_37915/10_2025/8wy4_37915.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wy4_37915/10_2025/8wy4_37915.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wy4_37915/10_2025/8wy4_37915.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wy4_37915/10_2025/8wy4_37915.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wy4_37915/10_2025/8wy4_37915.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wy4_37915/10_2025/8wy4_37915.map" } resolution = 2.81 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= 0.001 sd= 0.031 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 48 5.16 5 C 9504 2.51 5 N 2448 2.21 5 O 2852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14864 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3685 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 8, 'TRANS': 442} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, D, C Time building chain proxies: 3.15, per 1000 atoms: 0.21 Number of scatterers: 14864 At special positions: 0 Unit cell: (115.08, 190.68, 68.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 12 15.00 O 2852 8.00 N 2448 7.00 C 9504 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 730.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3416 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 16 sheets defined 42.8% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 31 through 47 removed outlier: 3.960A pdb=" N LEU A 39 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 83 through 91 removed outlier: 3.860A pdb=" N LYS A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 308 Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.612A pdb=" N LEU A 324 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR A 326 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 370 removed outlier: 3.784A pdb=" N SER A 368 " --> pdb=" O LYS A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 395 removed outlier: 3.558A pdb=" N LYS A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 413 through 423 removed outlier: 3.630A pdb=" N THR A 419 " --> pdb=" O HIS A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 457 removed outlier: 4.019A pdb=" N CYS A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 493 Processing helix chain 'A' and resid 493 through 503 removed outlier: 3.671A pdb=" N GLU A 503 " --> pdb=" O GLU A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 528 removed outlier: 3.592A pdb=" N SER A 518 " --> pdb=" O ASN A 514 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA A 519 " --> pdb=" O ASP A 515 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N GLU A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N SER A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE A 528 " --> pdb=" O MET A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 540 removed outlier: 3.662A pdb=" N TYR A 536 " --> pdb=" O ASP A 532 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER A 540 " --> pdb=" O TYR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 551 removed outlier: 3.632A pdb=" N ASN A 544 " --> pdb=" O SER A 540 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN A 551 " --> pdb=" O GLU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 562 removed outlier: 3.564A pdb=" N CYS A 557 " --> pdb=" O SER A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 574 Processing helix chain 'B' and resid 31 through 47 removed outlier: 3.960A pdb=" N LEU B 39 " --> pdb=" O LYS B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 52 Processing helix chain 'B' and resid 83 through 91 removed outlier: 3.861A pdb=" N LYS B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 308 Processing helix chain 'B' and resid 321 through 326 removed outlier: 3.612A pdb=" N LEU B 324 " --> pdb=" O SER B 321 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR B 326 " --> pdb=" O GLU B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 370 removed outlier: 3.784A pdb=" N SER B 368 " --> pdb=" O LYS B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 395 removed outlier: 3.558A pdb=" N LYS B 384 " --> pdb=" O GLY B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 402 Processing helix chain 'B' and resid 413 through 423 removed outlier: 3.630A pdb=" N THR B 419 " --> pdb=" O HIS B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 457 removed outlier: 4.019A pdb=" N CYS B 453 " --> pdb=" O GLY B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 493 Processing helix chain 'B' and resid 493 through 503 removed outlier: 3.671A pdb=" N GLU B 503 " --> pdb=" O GLU B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 528 removed outlier: 3.592A pdb=" N SER B 518 " --> pdb=" O ASN B 514 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA B 519 " --> pdb=" O ASP B 515 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N GLU B 522 " --> pdb=" O SER B 518 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N SER B 523 " --> pdb=" O ALA B 519 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE B 528 " --> pdb=" O MET B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 540 removed outlier: 3.662A pdb=" N TYR B 536 " --> pdb=" O ASP B 532 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER B 540 " --> pdb=" O TYR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 551 removed outlier: 3.632A pdb=" N ASN B 544 " --> pdb=" O SER B 540 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN B 551 " --> pdb=" O GLU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 562 removed outlier: 3.564A pdb=" N CYS B 557 " --> pdb=" O SER B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 574 Processing helix chain 'D' and resid 31 through 47 removed outlier: 3.960A pdb=" N LEU D 39 " --> pdb=" O LYS D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 52 Processing helix chain 'D' and resid 83 through 91 removed outlier: 3.859A pdb=" N LYS D 87 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 308 Processing helix chain 'D' and resid 321 through 326 removed outlier: 3.612A pdb=" N LEU D 324 " --> pdb=" O SER D 321 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR D 326 " --> pdb=" O GLU D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 370 removed outlier: 3.784A pdb=" N SER D 368 " --> pdb=" O LYS D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 395 removed outlier: 3.558A pdb=" N LYS D 384 " --> pdb=" O GLY D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 402 Processing helix chain 'D' and resid 413 through 423 removed outlier: 3.629A pdb=" N THR D 419 " --> pdb=" O HIS D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 457 removed outlier: 4.020A pdb=" N CYS D 453 " --> pdb=" O GLY D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 493 Processing helix chain 'D' and resid 493 through 503 removed outlier: 3.671A pdb=" N GLU D 503 " --> pdb=" O GLU D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 528 removed outlier: 3.592A pdb=" N SER D 518 " --> pdb=" O ASN D 514 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA D 519 " --> pdb=" O ASP D 515 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N GLU D 522 " --> pdb=" O SER D 518 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N SER D 523 " --> pdb=" O ALA D 519 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE D 528 " --> pdb=" O MET D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 540 removed outlier: 3.662A pdb=" N TYR D 536 " --> pdb=" O ASP D 532 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER D 540 " --> pdb=" O TYR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 551 removed outlier: 3.632A pdb=" N ASN D 544 " --> pdb=" O SER D 540 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN D 551 " --> pdb=" O GLU D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 562 removed outlier: 3.564A pdb=" N CYS D 557 " --> pdb=" O SER D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 574 Processing helix chain 'C' and resid 31 through 47 removed outlier: 3.959A pdb=" N LEU C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 52 Processing helix chain 'C' and resid 83 through 91 removed outlier: 3.860A pdb=" N LYS C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 308 Processing helix chain 'C' and resid 321 through 326 removed outlier: 3.612A pdb=" N LEU C 324 " --> pdb=" O SER C 321 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR C 326 " --> pdb=" O GLU C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 370 removed outlier: 3.784A pdb=" N SER C 368 " --> pdb=" O LYS C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 395 removed outlier: 3.558A pdb=" N LYS C 384 " --> pdb=" O GLY C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 402 Processing helix chain 'C' and resid 413 through 423 removed outlier: 3.630A pdb=" N THR C 419 " --> pdb=" O HIS C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 457 removed outlier: 4.019A pdb=" N CYS C 453 " --> pdb=" O GLY C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 493 Processing helix chain 'C' and resid 493 through 503 removed outlier: 3.671A pdb=" N GLU C 503 " --> pdb=" O GLU C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 528 removed outlier: 3.592A pdb=" N SER C 518 " --> pdb=" O ASN C 514 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA C 519 " --> pdb=" O ASP C 515 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N GLU C 522 " --> pdb=" O SER C 518 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N SER C 523 " --> pdb=" O ALA C 519 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE C 528 " --> pdb=" O MET C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 540 removed outlier: 3.662A pdb=" N TYR C 536 " --> pdb=" O ASP C 532 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER C 540 " --> pdb=" O TYR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 551 removed outlier: 3.633A pdb=" N ASN C 544 " --> pdb=" O SER C 540 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN C 551 " --> pdb=" O GLU C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 562 removed outlier: 3.565A pdb=" N CYS C 557 " --> pdb=" O SER C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 574 Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 20 removed outlier: 3.533A pdb=" N ILE A 8 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN A 5 " --> pdb=" O THR A 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY A 127 " --> pdb=" O TYR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 154 removed outlier: 6.726A pdb=" N VAL A 283 " --> pdb=" O TYR A 314 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N PHE A 316 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TYR A 285 " --> pdb=" O PHE A 316 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N SER A 318 " --> pdb=" O TYR A 285 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE A 287 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL A 26 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL A 336 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE A 28 " --> pdb=" O VAL A 336 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 403 through 407 removed outlier: 6.723A pdb=" N ARG A 374 " --> pdb=" O PHE A 404 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU A 406 " --> pdb=" O ARG A 374 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU A 376 " --> pdb=" O LEU A 406 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 435 through 437 Processing sheet with id=AA5, first strand: chain 'B' and resid 17 through 20 removed outlier: 3.533A pdb=" N ILE B 8 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN B 5 " --> pdb=" O THR B 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY B 127 " --> pdb=" O TYR B 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 154 removed outlier: 6.727A pdb=" N VAL B 283 " --> pdb=" O TYR B 314 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N PHE B 316 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TYR B 285 " --> pdb=" O PHE B 316 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N SER B 318 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE B 287 " --> pdb=" O SER B 318 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL B 26 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL B 336 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N PHE B 28 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 403 through 407 removed outlier: 6.724A pdb=" N ARG B 374 " --> pdb=" O PHE B 404 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU B 406 " --> pdb=" O ARG B 374 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU B 376 " --> pdb=" O LEU B 406 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 435 through 437 Processing sheet with id=AA9, first strand: chain 'D' and resid 17 through 20 removed outlier: 3.532A pdb=" N ILE D 8 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN D 5 " --> pdb=" O THR D 74 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY D 127 " --> pdb=" O TYR D 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 149 through 154 removed outlier: 6.726A pdb=" N VAL D 283 " --> pdb=" O TYR D 314 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N PHE D 316 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TYR D 285 " --> pdb=" O PHE D 316 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N SER D 318 " --> pdb=" O TYR D 285 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE D 287 " --> pdb=" O SER D 318 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL D 26 " --> pdb=" O ILE D 334 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL D 336 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N PHE D 28 " --> pdb=" O VAL D 336 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 403 through 407 removed outlier: 6.723A pdb=" N ARG D 374 " --> pdb=" O PHE D 404 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU D 406 " --> pdb=" O ARG D 374 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU D 376 " --> pdb=" O LEU D 406 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 435 through 437 Processing sheet with id=AB4, first strand: chain 'C' and resid 17 through 20 removed outlier: 3.534A pdb=" N ILE C 8 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN C 5 " --> pdb=" O THR C 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY C 127 " --> pdb=" O TYR C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 149 through 154 removed outlier: 4.299A pdb=" N TYR C 314 " --> pdb=" O VAL C 283 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL C 26 " --> pdb=" O ILE C 334 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL C 336 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE C 28 " --> pdb=" O VAL C 336 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 403 through 407 removed outlier: 6.723A pdb=" N ARG C 374 " --> pdb=" O PHE C 404 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU C 406 " --> pdb=" O ARG C 374 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU C 376 " --> pdb=" O LEU C 406 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 435 through 437 600 hydrogen bonds defined for protein. 1716 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: 3.06 Time building geometry restraints manager: 1.87 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: 4400 1.34 - 1.46: 2405 1.46 - 1.57: 8223 1.57 - 1.69: 20 1.69 - 1.81: 76 Bond restraints: 15124 Sorted by residual: bond pdb=" N GLU B 503 " pdb=" CA GLU B 503 " ideal model delta sigma weight residual 1.457 1.486 -0.029 6.40e-03 2.44e+04 2.06e+01 bond pdb=" N GLU A 503 " pdb=" CA GLU A 503 " ideal model delta sigma weight residual 1.457 1.486 -0.029 6.40e-03 2.44e+04 2.06e+01 bond pdb=" N GLU C 503 " pdb=" CA GLU C 503 " ideal model delta sigma weight residual 1.457 1.486 -0.029 6.40e-03 2.44e+04 2.06e+01 bond pdb=" N GLU D 503 " pdb=" CA GLU D 503 " ideal model delta sigma weight residual 1.457 1.485 -0.028 6.40e-03 2.44e+04 1.94e+01 bond pdb=" N VAL A 497 " pdb=" CA VAL A 497 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.19e-02 7.06e+03 8.75e+00 ... (remaining 15119 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 19535 2.41 - 4.82: 665 4.82 - 7.23: 124 7.23 - 9.64: 12 9.64 - 12.06: 8 Bond angle restraints: 20344 Sorted by residual: angle pdb=" C LYS A 116 " pdb=" N GLU A 117 " pdb=" CA GLU A 117 " ideal model delta sigma weight residual 121.54 130.91 -9.37 1.91e+00 2.74e-01 2.40e+01 angle pdb=" C LYS D 116 " pdb=" N GLU D 117 " pdb=" CA GLU D 117 " ideal model delta sigma weight residual 121.54 130.87 -9.33 1.91e+00 2.74e-01 2.39e+01 angle pdb=" C LYS B 116 " pdb=" N GLU B 117 " pdb=" CA GLU B 117 " ideal model delta sigma weight residual 121.54 130.87 -9.33 1.91e+00 2.74e-01 2.39e+01 angle pdb=" C LYS C 116 " pdb=" N GLU C 117 " pdb=" CA GLU C 117 " ideal model delta sigma weight residual 121.54 130.85 -9.31 1.91e+00 2.74e-01 2.38e+01 angle pdb=" N ASP B 22 " pdb=" CA ASP B 22 " pdb=" C ASP B 22 " ideal model delta sigma weight residual 108.45 102.61 5.84 1.26e+00 6.30e-01 2.15e+01 ... (remaining 20339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 8132 17.18 - 34.36: 900 34.36 - 51.55: 200 51.55 - 68.73: 36 68.73 - 85.91: 20 Dihedral angle restraints: 9288 sinusoidal: 3992 harmonic: 5296 Sorted by residual: dihedral pdb=" CA ASP B 76 " pdb=" C ASP B 76 " pdb=" N LEU B 77 " pdb=" CA LEU B 77 " ideal model delta harmonic sigma weight residual -180.00 -153.37 -26.63 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA ASP C 76 " pdb=" C ASP C 76 " pdb=" N LEU C 77 " pdb=" CA LEU C 77 " ideal model delta harmonic sigma weight residual 180.00 -153.39 -26.61 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA ASP D 76 " pdb=" C ASP D 76 " pdb=" N LEU D 77 " pdb=" CA LEU D 77 " ideal model delta harmonic sigma weight residual -180.00 -153.41 -26.59 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 9285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1641 0.057 - 0.114: 416 0.114 - 0.171: 168 0.171 - 0.228: 23 0.228 - 0.285: 8 Chirality restraints: 2256 Sorted by residual: chirality pdb=" CB ILE C 6 " pdb=" CA ILE C 6 " pdb=" CG1 ILE C 6 " pdb=" CG2 ILE C 6 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB ILE D 6 " pdb=" CA ILE D 6 " pdb=" CG1 ILE D 6 " pdb=" CG2 ILE D 6 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CB ILE B 6 " pdb=" CA ILE B 6 " pdb=" CG1 ILE B 6 " pdb=" CG2 ILE B 6 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 2253 not shown) Planarity restraints: 2564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 9 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.47e+00 pdb=" C LYS B 9 " 0.037 2.00e-02 2.50e+03 pdb=" O LYS B 9 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN B 10 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 9 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.30e+00 pdb=" C LYS C 9 " -0.036 2.00e-02 2.50e+03 pdb=" O LYS C 9 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN C 10 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 9 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.28e+00 pdb=" C LYS A 9 " -0.036 2.00e-02 2.50e+03 pdb=" O LYS A 9 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN A 10 " 0.012 2.00e-02 2.50e+03 ... (remaining 2561 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 4842 2.87 - 3.38: 12020 3.38 - 3.89: 24467 3.89 - 4.39: 27338 4.39 - 4.90: 47837 Nonbonded interactions: 116504 Sorted by model distance: nonbonded pdb=" OG SER D 4 " pdb=" OD2 ASP D 76 " model vdw 2.368 3.040 nonbonded pdb=" OG SER B 4 " pdb=" OD2 ASP B 76 " model vdw 2.369 3.040 nonbonded pdb=" OG SER C 4 " pdb=" OD2 ASP C 76 " model vdw 2.369 3.040 nonbonded pdb=" OG SER A 4 " pdb=" OD2 ASP A 76 " model vdw 2.370 3.040 nonbonded pdb=" OG1 THR A 339 " pdb=" O LYS A 341 " model vdw 2.378 3.040 ... (remaining 116499 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'C' } 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: 5.420 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 15.510 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 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 : 0.006 0.056 15128 Z= 0.323 Angle : 1.057 12.055 20344 Z= 0.595 Chirality : 0.061 0.285 2256 Planarity : 0.006 0.045 2564 Dihedral : 15.320 85.911 5872 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.49 (0.16), residues: 1788 helix: -3.71 (0.09), residues: 732 sheet: 0.05 (0.27), residues: 392 loop : -1.83 (0.20), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 332 TYR 0.022 0.002 TYR A 326 PHE 0.031 0.002 PHE A 315 TRP 0.019 0.006 TRP D 126 HIS 0.006 0.002 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00604 (15124) covalent geometry : angle 1.05686 (20344) hydrogen bonds : bond 0.20188 ( 600) hydrogen bonds : angle 8.34691 ( 1716) Misc. bond : bond 0.02436 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.617 Fit side-chains REVERT: A 141 ASN cc_start: 0.6872 (m-40) cc_final: 0.6356 (m-40) REVERT: A 422 ASP cc_start: 0.7603 (m-30) cc_final: 0.7394 (t0) REVERT: A 474 LYS cc_start: 0.7773 (mttt) cc_final: 0.7516 (mttt) REVERT: B 141 ASN cc_start: 0.6822 (m-40) cc_final: 0.6322 (m-40) REVERT: B 422 ASP cc_start: 0.7606 (m-30) cc_final: 0.7400 (t0) REVERT: D 141 ASN cc_start: 0.6873 (m-40) cc_final: 0.6357 (m-40) REVERT: D 422 ASP cc_start: 0.7605 (m-30) cc_final: 0.7395 (t0) REVERT: D 474 LYS cc_start: 0.7753 (mttt) cc_final: 0.7523 (mttt) REVERT: C 141 ASN cc_start: 0.6874 (m-40) cc_final: 0.6357 (m-40) REVERT: C 422 ASP cc_start: 0.7604 (m-30) cc_final: 0.7387 (t0) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.6648 time to fit residues: 195.6764 Evaluate side-chains 167 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.0070 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.230596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.200618 restraints weight = 17035.693| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 1.75 r_work: 0.4113 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.4005 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15128 Z= 0.134 Angle : 0.602 8.532 20344 Z= 0.324 Chirality : 0.046 0.168 2256 Planarity : 0.003 0.025 2564 Dihedral : 8.623 50.368 2076 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.99 % Allowed : 8.03 % Favored : 89.98 % 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 aren not related in a simple way. whole: -1.50 (0.18), residues: 1788 helix: -1.16 (0.16), residues: 700 sheet: 0.11 (0.27), residues: 404 loop : -1.30 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 332 TYR 0.015 0.001 TYR C 314 PHE 0.010 0.001 PHE A 316 TRP 0.003 0.001 TRP B 126 HIS 0.005 0.001 HIS D 415 Details of bonding type rmsd covalent geometry : bond 0.00285 (15124) covalent geometry : angle 0.60236 (20344) hydrogen bonds : bond 0.04867 ( 600) hydrogen bonds : angle 5.55508 ( 1716) Misc. bond : bond 0.00156 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 183 time to evaluate : 0.618 Fit side-chains REVERT: A 1 MET cc_start: 0.7251 (OUTLIER) cc_final: 0.6400 (tmt) REVERT: A 141 ASN cc_start: 0.6915 (m-40) cc_final: 0.6300 (m-40) REVERT: A 285 TYR cc_start: 0.7742 (m-80) cc_final: 0.7489 (m-80) REVERT: A 422 ASP cc_start: 0.7843 (m-30) cc_final: 0.7538 (t0) REVERT: A 474 LYS cc_start: 0.7634 (mttt) cc_final: 0.7241 (mtmt) REVERT: B 141 ASN cc_start: 0.6902 (m-40) cc_final: 0.6465 (m-40) REVERT: B 285 TYR cc_start: 0.7743 (m-80) cc_final: 0.7492 (m-80) REVERT: B 422 ASP cc_start: 0.7853 (m-30) cc_final: 0.7543 (t0) REVERT: D 1 MET cc_start: 0.7230 (OUTLIER) cc_final: 0.6252 (tmt) REVERT: D 141 ASN cc_start: 0.6909 (m-40) cc_final: 0.6320 (m-40) REVERT: D 285 TYR cc_start: 0.7745 (m-80) cc_final: 0.7491 (m-80) REVERT: D 422 ASP cc_start: 0.7818 (m-30) cc_final: 0.7516 (t0) REVERT: D 474 LYS cc_start: 0.7625 (mttt) cc_final: 0.7225 (mtmt) REVERT: C 1 MET cc_start: 0.7203 (OUTLIER) cc_final: 0.6330 (tmt) REVERT: C 141 ASN cc_start: 0.6908 (m-40) cc_final: 0.6305 (m-40) REVERT: C 285 TYR cc_start: 0.7694 (m-80) cc_final: 0.7473 (m-80) REVERT: C 422 ASP cc_start: 0.7857 (m-30) cc_final: 0.7540 (t0) outliers start: 33 outliers final: 9 residues processed: 198 average time/residue: 0.6447 time to fit residues: 139.6725 Evaluate side-chains 175 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 163 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain C residue 549 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 168 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 146 optimal weight: 0.0020 chunk 118 optimal weight: 1.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS A 551 ASN B 415 HIS B 551 ASN D 415 HIS D 551 ASN C 415 HIS C 551 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.223859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.192341 restraints weight = 17254.022| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 1.74 r_work: 0.4015 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3907 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15128 Z= 0.213 Angle : 0.712 9.738 20344 Z= 0.374 Chirality : 0.048 0.163 2256 Planarity : 0.005 0.068 2564 Dihedral : 8.087 54.043 2076 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.26 % Allowed : 10.57 % Favored : 86.17 % 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 aren not related in a simple way. whole: -0.86 (0.19), residues: 1788 helix: 0.00 (0.19), residues: 688 sheet: -0.05 (0.26), residues: 396 loop : -1.35 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 332 TYR 0.025 0.002 TYR C 314 PHE 0.016 0.002 PHE B 371 TRP 0.003 0.001 TRP B 126 HIS 0.006 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00489 (15124) covalent geometry : angle 0.71229 (20344) hydrogen bonds : bond 0.05764 ( 600) hydrogen bonds : angle 5.42628 ( 1716) Misc. bond : bond 0.00205 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 189 time to evaluate : 0.602 Fit side-chains REVERT: A 141 ASN cc_start: 0.7180 (m-40) cc_final: 0.6955 (m-40) REVERT: A 373 GLU cc_start: 0.6631 (mm-30) cc_final: 0.6090 (pt0) REVERT: A 414 ASN cc_start: 0.7159 (p0) cc_final: 0.6944 (t160) REVERT: A 474 LYS cc_start: 0.7503 (mttt) cc_final: 0.7061 (mttt) REVERT: B 59 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7265 (p0) REVERT: B 139 ARG cc_start: 0.6749 (mmm160) cc_final: 0.6276 (mmm160) REVERT: B 141 ASN cc_start: 0.7184 (m-40) cc_final: 0.6946 (m-40) REVERT: B 414 ASN cc_start: 0.7177 (p0) cc_final: 0.6959 (t160) REVERT: D 59 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7381 (p0) REVERT: D 141 ASN cc_start: 0.7163 (m-40) cc_final: 0.6958 (m-40) REVERT: D 414 ASN cc_start: 0.7175 (p0) cc_final: 0.6956 (t160) REVERT: D 422 ASP cc_start: 0.7919 (m-30) cc_final: 0.7625 (t0) REVERT: D 474 LYS cc_start: 0.7487 (mttt) cc_final: 0.7044 (mttt) REVERT: C 59 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7367 (p0) REVERT: C 141 ASN cc_start: 0.7168 (m-40) cc_final: 0.6941 (m-40) REVERT: C 414 ASN cc_start: 0.7152 (p0) cc_final: 0.6932 (t160) outliers start: 54 outliers final: 20 residues processed: 223 average time/residue: 0.6825 time to fit residues: 165.6699 Evaluate side-chains 191 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 549 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 56 optimal weight: 0.2980 chunk 118 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 13 optimal weight: 0.0570 chunk 94 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 chunk 46 optimal weight: 0.0980 chunk 3 optimal weight: 0.8980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.226092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.195799 restraints weight = 17314.199| |-----------------------------------------------------------------------------| r_work (start): 0.4172 rms_B_bonded: 1.70 r_work: 0.4069 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3960 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15128 Z= 0.112 Angle : 0.557 9.887 20344 Z= 0.293 Chirality : 0.045 0.156 2256 Planarity : 0.003 0.033 2564 Dihedral : 7.414 53.225 2076 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.08 % Allowed : 14.43 % Favored : 82.49 % 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 aren not related in a simple way. whole: -0.24 (0.20), residues: 1788 helix: 0.77 (0.20), residues: 700 sheet: -0.00 (0.27), residues: 396 loop : -1.15 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 332 TYR 0.011 0.001 TYR C 314 PHE 0.011 0.001 PHE C 315 TRP 0.001 0.000 TRP B 126 HIS 0.002 0.000 HIS D 415 Details of bonding type rmsd covalent geometry : bond 0.00235 (15124) covalent geometry : angle 0.55662 (20344) hydrogen bonds : bond 0.04051 ( 600) hydrogen bonds : angle 4.91322 ( 1716) Misc. bond : bond 0.00132 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 173 time to evaluate : 0.642 Fit side-chains REVERT: A 373 GLU cc_start: 0.6710 (mm-30) cc_final: 0.6100 (pt0) REVERT: A 392 ASP cc_start: 0.7677 (p0) cc_final: 0.7397 (p0) REVERT: A 474 LYS cc_start: 0.7366 (mttt) cc_final: 0.6983 (mttt) REVERT: A 549 VAL cc_start: 0.8264 (OUTLIER) cc_final: 0.7981 (m) REVERT: B 373 GLU cc_start: 0.6626 (mm-30) cc_final: 0.6104 (pt0) REVERT: B 392 ASP cc_start: 0.7615 (p0) cc_final: 0.7332 (p0) REVERT: B 549 VAL cc_start: 0.8248 (OUTLIER) cc_final: 0.7981 (m) REVERT: D 373 GLU cc_start: 0.6618 (mm-30) cc_final: 0.6066 (pt0) REVERT: D 392 ASP cc_start: 0.7634 (p0) cc_final: 0.7353 (p0) REVERT: D 474 LYS cc_start: 0.7387 (mttt) cc_final: 0.6888 (mttt) REVERT: D 549 VAL cc_start: 0.8287 (OUTLIER) cc_final: 0.8012 (m) REVERT: C 285 TYR cc_start: 0.7811 (m-80) cc_final: 0.7437 (m-80) REVERT: C 373 GLU cc_start: 0.6646 (mm-30) cc_final: 0.6097 (pt0) REVERT: C 392 ASP cc_start: 0.7644 (p0) cc_final: 0.7372 (p0) REVERT: C 549 VAL cc_start: 0.8243 (OUTLIER) cc_final: 0.7965 (m) outliers start: 51 outliers final: 16 residues processed: 202 average time/residue: 0.6582 time to fit residues: 144.7375 Evaluate side-chains 186 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 523 SER Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain C residue 523 SER Chi-restraints excluded: chain C residue 549 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 152 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 117 optimal weight: 0.4980 chunk 94 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 6 optimal weight: 0.1980 chunk 31 optimal weight: 7.9990 chunk 153 optimal weight: 0.2980 chunk 132 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.226107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.195804 restraints weight = 17221.330| |-----------------------------------------------------------------------------| r_work (start): 0.4168 rms_B_bonded: 1.68 r_work: 0.4066 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3959 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15128 Z= 0.116 Angle : 0.553 10.165 20344 Z= 0.289 Chirality : 0.044 0.149 2256 Planarity : 0.003 0.037 2564 Dihedral : 7.261 55.302 2076 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.62 % Allowed : 15.28 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.20), residues: 1788 helix: 1.19 (0.20), residues: 696 sheet: -0.03 (0.27), residues: 404 loop : -1.01 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 332 TYR 0.014 0.001 TYR C 314 PHE 0.011 0.001 PHE C 315 TRP 0.002 0.001 TRP C 126 HIS 0.003 0.001 HIS C 415 Details of bonding type rmsd covalent geometry : bond 0.00249 (15124) covalent geometry : angle 0.55290 (20344) hydrogen bonds : bond 0.04051 ( 600) hydrogen bonds : angle 4.78001 ( 1716) Misc. bond : bond 0.00127 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 178 time to evaluate : 0.667 Fit side-chains REVERT: A 285 TYR cc_start: 0.7893 (m-80) cc_final: 0.7456 (m-80) REVERT: A 373 GLU cc_start: 0.6725 (mm-30) cc_final: 0.6184 (pt0) REVERT: A 392 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7241 (p0) REVERT: A 474 LYS cc_start: 0.7278 (mttt) cc_final: 0.6937 (mttt) REVERT: B 285 TYR cc_start: 0.7875 (m-80) cc_final: 0.7443 (m-80) REVERT: B 373 GLU cc_start: 0.6638 (mm-30) cc_final: 0.6110 (pt0) REVERT: B 392 ASP cc_start: 0.7556 (OUTLIER) cc_final: 0.7232 (p0) REVERT: D 285 TYR cc_start: 0.7876 (m-80) cc_final: 0.7437 (m-80) REVERT: D 373 GLU cc_start: 0.6596 (mm-30) cc_final: 0.6068 (pt0) REVERT: D 392 ASP cc_start: 0.7561 (OUTLIER) cc_final: 0.7234 (p0) REVERT: D 474 LYS cc_start: 0.7291 (mttt) cc_final: 0.6961 (mttt) REVERT: C 285 TYR cc_start: 0.7853 (m-80) cc_final: 0.7475 (m-80) REVERT: C 373 GLU cc_start: 0.6662 (mm-30) cc_final: 0.6172 (pt0) REVERT: C 392 ASP cc_start: 0.7580 (OUTLIER) cc_final: 0.7249 (p0) REVERT: C 549 VAL cc_start: 0.8262 (OUTLIER) cc_final: 0.8039 (m) outliers start: 60 outliers final: 20 residues processed: 221 average time/residue: 0.6539 time to fit residues: 158.0808 Evaluate side-chains 187 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain D residue 523 SER Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain C residue 523 SER Chi-restraints excluded: chain C residue 549 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 121 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 84 optimal weight: 7.9990 chunk 162 optimal weight: 0.0770 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.224274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.193808 restraints weight = 17175.703| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 1.67 r_work: 0.4046 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3938 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15128 Z= 0.148 Angle : 0.596 9.999 20344 Z= 0.311 Chirality : 0.045 0.152 2256 Planarity : 0.003 0.052 2564 Dihedral : 7.310 56.587 2076 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.90 % Allowed : 16.49 % Favored : 80.62 % 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 aren not related in a simple way. whole: 0.15 (0.20), residues: 1788 helix: 1.30 (0.20), residues: 684 sheet: 0.04 (0.27), residues: 396 loop : -1.02 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 481 TYR 0.016 0.001 TYR C 314 PHE 0.012 0.001 PHE A 315 TRP 0.003 0.001 TRP B 126 HIS 0.003 0.001 HIS B 415 Details of bonding type rmsd covalent geometry : bond 0.00336 (15124) covalent geometry : angle 0.59593 (20344) hydrogen bonds : bond 0.04423 ( 600) hydrogen bonds : angle 4.84516 ( 1716) Misc. bond : bond 0.00136 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 177 time to evaluate : 0.691 Fit side-chains REVERT: A 285 TYR cc_start: 0.7945 (m-80) cc_final: 0.7475 (m-80) REVERT: A 373 GLU cc_start: 0.6729 (mm-30) cc_final: 0.6190 (pt0) REVERT: A 392 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7280 (p0) REVERT: A 474 LYS cc_start: 0.7169 (mttt) cc_final: 0.6768 (mttt) REVERT: B 285 TYR cc_start: 0.7934 (m-80) cc_final: 0.7469 (m-80) REVERT: B 373 GLU cc_start: 0.6682 (mm-30) cc_final: 0.6191 (pt0) REVERT: B 392 ASP cc_start: 0.7578 (OUTLIER) cc_final: 0.7268 (p0) REVERT: D 285 TYR cc_start: 0.7925 (m-80) cc_final: 0.7452 (m-80) REVERT: D 373 GLU cc_start: 0.6644 (mm-30) cc_final: 0.6143 (pt0) REVERT: D 392 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7273 (p0) REVERT: D 474 LYS cc_start: 0.7197 (mttt) cc_final: 0.6808 (mttt) REVERT: C 285 TYR cc_start: 0.7852 (m-80) cc_final: 0.7445 (m-80) REVERT: C 334 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8128 (mt) REVERT: C 373 GLU cc_start: 0.6683 (mm-30) cc_final: 0.6185 (pt0) REVERT: C 392 ASP cc_start: 0.7586 (OUTLIER) cc_final: 0.7274 (p0) outliers start: 48 outliers final: 21 residues processed: 213 average time/residue: 0.6288 time to fit residues: 146.9927 Evaluate side-chains 197 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 523 SER Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 523 SER Chi-restraints excluded: chain C residue 549 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 100 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 166 optimal weight: 10.0000 chunk 168 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN A 414 ASN A 455 ASN B 414 ASN B 455 ASN D 414 ASN D 455 ASN C 414 ASN C 455 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.221745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.191032 restraints weight = 17118.962| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 1.66 r_work: 0.4019 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3912 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15128 Z= 0.194 Angle : 0.661 10.438 20344 Z= 0.343 Chirality : 0.047 0.160 2256 Planarity : 0.004 0.070 2564 Dihedral : 7.499 58.395 2076 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.62 % Allowed : 16.67 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.20), residues: 1788 helix: 1.28 (0.20), residues: 680 sheet: -0.13 (0.26), residues: 396 loop : -1.04 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 332 TYR 0.020 0.002 TYR C 314 PHE 0.015 0.002 PHE C 315 TRP 0.005 0.001 TRP B 126 HIS 0.003 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00453 (15124) covalent geometry : angle 0.66056 (20344) hydrogen bonds : bond 0.05050 ( 600) hydrogen bonds : angle 5.02598 ( 1716) Misc. bond : bond 0.00142 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 173 time to evaluate : 0.656 Fit side-chains REVERT: A 285 TYR cc_start: 0.7980 (m-80) cc_final: 0.7494 (m-80) REVERT: A 373 GLU cc_start: 0.6707 (mm-30) cc_final: 0.6194 (pt0) REVERT: A 392 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.7347 (p0) REVERT: A 474 LYS cc_start: 0.7161 (mttt) cc_final: 0.6846 (mmpt) REVERT: B 285 TYR cc_start: 0.7977 (m-80) cc_final: 0.7494 (m-80) REVERT: B 373 GLU cc_start: 0.6596 (mm-30) cc_final: 0.6118 (pt0) REVERT: B 392 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7327 (p0) REVERT: D 285 TYR cc_start: 0.7975 (m-80) cc_final: 0.7480 (m-80) REVERT: D 373 GLU cc_start: 0.6565 (mm-30) cc_final: 0.6093 (pt0) REVERT: D 392 ASP cc_start: 0.7671 (OUTLIER) cc_final: 0.7344 (p0) REVERT: D 474 LYS cc_start: 0.7179 (mttt) cc_final: 0.6852 (mmpt) REVERT: C 285 TYR cc_start: 0.7866 (m-80) cc_final: 0.7447 (m-80) REVERT: C 334 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8153 (mt) REVERT: C 373 GLU cc_start: 0.6587 (mm-30) cc_final: 0.6123 (pt0) REVERT: C 392 ASP cc_start: 0.7670 (OUTLIER) cc_final: 0.7346 (p0) outliers start: 60 outliers final: 23 residues processed: 210 average time/residue: 0.6125 time to fit residues: 141.5416 Evaluate side-chains 199 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 523 SER Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 523 SER Chi-restraints excluded: chain C residue 549 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 37 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 53 optimal weight: 0.0470 chunk 177 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN B 330 ASN D 330 ASN D 414 ASN C 330 ASN C 414 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.224050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.193550 restraints weight = 17179.465| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 1.68 r_work: 0.4041 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3933 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15128 Z= 0.134 Angle : 0.603 11.312 20344 Z= 0.312 Chirality : 0.045 0.149 2256 Planarity : 0.003 0.049 2564 Dihedral : 7.368 59.178 2076 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.26 % Allowed : 17.21 % Favored : 79.53 % 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 aren not related in a simple way. whole: 0.25 (0.21), residues: 1788 helix: 1.50 (0.20), residues: 680 sheet: -0.11 (0.27), residues: 396 loop : -0.94 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 481 TYR 0.013 0.001 TYR A 314 PHE 0.013 0.001 PHE B 315 TRP 0.003 0.001 TRP B 126 HIS 0.004 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00300 (15124) covalent geometry : angle 0.60265 (20344) hydrogen bonds : bond 0.04280 ( 600) hydrogen bonds : angle 4.82804 ( 1716) Misc. bond : bond 0.00125 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 171 time to evaluate : 0.617 Fit side-chains REVERT: A 285 TYR cc_start: 0.7977 (m-80) cc_final: 0.7478 (m-80) REVERT: A 317 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8575 (tp) REVERT: A 373 GLU cc_start: 0.6686 (mm-30) cc_final: 0.6164 (pt0) REVERT: A 392 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7371 (p0) REVERT: A 474 LYS cc_start: 0.7144 (mttt) cc_final: 0.6826 (mttt) REVERT: B 285 TYR cc_start: 0.7946 (m-80) cc_final: 0.7450 (m-80) REVERT: B 317 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8577 (tp) REVERT: B 373 GLU cc_start: 0.6596 (mm-30) cc_final: 0.6102 (pt0) REVERT: B 392 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.7360 (p0) REVERT: D 285 TYR cc_start: 0.7944 (m-80) cc_final: 0.7438 (m-80) REVERT: D 317 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8574 (tp) REVERT: D 373 GLU cc_start: 0.6556 (mm-30) cc_final: 0.6080 (pt0) REVERT: D 392 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7375 (p0) REVERT: D 474 LYS cc_start: 0.7136 (mttt) cc_final: 0.6823 (mttt) REVERT: C 110 GLU cc_start: 0.7016 (mp0) cc_final: 0.6777 (mp0) REVERT: C 285 TYR cc_start: 0.7843 (m-80) cc_final: 0.7452 (m-80) REVERT: C 373 GLU cc_start: 0.6593 (mm-30) cc_final: 0.6088 (pt0) REVERT: C 392 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7362 (p0) outliers start: 54 outliers final: 18 residues processed: 208 average time/residue: 0.6220 time to fit residues: 142.5319 Evaluate side-chains 188 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 523 SER Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 523 SER Chi-restraints excluded: chain C residue 549 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 chunk 117 optimal weight: 0.0770 chunk 116 optimal weight: 0.9990 chunk 175 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.224185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.193647 restraints weight = 17258.769| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 1.68 r_work: 0.4040 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3931 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15128 Z= 0.134 Angle : 0.597 11.448 20344 Z= 0.308 Chirality : 0.045 0.148 2256 Planarity : 0.003 0.047 2564 Dihedral : 7.291 59.587 2076 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.48 % Allowed : 18.06 % Favored : 79.47 % 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 aren not related in a simple way. whole: 0.40 (0.21), residues: 1788 helix: 1.65 (0.21), residues: 680 sheet: -0.09 (0.27), residues: 396 loop : -0.84 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 481 TYR 0.014 0.001 TYR C 314 PHE 0.012 0.001 PHE C 315 TRP 0.003 0.001 TRP B 126 HIS 0.004 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00302 (15124) covalent geometry : angle 0.59682 (20344) hydrogen bonds : bond 0.04216 ( 600) hydrogen bonds : angle 4.77695 ( 1716) Misc. bond : bond 0.00121 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 174 time to evaluate : 0.636 Fit side-chains REVERT: A 110 GLU cc_start: 0.7381 (mp0) cc_final: 0.7152 (mp0) REVERT: A 285 TYR cc_start: 0.7978 (m-80) cc_final: 0.7489 (m-80) REVERT: A 317 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8570 (tp) REVERT: A 373 GLU cc_start: 0.6686 (mm-30) cc_final: 0.6164 (pt0) REVERT: A 392 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7390 (p0) REVERT: A 474 LYS cc_start: 0.7018 (mttt) cc_final: 0.6743 (mmpt) REVERT: B 285 TYR cc_start: 0.7957 (m-80) cc_final: 0.7476 (m-80) REVERT: B 317 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8572 (tp) REVERT: B 373 GLU cc_start: 0.6586 (mm-30) cc_final: 0.6108 (pt0) REVERT: B 392 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.7387 (p0) REVERT: D 285 TYR cc_start: 0.7960 (m-80) cc_final: 0.7468 (m-80) REVERT: D 317 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8572 (tp) REVERT: D 373 GLU cc_start: 0.6544 (mm-30) cc_final: 0.6080 (pt0) REVERT: D 392 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7413 (p0) REVERT: D 474 LYS cc_start: 0.7067 (mttt) cc_final: 0.6735 (mttt) REVERT: C 285 TYR cc_start: 0.7852 (m-80) cc_final: 0.7446 (m-80) REVERT: C 373 GLU cc_start: 0.6638 (mm-30) cc_final: 0.6124 (pt0) REVERT: C 392 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7401 (p0) outliers start: 41 outliers final: 20 residues processed: 197 average time/residue: 0.6090 time to fit residues: 132.0437 Evaluate side-chains 195 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain D residue 523 SER Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 523 SER Chi-restraints excluded: chain C residue 549 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 67 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 66 optimal weight: 0.0670 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.222060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.191260 restraints weight = 17228.698| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 1.68 r_work: 0.4020 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3911 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15128 Z= 0.176 Angle : 0.654 11.667 20344 Z= 0.336 Chirality : 0.047 0.154 2256 Planarity : 0.004 0.064 2564 Dihedral : 7.407 59.923 2076 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 1.99 % Allowed : 18.54 % Favored : 79.47 % 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 aren not related in a simple way. whole: 0.27 (0.20), residues: 1788 helix: 1.51 (0.20), residues: 680 sheet: -0.17 (0.27), residues: 396 loop : -0.88 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 332 TYR 0.017 0.001 TYR C 314 PHE 0.014 0.002 PHE D 315 TRP 0.005 0.001 TRP B 126 HIS 0.003 0.001 HIS D 415 Details of bonding type rmsd covalent geometry : bond 0.00412 (15124) covalent geometry : angle 0.65450 (20344) hydrogen bonds : bond 0.04705 ( 600) hydrogen bonds : angle 4.91045 ( 1716) Misc. bond : bond 0.00129 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 0.489 Fit side-chains REVERT: A 110 GLU cc_start: 0.7429 (mp0) cc_final: 0.7133 (mp0) REVERT: A 285 TYR cc_start: 0.8004 (m-80) cc_final: 0.7523 (m-80) REVERT: A 317 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8592 (tp) REVERT: A 373 GLU cc_start: 0.6691 (mm-30) cc_final: 0.6165 (pt0) REVERT: A 392 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7422 (p0) REVERT: A 474 LYS cc_start: 0.7019 (mttt) cc_final: 0.6757 (mmpt) REVERT: B 285 TYR cc_start: 0.7987 (m-80) cc_final: 0.7510 (m-80) REVERT: B 317 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8589 (tp) REVERT: B 373 GLU cc_start: 0.6605 (mm-30) cc_final: 0.6131 (pt0) REVERT: B 392 ASP cc_start: 0.7718 (OUTLIER) cc_final: 0.7412 (p0) REVERT: D 285 TYR cc_start: 0.7990 (m-80) cc_final: 0.7506 (m-80) REVERT: D 317 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8589 (tp) REVERT: D 373 GLU cc_start: 0.6582 (mm-30) cc_final: 0.6111 (pt0) REVERT: D 392 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.7423 (p0) REVERT: D 474 LYS cc_start: 0.7046 (mttt) cc_final: 0.6765 (mmpt) REVERT: C 285 TYR cc_start: 0.7885 (m-80) cc_final: 0.7481 (m-80) REVERT: C 373 GLU cc_start: 0.6601 (mm-30) cc_final: 0.6106 (pt0) REVERT: C 392 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7421 (p0) outliers start: 33 outliers final: 19 residues processed: 187 average time/residue: 0.6603 time to fit residues: 135.3205 Evaluate side-chains 194 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 523 SER Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 523 SER Chi-restraints excluded: chain C residue 549 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.219851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.188881 restraints weight = 17199.011| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 1.67 r_work: 0.4000 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3896 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15128 Z= 0.220 Angle : 0.725 11.701 20344 Z= 0.371 Chirality : 0.048 0.159 2256 Planarity : 0.005 0.076 2564 Dihedral : 7.638 57.225 2076 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 2.66 % Allowed : 18.18 % Favored : 79.17 % 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 aren not related in a simple way. whole: -0.01 (0.20), residues: 1788 helix: 1.24 (0.20), residues: 680 sheet: -0.14 (0.26), residues: 380 loop : -1.09 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 332 TYR 0.021 0.002 TYR C 314 PHE 0.016 0.002 PHE D 315 TRP 0.006 0.001 TRP B 126 HIS 0.003 0.001 HIS B 415 Details of bonding type rmsd covalent geometry : bond 0.00523 (15124) covalent geometry : angle 0.72491 (20344) hydrogen bonds : bond 0.05386 ( 600) hydrogen bonds : angle 5.13132 ( 1716) Misc. bond : bond 0.00137 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5516.20 seconds wall clock time: 94 minutes 50.15 seconds (5690.15 seconds total)