Starting phenix.real_space_refine on Thu Aug 6 19:49:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x5i_38070/08_2026/8x5i_38070.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x5i_38070/08_2026/8x5i_38070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8x5i_38070/08_2026/8x5i_38070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x5i_38070/08_2026/8x5i_38070.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x5i_38070/08_2026/8x5i_38070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x5i_38070/08_2026/8x5i_38070.map" } resolution = 3.01 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= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 55 5.16 5 C 10851 2.51 5 N 2808 2.21 5 O 3276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17006 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3904 Classifications: {'peptide': 477} Link IDs: {'PTRANS': 8, 'TRANS': 468} Chain breaks: 1 Chain: "B" Number of atoms: 4537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4537 Classifications: {'peptide': 555} Link IDs: {'PTRANS': 8, 'TRANS': 546} Chain breaks: 1 Chain: "C" Number of atoms: 3888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3888 Classifications: {'peptide': 474} Link IDs: {'PTRANS': 8, 'TRANS': 465} Chain breaks: 1 Chain: "D" Number of atoms: 4549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4549 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 10, 'TRANS': 546} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.52, per 1000 atoms: 0.21 Number of scatterers: 17006 At special positions: 0 Unit cell: (87.36, 112.56, 193.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 55 16.00 P 12 15.00 Mg 4 11.99 O 3276 8.00 N 2808 7.00 C 10851 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 873.8 milliseconds 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3896 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 20 sheets defined 45.2% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 34 through 46 removed outlier: 3.573A pdb=" N LEU A 39 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 removed outlier: 3.529A pdb=" N ARG A 51 " --> pdb=" O ASP A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 64 removed outlier: 3.635A pdb=" N HIS A 63 " --> pdb=" O TYR A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 94 removed outlier: 4.102A pdb=" N LYS A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 98 through 102 Processing helix chain 'A' and resid 143 through 147 removed outlier: 3.525A pdb=" N ASN A 147 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 277 Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.533A pdb=" N GLN A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.920A pdb=" N TYR A 326 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 370 removed outlier: 3.674A pdb=" N SER A 368 " --> pdb=" O LYS A 364 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 394 removed outlier: 3.604A pdb=" N LYS A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 423 removed outlier: 3.643A pdb=" N LEU A 423 " --> pdb=" O THR A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 458 Processing helix chain 'A' and resid 475 through 493 removed outlier: 3.943A pdb=" N LYS A 479 " --> pdb=" O GLY A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 503 removed outlier: 3.610A pdb=" N GLU A 503 " --> pdb=" O GLU A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 529 removed outlier: 3.933A pdb=" N ASP A 515 " --> pdb=" O ASP A 511 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A 519 " --> pdb=" O ASP A 515 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLU A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N SER A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 538 removed outlier: 3.755A pdb=" N GLN A 538 " --> pdb=" O VAL A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 550 removed outlier: 3.507A pdb=" N MET A 545 " --> pdb=" O LYS A 541 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 562 Processing helix chain 'A' and resid 566 through 574 removed outlier: 4.186A pdb=" N LYS A 570 " --> pdb=" O PHE A 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 47 removed outlier: 3.835A pdb=" N LEU B 42 " --> pdb=" O PHE B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 52 Processing helix chain 'B' and resid 60 through 64 removed outlier: 3.651A pdb=" N HIS B 63 " --> pdb=" O TYR B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 91 removed outlier: 4.121A pdb=" N LYS B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 97 removed outlier: 4.287A pdb=" N ARG B 97 " --> pdb=" O LYS B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 177 removed outlier: 4.394A pdb=" N LEU B 163 " --> pdb=" O ASP B 159 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN B 166 " --> pdb=" O LYS B 162 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS B 169 " --> pdb=" O ALA B 165 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N PHE B 172 " --> pdb=" O LYS B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 194 Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.824A pdb=" N PHE B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THR B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 277 removed outlier: 3.628A pdb=" N SER B 268 " --> pdb=" O MET B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 281 removed outlier: 3.529A pdb=" N LYS B 281 " --> pdb=" O TYR B 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 278 through 281' Processing helix chain 'B' and resid 295 through 308 Processing helix chain 'B' and resid 321 through 326 removed outlier: 3.699A pdb=" N LEU B 324 " --> pdb=" O SER B 321 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR B 326 " --> pdb=" O GLU B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 357 No H-bonds generated for 'chain 'B' and resid 355 through 357' Processing helix chain 'B' and resid 358 through 370 removed outlier: 4.610A pdb=" N SER B 368 " --> pdb=" O LYS B 364 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA B 369 " --> pdb=" O ALA B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 394 removed outlier: 3.612A pdb=" N LYS B 384 " --> pdb=" O GLY B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 402 removed outlier: 3.548A pdb=" N ASN B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY B 402 " --> pdb=" O TYR B 398 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 397 through 402' Processing helix chain 'B' and resid 412 through 423 removed outlier: 4.027A pdb=" N TYR B 416 " --> pdb=" O TYR B 412 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 423 " --> pdb=" O THR B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 457 removed outlier: 3.719A pdb=" N LEU B 457 " --> pdb=" O CYS B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 493 removed outlier: 3.639A pdb=" N GLU B 480 " --> pdb=" O LYS B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 503 Processing helix chain 'B' and resid 511 through 529 removed outlier: 3.884A pdb=" N ASP B 515 " --> pdb=" O ASP B 511 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N GLU B 522 " --> pdb=" O SER B 518 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N SER B 523 " --> pdb=" O ALA B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 538 removed outlier: 3.599A pdb=" N TYR B 536 " --> pdb=" O ASP B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 550 removed outlier: 3.518A pdb=" N GLU B 547 " --> pdb=" O PHE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 562 removed outlier: 3.595A pdb=" N CYS B 557 " --> pdb=" O SER B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 574 removed outlier: 4.165A pdb=" N LYS B 570 " --> pdb=" O PHE B 566 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY B 574 " --> pdb=" O LYS B 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 47 removed outlier: 3.519A pdb=" N LEU C 42 " --> pdb=" O PHE C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 52 Processing helix chain 'C' and resid 60 through 64 removed outlier: 3.684A pdb=" N HIS C 63 " --> pdb=" O TYR C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 94 removed outlier: 4.305A pdb=" N LYS C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 278 removed outlier: 3.661A pdb=" N TYR C 270 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR C 278 " --> pdb=" O ALA C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 308 Processing helix chain 'C' and resid 321 through 326 removed outlier: 3.767A pdb=" N LEU C 324 " --> pdb=" O SER C 321 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR C 326 " --> pdb=" O GLU C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 370 removed outlier: 4.695A pdb=" N SER C 368 " --> pdb=" O LYS C 364 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA C 369 " --> pdb=" O ALA C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 394 removed outlier: 3.695A pdb=" N LYS C 384 " --> pdb=" O GLY C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 424 removed outlier: 3.555A pdb=" N VAL C 417 " --> pdb=" O PHE C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 458 removed outlier: 4.274A pdb=" N LEU C 456 " --> pdb=" O ARG C 452 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU C 457 " --> pdb=" O CYS C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 493 removed outlier: 3.688A pdb=" N GLU C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 503 Processing helix chain 'C' and resid 511 through 520 removed outlier: 3.681A pdb=" N ASP C 515 " --> pdb=" O ASP C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 529 removed outlier: 3.644A pdb=" N LYS C 525 " --> pdb=" O GLY C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 538 removed outlier: 3.802A pdb=" N TYR C 536 " --> pdb=" O ASP C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 551 removed outlier: 3.617A pdb=" N MET C 545 " --> pdb=" O LYS C 541 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL C 546 " --> pdb=" O LEU C 542 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN C 551 " --> pdb=" O GLU C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 562 Processing helix chain 'C' and resid 563 through 565 No H-bonds generated for 'chain 'C' and resid 563 through 565' Processing helix chain 'C' and resid 566 through 574 removed outlier: 4.172A pdb=" N LYS C 570 " --> pdb=" O PHE C 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 47 removed outlier: 3.746A pdb=" N LEU D 42 " --> pdb=" O PHE D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 52 removed outlier: 3.554A pdb=" N ARG D 51 " --> pdb=" O ASP D 47 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS D 52 " --> pdb=" O LYS D 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 47 through 52' Processing helix chain 'D' and resid 60 through 64 removed outlier: 3.953A pdb=" N ASP D 64 " --> pdb=" O HIS D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 91 removed outlier: 4.256A pdb=" N LYS D 87 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 147 No H-bonds generated for 'chain 'D' and resid 145 through 147' Processing helix chain 'D' and resid 159 through 168 Processing helix chain 'D' and resid 181 through 192 Processing helix chain 'D' and resid 205 through 211 Processing helix chain 'D' and resid 260 through 277 removed outlier: 3.608A pdb=" N MET D 264 " --> pdb=" O GLY D 260 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER D 266 " --> pdb=" O ARG D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 308 Processing helix chain 'D' and resid 321 through 326 removed outlier: 3.742A pdb=" N LEU D 324 " --> pdb=" O SER D 321 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR D 326 " --> pdb=" O GLU D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 370 removed outlier: 4.637A pdb=" N SER D 368 " --> pdb=" O LYS D 364 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA D 369 " --> pdb=" O ALA D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 394 removed outlier: 3.638A pdb=" N LYS D 384 " --> pdb=" O GLY D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 423 removed outlier: 3.895A pdb=" N TYR D 416 " --> pdb=" O TYR D 412 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL D 417 " --> pdb=" O PHE D 413 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU D 423 " --> pdb=" O THR D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 457 removed outlier: 3.519A pdb=" N LEU D 457 " --> pdb=" O CYS D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 493 Processing helix chain 'D' and resid 493 through 503 removed outlier: 3.796A pdb=" N GLU D 503 " --> pdb=" O GLU D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 529 removed outlier: 3.989A pdb=" N ASP D 515 " --> pdb=" O ASP D 511 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA D 519 " --> pdb=" O ASP D 515 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N GLU D 522 " --> pdb=" O SER D 518 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER D 523 " --> pdb=" O ALA D 519 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU D 529 " --> pdb=" O LYS D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 540 removed outlier: 4.163A pdb=" N SER D 540 " --> pdb=" O TYR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 550 removed outlier: 3.579A pdb=" N VAL D 546 " --> pdb=" O LEU D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 562 Processing helix chain 'D' and resid 566 through 574 removed outlier: 4.226A pdb=" N LYS D 570 " --> pdb=" O PHE D 566 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY D 574 " --> pdb=" O LYS D 570 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 20 removed outlier: 3.746A pdb=" N ASN A 5 " --> pdb=" O THR A 74 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLU A 70 " --> pdb=" O LYS A 9 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS A 112 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN A 121 " --> pdb=" O LYS A 112 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 154 removed outlier: 8.321A pdb=" N PHE A 316 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TYR A 285 " --> pdb=" O PHE A 316 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N SER A 318 " --> pdb=" O TYR A 285 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE A 287 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ASN A 25 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL A 26 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL A 336 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 7.147A 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: 8.429A pdb=" N TYR A 506 " --> pdb=" O HIS A 427 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE A 429 " --> pdb=" O TYR A 506 " (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 14 through 20 removed outlier: 6.622A pdb=" N LYS B 16 " --> pdb=" O LYS B 9 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LYS B 9 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN B 18 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR B 7 " --> pdb=" O ASN B 18 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASN B 20 " --> pdb=" O ASN B 5 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ASN B 5 " --> pdb=" O ASN B 20 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR B 74 " --> pdb=" O SER B 4 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE B 6 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE B 72 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE B 8 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N GLU B 70 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS B 112 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN B 121 " --> pdb=" O LYS B 112 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 154 removed outlier: 8.256A pdb=" N PHE B 316 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N TYR B 285 " --> pdb=" O PHE B 316 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N SER B 318 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE B 287 " --> pdb=" O SER B 318 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS B 24 " --> pdb=" O ARG B 332 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ILE B 334 " --> pdb=" O LYS B 24 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL B 26 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N VAL B 336 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N PHE B 28 " --> pdb=" O VAL B 336 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N SER B 338 " --> pdb=" O PHE B 28 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 138 through 139 removed outlier: 3.717A pdb=" N ILE B 142 " --> pdb=" O ARG B 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 224 through 229 Processing sheet with id=AA9, first strand: chain 'B' and resid 403 through 407 removed outlier: 6.659A pdb=" N ARG B 374 " --> pdb=" O PHE B 404 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N LEU B 406 " --> pdb=" O ARG B 374 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU B 376 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 430 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N TYR B 506 " --> pdb=" O HIS B 427 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE B 429 " --> pdb=" O TYR B 506 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 435 through 437 Processing sheet with id=AB2, first strand: chain 'C' and resid 17 through 20 removed outlier: 6.805A pdb=" N THR C 74 " --> pdb=" O SER C 4 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE C 6 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE C 72 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ILE C 8 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLU C 70 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS C 112 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN C 121 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE C 134 " --> pdb=" O TRP C 126 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 149 through 154 removed outlier: 4.466A pdb=" N TYR C 314 " --> pdb=" O VAL C 283 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL C 26 " --> pdb=" O ILE C 334 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N VAL C 336 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE C 28 " --> pdb=" O VAL C 336 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 403 through 407 removed outlier: 6.659A pdb=" N ARG C 374 " --> pdb=" O PHE C 404 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LEU C 406 " --> pdb=" O ARG C 374 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU C 376 " --> pdb=" O LEU C 406 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 435 through 437 Processing sheet with id=AB6, first strand: chain 'D' and resid 14 through 20 removed outlier: 6.622A pdb=" N GLU D 15 " --> pdb=" O ASN D 10 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR D 74 " --> pdb=" O SER D 4 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE D 6 " --> pdb=" O ILE D 72 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE D 72 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ILE D 8 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLU D 70 " --> pdb=" O ILE D 8 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 149 through 154 removed outlier: 8.213A pdb=" N PHE D 316 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TYR D 285 " --> pdb=" O PHE D 316 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N SER D 318 " --> pdb=" O TYR D 285 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE D 287 " --> pdb=" O SER D 318 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS D 24 " --> pdb=" O ARG D 332 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ILE D 334 " --> pdb=" O LYS D 24 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N VAL D 26 " --> pdb=" O ILE D 334 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VAL D 336 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N PHE D 28 " --> pdb=" O VAL D 336 " (cutoff:3.500A) removed outlier: 8.932A pdb=" N SER D 338 " --> pdb=" O PHE D 28 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 113 through 114 Processing sheet with id=AB9, first strand: chain 'D' and resid 138 through 139 removed outlier: 3.832A pdb=" N ILE D 142 " --> pdb=" O ARG D 139 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 403 through 407 removed outlier: 6.596A pdb=" N ARG D 374 " --> pdb=" O PHE D 404 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N LEU D 406 " --> pdb=" O ARG D 374 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU D 376 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS D 430 " --> pdb=" O LEU D 377 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N TYR D 506 " --> pdb=" O HIS D 427 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE D 429 " --> pdb=" O TYR D 506 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 435 through 437 700 hydrogen bonds defined for protein. 1983 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: 3.10 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4319 1.33 - 1.45: 3116 1.45 - 1.57: 9752 1.57 - 1.69: 17 1.69 - 1.81: 90 Bond restraints: 17294 Sorted by residual: bond pdb=" N VAL A 358 " pdb=" CA VAL A 358 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.25e-02 6.40e+03 1.15e+01 bond pdb=" N ILE A 467 " pdb=" CA ILE A 467 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.14e-02 7.69e+03 1.10e+01 bond pdb=" C VAL A 358 " pdb=" O VAL A 358 " ideal model delta sigma weight residual 1.236 1.274 -0.037 1.19e-02 7.06e+03 9.91e+00 bond pdb=" N VAL D 93 " pdb=" CA VAL D 93 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.59e+00 bond pdb=" N VAL B 93 " pdb=" CA VAL B 93 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.58e+00 ... (remaining 17289 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 22516 2.62 - 5.23: 606 5.23 - 7.85: 85 7.85 - 10.46: 29 10.46 - 13.08: 3 Bond angle restraints: 23239 Sorted by residual: angle pdb=" C GLU C 471 " pdb=" N ASP C 472 " pdb=" CA ASP C 472 " ideal model delta sigma weight residual 121.54 134.62 -13.08 1.91e+00 2.74e-01 4.69e+01 angle pdb=" C THR C 554 " pdb=" N LYS C 555 " pdb=" CA LYS C 555 " ideal model delta sigma weight residual 121.54 133.91 -12.37 1.91e+00 2.74e-01 4.19e+01 angle pdb=" C PHE A 528 " pdb=" N GLU A 529 " pdb=" CA GLU A 529 " ideal model delta sigma weight residual 122.08 131.48 -9.40 1.47e+00 4.63e-01 4.09e+01 angle pdb=" C ASP C 64 " pdb=" N THR C 65 " pdb=" CA THR C 65 " ideal model delta sigma weight residual 122.61 132.44 -9.83 1.56e+00 4.11e-01 3.97e+01 angle pdb=" N ASP A 32 " pdb=" CA ASP A 32 " pdb=" C ASP A 32 " ideal model delta sigma weight residual 111.52 119.96 -8.44 1.40e+00 5.10e-01 3.63e+01 ... (remaining 23234 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 9413 17.90 - 35.79: 966 35.79 - 53.69: 202 53.69 - 71.58: 35 71.58 - 89.48: 15 Dihedral angle restraints: 10631 sinusoidal: 4574 harmonic: 6057 Sorted by residual: dihedral pdb=" CA GLN B 198 " pdb=" C GLN B 198 " pdb=" N ILE B 199 " pdb=" CA ILE B 199 " ideal model delta harmonic sigma weight residual 180.00 152.10 27.90 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA GLU B 201 " pdb=" C GLU B 201 " pdb=" N MET B 202 " pdb=" CA MET B 202 " ideal model delta harmonic sigma weight residual 180.00 152.81 27.19 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA LYS C 35 " pdb=" C LYS C 35 " pdb=" N THR C 36 " pdb=" CA THR C 36 " ideal model delta harmonic sigma weight residual 180.00 154.58 25.42 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 10628 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 2358 0.114 - 0.228: 177 0.228 - 0.342: 12 0.342 - 0.456: 3 0.456 - 0.570: 1 Chirality restraints: 2551 Sorted by residual: chirality pdb=" CB VAL B 549 " pdb=" CA VAL B 549 " pdb=" CG1 VAL B 549 " pdb=" CG2 VAL B 549 " both_signs ideal model delta sigma weight residual False -2.63 -2.06 -0.57 2.00e-01 2.50e+01 8.11e+00 chirality pdb=" CB ILE D 199 " pdb=" CA ILE D 199 " pdb=" CG1 ILE D 199 " pdb=" CG2 ILE D 199 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.62e+00 chirality pdb=" CA ASP A 32 " pdb=" N ASP A 32 " pdb=" C ASP A 32 " pdb=" CB ASP A 32 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.44e+00 ... (remaining 2548 not shown) Planarity restraints: 2940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 358 " -0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C VAL C 358 " 0.061 2.00e-02 2.50e+03 pdb=" O VAL C 358 " -0.023 2.00e-02 2.50e+03 pdb=" N LYS C 359 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 90 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.88e+00 pdb=" C ILE D 90 " -0.049 2.00e-02 2.50e+03 pdb=" O ILE D 90 " 0.018 2.00e-02 2.50e+03 pdb=" N SER D 91 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 90 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.86e+00 pdb=" C ILE B 90 " 0.048 2.00e-02 2.50e+03 pdb=" O ILE B 90 " -0.018 2.00e-02 2.50e+03 pdb=" N SER B 91 " -0.016 2.00e-02 2.50e+03 ... (remaining 2937 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 188 2.67 - 3.23: 13731 3.23 - 3.79: 24175 3.79 - 4.34: 36253 4.34 - 4.90: 58753 Nonbonded interactions: 133100 Sorted by model distance: nonbonded pdb=" O1G ATP A 601 " pdb="MG MG A 602 " model vdw 2.113 2.170 nonbonded pdb=" OG1 THR D 36 " pdb="MG MG D 602 " model vdw 2.127 2.170 nonbonded pdb=" OG1 THR B 36 " pdb="MG MG B 602 " model vdw 2.130 2.170 nonbonded pdb=" OG1 THR A 36 " pdb="MG MG A 602 " model vdw 2.160 2.170 nonbonded pdb=" O2B ATP A 601 " pdb="MG MG A 602 " model vdw 2.197 2.170 ... (remaining 133095 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 156 or resid 261 through 602)) selection = (chain 'B' and (resid 1 through 156 or resid 261 through 602)) selection = chain 'C' selection = (chain 'D' and (resid 1 through 156 or resid 261 through 602)) } 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: 5.240 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: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.150 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 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 : 0.007 0.062 17294 Z= 0.348 Angle : 1.045 13.081 23239 Z= 0.595 Chirality : 0.064 0.570 2551 Planarity : 0.006 0.059 2940 Dihedral : 15.256 89.476 6735 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.79 % Favored : 95.16 % Rotamer: Outliers : 0.64 % Allowed : 0.95 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.57 (0.15), residues: 2047 helix: -3.88 (0.08), residues: 807 sheet: 0.41 (0.26), residues: 393 loop : -2.00 (0.18), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 51 TYR 0.021 0.002 TYR B 272 PHE 0.038 0.003 PHE C 315 TRP 0.004 0.001 TRP D 126 HIS 0.012 0.002 HIS C 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00677 / 0.35 (17294) covalent geometry : angle 1.04530 / 0.59 (23239) hydrogen bonds : bond 0.18392 / 11.50 ( 700) hydrogen bonds : angle 8.41163 / 5.79 ( 1983) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 322 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8163 (tt0) cc_final: 0.7821 (tp30) REVERT: A 143 ASN cc_start: 0.8520 (p0) cc_final: 0.8312 (p0) REVERT: A 480 GLU cc_start: 0.7159 (mp0) cc_final: 0.6626 (tp30) REVERT: A 481 ARG cc_start: 0.7940 (tpp80) cc_final: 0.7569 (tpp80) REVERT: A 511 ASP cc_start: 0.7775 (m-30) cc_final: 0.7559 (m-30) REVERT: B 132 ASN cc_start: 0.8754 (t0) cc_final: 0.8527 (t0) REVERT: B 197 GLN cc_start: 0.8395 (tm-30) cc_final: 0.7888 (tm-30) REVERT: B 210 GLN cc_start: 0.8575 (tm-30) cc_final: 0.8354 (tm-30) REVERT: B 211 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7838 (mt-10) REVERT: B 229 LYS cc_start: 0.8178 (ptpt) cc_final: 0.7944 (ptpt) REVERT: B 232 MET cc_start: 0.8234 (ppp) cc_final: 0.7987 (ptm) REVERT: B 422 ASP cc_start: 0.8446 (m-30) cc_final: 0.8093 (m-30) REVERT: B 476 LYS cc_start: 0.7322 (tttt) cc_final: 0.6949 (mptt) REVERT: B 492 GLN cc_start: 0.8152 (tt0) cc_final: 0.7929 (tt0) REVERT: C 62 LYS cc_start: 0.8370 (mttt) cc_final: 0.7661 (mmtt) REVERT: C 70 GLU cc_start: 0.7994 (tt0) cc_final: 0.7765 (tt0) REVERT: C 94 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7659 (tppt) REVERT: C 348 MET cc_start: 0.9114 (tpt) cc_final: 0.8771 (tpp) REVERT: C 464 GLU cc_start: 0.7646 (pp20) cc_final: 0.6922 (pp20) REVERT: C 465 ILE cc_start: 0.8434 (pt) cc_final: 0.7948 (tp) REVERT: C 477 LYS cc_start: 0.8652 (mmmm) cc_final: 0.7732 (pttm) REVERT: C 481 ARG cc_start: 0.7719 (mtp180) cc_final: 0.7433 (ttp-170) REVERT: D 67 LYS cc_start: 0.8110 (mmpt) cc_final: 0.7366 (mtmm) REVERT: D 87 LYS cc_start: 0.8100 (mttt) cc_final: 0.7615 (mtmt) REVERT: D 114 ASP cc_start: 0.7668 (t0) cc_final: 0.7379 (t0) REVERT: D 278 TYR cc_start: 0.8749 (m-80) cc_final: 0.8459 (m-80) REVERT: D 279 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7730 (tm-30) REVERT: D 280 ASP cc_start: 0.7533 (m-30) cc_final: 0.7267 (m-30) REVERT: D 434 ASP cc_start: 0.8406 (m-30) cc_final: 0.8134 (m-30) REVERT: D 438 LYS cc_start: 0.8255 (pttm) cc_final: 0.8008 (pttm) REVERT: D 526 ARG cc_start: 0.7863 (ttp-170) cc_final: 0.7505 (ttp-170) outliers start: 12 outliers final: 2 residues processed: 332 average time/residue: 0.1459 time to fit residues: 69.8257 Evaluate side-chains 219 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 216 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain C residue 103 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 492 GLN B 178 ASN B 186 ASN B 455 ASN C 5 ASN C 13 ASN C 56 ASN C 147 ASN ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 HIS D 186 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.151883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.110036 restraints weight = 21014.404| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.55 r_work: 0.3060 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17294 Z= 0.210 Angle : 0.607 8.042 23239 Z= 0.325 Chirality : 0.046 0.174 2551 Planarity : 0.004 0.034 2940 Dihedral : 8.907 89.053 2378 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.25 % Favored : 95.70 % Rotamer: Outliers : 1.32 % Allowed : 7.57 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.17), residues: 2047 helix: -1.35 (0.15), residues: 824 sheet: 0.47 (0.26), residues: 394 loop : -1.66 (0.19), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 139 TYR 0.013 0.002 TYR B 272 PHE 0.031 0.002 PHE C 315 TRP 0.012 0.002 TRP D 126 HIS 0.012 0.002 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.21 (17294) covalent geometry : angle 0.60685 / 0.32 (23239) hydrogen bonds : bond 0.04701 / 3.02 ( 700) hydrogen bonds : angle 5.21480 / 3.60 ( 1983) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 222 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 511 ASP cc_start: 0.8032 (m-30) cc_final: 0.7825 (m-30) REVERT: A 530 ASN cc_start: 0.7900 (t0) cc_final: 0.7664 (t0) REVERT: B 106 TYR cc_start: 0.8780 (m-80) cc_final: 0.8371 (m-80) REVERT: B 129 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7463 (mm-30) REVERT: B 197 GLN cc_start: 0.8614 (tm-30) cc_final: 0.8091 (tm-30) REVERT: B 211 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7862 (mt-10) REVERT: B 217 ARG cc_start: 0.8377 (mtp85) cc_final: 0.8170 (mtp85) REVERT: B 232 MET cc_start: 0.8395 (ppp) cc_final: 0.8114 (ptm) REVERT: B 446 GLU cc_start: 0.8331 (tt0) cc_final: 0.8125 (tt0) REVERT: B 547 GLU cc_start: 0.8535 (tt0) cc_final: 0.8298 (tt0) REVERT: C 94 LYS cc_start: 0.8656 (ttpp) cc_final: 0.7859 (tppt) REVERT: C 278 TYR cc_start: 0.7779 (m-80) cc_final: 0.7529 (m-80) REVERT: C 397 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7846 (mt-10) REVERT: C 439 LYS cc_start: 0.8110 (tttm) cc_final: 0.7781 (tttm) REVERT: C 464 GLU cc_start: 0.8134 (pp20) cc_final: 0.7327 (pp20) REVERT: C 465 ILE cc_start: 0.8305 (pt) cc_final: 0.8102 (tt) REVERT: C 480 GLU cc_start: 0.7556 (pm20) cc_final: 0.7150 (pm20) REVERT: C 481 ARG cc_start: 0.8196 (mtp180) cc_final: 0.7981 (ttp-170) REVERT: D 30 MET cc_start: 0.8511 (mmt) cc_final: 0.8264 (tpt) REVERT: D 67 LYS cc_start: 0.8088 (mmpt) cc_final: 0.7392 (mtmm) REVERT: D 87 LYS cc_start: 0.8453 (mttt) cc_final: 0.8247 (mtmt) REVERT: D 246 LYS cc_start: 0.8335 (mtpt) cc_final: 0.7968 (mtmt) REVERT: D 279 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8257 (tm-30) REVERT: D 379 GLU cc_start: 0.8089 (tp30) cc_final: 0.7871 (tp30) REVERT: D 526 ARG cc_start: 0.8156 (ttp-170) cc_final: 0.7579 (ttt-90) outliers start: 25 outliers final: 19 residues processed: 242 average time/residue: 0.1530 time to fit residues: 53.0525 Evaluate side-chains 207 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 188 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain D residue 455 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 173 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 146 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 55.891 > 50:) chunk 195 optimal weight: 0.4980 chunk 179 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 189 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 535 HIS B 147 ASN C 5 ASN C 13 ASN C 56 ASN C 147 ASN ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 551 ASN D 198 GLN D 538 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.152100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.110492 restraints weight = 21189.042| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.65 r_work: 0.3069 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17294 Z= 0.148 Angle : 0.519 6.826 23239 Z= 0.281 Chirality : 0.044 0.165 2551 Planarity : 0.003 0.031 2940 Dihedral : 8.144 77.081 2372 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.81 % Favored : 96.14 % Rotamer: Outliers : 1.54 % Allowed : 10.22 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.18), residues: 2047 helix: -0.06 (0.18), residues: 824 sheet: 0.52 (0.26), residues: 392 loop : -1.40 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 139 TYR 0.012 0.001 TYR B 272 PHE 0.023 0.001 PHE C 315 TRP 0.006 0.001 TRP D 126 HIS 0.006 0.001 HIS C 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (17294) covalent geometry : angle 0.51917 / 0.28 (23239) hydrogen bonds : bond 0.03889 / 2.51 ( 700) hydrogen bonds : angle 4.79448 / 3.30 ( 1983) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 202 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 511 ASP cc_start: 0.8060 (m-30) cc_final: 0.7837 (m-30) REVERT: A 530 ASN cc_start: 0.7904 (t0) cc_final: 0.7097 (t0) REVERT: B 197 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8231 (tm-30) REVERT: B 211 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7863 (mt-10) REVERT: B 232 MET cc_start: 0.8379 (ppp) cc_final: 0.8026 (ptm) REVERT: B 547 GLU cc_start: 0.8554 (tt0) cc_final: 0.8251 (tt0) REVERT: C 147 ASN cc_start: 0.8806 (t0) cc_final: 0.8541 (t0) REVERT: C 278 TYR cc_start: 0.7779 (m-80) cc_final: 0.7538 (m-80) REVERT: C 439 LYS cc_start: 0.8150 (tttm) cc_final: 0.7790 (tttm) REVERT: C 464 GLU cc_start: 0.8058 (pp20) cc_final: 0.7369 (pp20) REVERT: C 465 ILE cc_start: 0.8285 (pt) cc_final: 0.8045 (tt) REVERT: C 481 ARG cc_start: 0.8159 (mtp180) cc_final: 0.7874 (ttp-170) REVERT: D 30 MET cc_start: 0.8495 (mmt) cc_final: 0.8225 (tpt) REVERT: D 67 LYS cc_start: 0.8169 (mmpt) cc_final: 0.7344 (mtmm) REVERT: D 87 LYS cc_start: 0.8474 (mttt) cc_final: 0.8273 (mttp) REVERT: D 198 GLN cc_start: 0.6783 (OUTLIER) cc_final: 0.5937 (pm20) REVERT: D 279 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8299 (tm-30) REVERT: D 526 ARG cc_start: 0.8147 (ttp-170) cc_final: 0.7572 (ttt-90) REVERT: D 564 GLU cc_start: 0.8066 (tp30) cc_final: 0.7859 (tp30) outliers start: 29 outliers final: 21 residues processed: 223 average time/residue: 0.1446 time to fit residues: 46.1047 Evaluate side-chains 211 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 198 GLN Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain D residue 418 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 40 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 193 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 66 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 5 ASN C 56 ASN ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.149969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.109379 restraints weight = 21203.761| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.54 r_work: 0.3045 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17294 Z= 0.196 Angle : 0.558 7.086 23239 Z= 0.298 Chirality : 0.045 0.176 2551 Planarity : 0.003 0.034 2940 Dihedral : 8.087 78.044 2372 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.74 % Favored : 95.21 % Rotamer: Outliers : 2.01 % Allowed : 11.59 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.18), residues: 2047 helix: 0.46 (0.18), residues: 813 sheet: 0.47 (0.26), residues: 392 loop : -1.23 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 481 TYR 0.011 0.001 TYR A 517 PHE 0.027 0.001 PHE C 315 TRP 0.007 0.001 TRP D 126 HIS 0.006 0.001 HIS C 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 (17294) covalent geometry : angle 0.55832 / 0.30 (23239) hydrogen bonds : bond 0.04171 / 2.71 ( 700) hydrogen bonds : angle 4.78233 / 3.27 ( 1983) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 204 time to evaluate : 0.601 Fit side-chains revert: symmetry clash REVERT: A 511 ASP cc_start: 0.8049 (m-30) cc_final: 0.7824 (m-30) REVERT: A 530 ASN cc_start: 0.8014 (t0) cc_final: 0.7194 (t0) REVERT: B 106 TYR cc_start: 0.8809 (m-80) cc_final: 0.8334 (m-80) REVERT: B 129 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7538 (mm-30) REVERT: B 197 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8055 (tm-30) REVERT: B 206 LYS cc_start: 0.8467 (mmtt) cc_final: 0.8208 (mmtt) REVERT: B 211 GLU cc_start: 0.8356 (mt-10) cc_final: 0.7798 (mt-10) REVERT: B 232 MET cc_start: 0.8360 (ppp) cc_final: 0.7995 (ptm) REVERT: B 481 ARG cc_start: 0.8356 (tpp80) cc_final: 0.8001 (mmm-85) REVERT: C 147 ASN cc_start: 0.8785 (t0) cc_final: 0.8503 (t0) REVERT: C 278 TYR cc_start: 0.7798 (m-80) cc_final: 0.7569 (m-80) REVERT: C 464 GLU cc_start: 0.8084 (pp20) cc_final: 0.7408 (pp20) REVERT: C 465 ILE cc_start: 0.8242 (pt) cc_final: 0.8005 (tt) REVERT: C 477 LYS cc_start: 0.8561 (mmmm) cc_final: 0.8059 (ptmm) REVERT: C 491 LYS cc_start: 0.8319 (ttmm) cc_final: 0.7904 (mtpp) REVERT: C 499 GLU cc_start: 0.8414 (tp30) cc_final: 0.8183 (tt0) REVERT: C 538 GLN cc_start: 0.8426 (mm110) cc_final: 0.8206 (mm110) REVERT: D 67 LYS cc_start: 0.8161 (mmpt) cc_final: 0.7312 (mtmm) REVERT: D 526 ARG cc_start: 0.8165 (ttp-170) cc_final: 0.7608 (ttp80) REVERT: D 564 GLU cc_start: 0.8048 (tp30) cc_final: 0.7792 (tp30) outliers start: 38 outliers final: 29 residues processed: 233 average time/residue: 0.1354 time to fit residues: 45.4813 Evaluate side-chains 224 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain D residue 418 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 120 optimal weight: 0.2980 chunk 88 optimal weight: 0.0570 chunk 100 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 5 ASN C 56 ASN ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.152870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.112395 restraints weight = 21080.142| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.37 r_work: 0.3092 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17294 Z= 0.108 Angle : 0.480 7.929 23239 Z= 0.260 Chirality : 0.043 0.155 2551 Planarity : 0.002 0.036 2940 Dihedral : 7.551 86.930 2372 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.81 % Favored : 96.14 % Rotamer: Outliers : 1.96 % Allowed : 12.55 % Favored : 85.49 % 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 are not related in a simple way. whole: 0.02 (0.19), residues: 2047 helix: 0.88 (0.19), residues: 818 sheet: 0.53 (0.26), residues: 392 loop : -1.08 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 481 TYR 0.019 0.001 TYR D 253 PHE 0.018 0.001 PHE C 315 TRP 0.004 0.001 TRP A 126 HIS 0.004 0.001 HIS C 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (17294) covalent geometry : angle 0.47977 / 0.26 (23239) hydrogen bonds : bond 0.03295 / 2.13 ( 700) hydrogen bonds : angle 4.51846 / 3.09 ( 1983) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 211 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 511 ASP cc_start: 0.8017 (m-30) cc_final: 0.7806 (m-30) REVERT: A 530 ASN cc_start: 0.8014 (t0) cc_final: 0.7287 (t0) REVERT: B 106 TYR cc_start: 0.8768 (m-80) cc_final: 0.8327 (m-80) REVERT: B 197 GLN cc_start: 0.8709 (tm-30) cc_final: 0.8268 (tm-30) REVERT: B 211 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7836 (mt-10) REVERT: B 221 LYS cc_start: 0.8989 (mtmm) cc_final: 0.8667 (mppt) REVERT: B 232 MET cc_start: 0.8326 (ppp) cc_final: 0.7993 (ptm) REVERT: B 379 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8129 (tp30) REVERT: B 481 ARG cc_start: 0.8308 (tpp80) cc_final: 0.7994 (mmm-85) REVERT: C 147 ASN cc_start: 0.8793 (t0) cc_final: 0.8491 (t0) REVERT: C 278 TYR cc_start: 0.7740 (m-80) cc_final: 0.7528 (m-80) REVERT: C 397 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7506 (mt-10) REVERT: C 464 GLU cc_start: 0.8013 (pp20) cc_final: 0.7362 (pp20) REVERT: C 481 ARG cc_start: 0.7958 (ttp-170) cc_final: 0.7712 (ttp-170) REVERT: C 491 LYS cc_start: 0.8292 (ttmm) cc_final: 0.7899 (mtpp) REVERT: C 499 GLU cc_start: 0.8430 (tp30) cc_final: 0.8215 (tt0) REVERT: D 30 MET cc_start: 0.8573 (mmt) cc_final: 0.8256 (tpt) REVERT: D 67 LYS cc_start: 0.8203 (mmpt) cc_final: 0.7477 (mtmt) REVERT: D 87 LYS cc_start: 0.8464 (mttt) cc_final: 0.8263 (mttp) REVERT: D 198 GLN cc_start: 0.6739 (OUTLIER) cc_final: 0.6341 (pm20) REVERT: D 526 ARG cc_start: 0.8167 (ttp-170) cc_final: 0.7596 (ttt-90) REVERT: D 564 GLU cc_start: 0.8030 (tp30) cc_final: 0.7760 (tp30) outliers start: 37 outliers final: 25 residues processed: 239 average time/residue: 0.1386 time to fit residues: 48.2189 Evaluate side-chains 217 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 198 GLN Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 418 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 112 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 88 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 168 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 53 optimal weight: 0.0370 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 ASN C 56 ASN ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.152996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.112670 restraints weight = 20968.080| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.31 r_work: 0.3104 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17294 Z= 0.107 Angle : 0.478 7.044 23239 Z= 0.259 Chirality : 0.043 0.150 2551 Planarity : 0.002 0.035 2940 Dihedral : 7.364 88.591 2372 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.86 % Favored : 96.09 % Rotamer: Outliers : 1.96 % Allowed : 13.23 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.19), residues: 2047 helix: 1.06 (0.19), residues: 819 sheet: 0.61 (0.26), residues: 391 loop : -1.01 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 481 TYR 0.010 0.001 TYR D 253 PHE 0.019 0.001 PHE C 315 TRP 0.004 0.001 TRP A 126 HIS 0.004 0.001 HIS C 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (17294) covalent geometry : angle 0.47780 / 0.26 (23239) hydrogen bonds : bond 0.03230 / 2.08 ( 700) hydrogen bonds : angle 4.44876 / 3.04 ( 1983) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 205 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 LYS cc_start: 0.6723 (mptt) cc_final: 0.6205 (ttpt) REVERT: A 511 ASP cc_start: 0.7999 (m-30) cc_final: 0.7771 (m-30) REVERT: A 530 ASN cc_start: 0.8150 (t0) cc_final: 0.7324 (t0) REVERT: B 106 TYR cc_start: 0.8772 (m-80) cc_final: 0.8381 (m-80) REVERT: B 197 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8282 (tm-30) REVERT: B 206 LYS cc_start: 0.8513 (mmtt) cc_final: 0.8270 (mmtt) REVERT: B 211 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7791 (mt-10) REVERT: B 221 LYS cc_start: 0.8990 (mtmm) cc_final: 0.8675 (mppt) REVERT: B 232 MET cc_start: 0.8339 (ppp) cc_final: 0.7968 (ptm) REVERT: B 379 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8118 (tp30) REVERT: C 147 ASN cc_start: 0.8785 (t0) cc_final: 0.8483 (t0) REVERT: C 278 TYR cc_start: 0.7749 (m-80) cc_final: 0.7536 (m-80) REVERT: C 464 GLU cc_start: 0.8011 (pp20) cc_final: 0.7431 (pp20) REVERT: C 476 LYS cc_start: 0.7909 (mmmm) cc_final: 0.7356 (mptt) REVERT: C 481 ARG cc_start: 0.7945 (ttp-170) cc_final: 0.7739 (ttp-170) REVERT: C 491 LYS cc_start: 0.8280 (ttmm) cc_final: 0.7896 (mtpp) REVERT: D 30 MET cc_start: 0.8558 (mmt) cc_final: 0.8243 (tpt) REVERT: D 67 LYS cc_start: 0.8202 (mmpt) cc_final: 0.7484 (mtmt) REVERT: D 87 LYS cc_start: 0.8440 (mttt) cc_final: 0.8236 (mttp) REVERT: D 526 ARG cc_start: 0.8174 (ttp-170) cc_final: 0.7537 (ttt-90) REVERT: D 564 GLU cc_start: 0.8019 (tp30) cc_final: 0.7738 (tp30) outliers start: 37 outliers final: 32 residues processed: 231 average time/residue: 0.1437 time to fit residues: 48.0406 Evaluate side-chains 228 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 198 GLN Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 418 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 95 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 100 optimal weight: 0.5980 chunk 200 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 170 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 535 HIS C 5 ASN C 56 ASN C 79 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.148613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.108071 restraints weight = 21060.219| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.56 r_work: 0.3034 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 17294 Z= 0.243 Angle : 0.605 7.415 23239 Z= 0.317 Chirality : 0.047 0.167 2551 Planarity : 0.003 0.035 2940 Dihedral : 7.930 83.159 2372 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.03 % Favored : 94.92 % Rotamer: Outliers : 2.28 % Allowed : 13.39 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.19), residues: 2047 helix: 0.94 (0.19), residues: 811 sheet: 0.38 (0.26), residues: 395 loop : -1.05 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 526 TYR 0.012 0.002 TYR A 517 PHE 0.028 0.002 PHE C 315 TRP 0.006 0.002 TRP D 126 HIS 0.007 0.001 HIS C 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.24 (17294) covalent geometry : angle 0.60489 / 0.32 (23239) hydrogen bonds : bond 0.04413 / 2.87 ( 700) hydrogen bonds : angle 4.77756 / 3.25 ( 1983) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 199 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 LYS cc_start: 0.6756 (mptt) cc_final: 0.6212 (ttpt) REVERT: A 511 ASP cc_start: 0.8052 (m-30) cc_final: 0.7813 (m-30) REVERT: A 530 ASN cc_start: 0.8277 (t0) cc_final: 0.7412 (t0) REVERT: B 106 TYR cc_start: 0.8842 (m-80) cc_final: 0.8339 (m-80) REVERT: B 197 GLN cc_start: 0.8769 (tm-30) cc_final: 0.8301 (tm-30) REVERT: B 206 LYS cc_start: 0.8497 (mmtt) cc_final: 0.7685 (mmtt) REVERT: B 210 GLN cc_start: 0.8198 (mt0) cc_final: 0.7794 (mp10) REVERT: B 211 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7761 (mt-10) REVERT: B 221 LYS cc_start: 0.8979 (mtmm) cc_final: 0.8654 (mppt) REVERT: B 232 MET cc_start: 0.8416 (ppp) cc_final: 0.7918 (ptm) REVERT: B 494 LYS cc_start: 0.8373 (ttpp) cc_final: 0.7947 (pttm) REVERT: C 147 ASN cc_start: 0.8752 (t0) cc_final: 0.8428 (t0) REVERT: C 278 TYR cc_start: 0.7786 (m-80) cc_final: 0.7564 (m-80) REVERT: C 464 GLU cc_start: 0.8178 (pp20) cc_final: 0.7553 (pp20) REVERT: C 465 ILE cc_start: 0.8014 (tp) cc_final: 0.7506 (tp) REVERT: C 491 LYS cc_start: 0.8304 (ttmm) cc_final: 0.7929 (mtpp) REVERT: D 67 LYS cc_start: 0.8207 (mmpt) cc_final: 0.7317 (mtmm) REVERT: D 379 GLU cc_start: 0.8009 (tp30) cc_final: 0.7243 (mp0) REVERT: D 526 ARG cc_start: 0.8204 (ttp-170) cc_final: 0.7606 (ttt-90) REVERT: D 564 GLU cc_start: 0.8123 (tp30) cc_final: 0.7835 (tp30) outliers start: 43 outliers final: 35 residues processed: 232 average time/residue: 0.1352 time to fit residues: 45.4838 Evaluate side-chains 227 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 191 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 198 GLN Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain D residue 428 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 93 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 153 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 64 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 chunk 169 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 135 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 132 ASN C 5 ASN C 56 ASN ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.151382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.111847 restraints weight = 21212.629| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.45 r_work: 0.3070 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17294 Z= 0.130 Angle : 0.515 7.662 23239 Z= 0.276 Chirality : 0.043 0.155 2551 Planarity : 0.003 0.032 2940 Dihedral : 7.520 88.352 2372 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.35 % Favored : 95.60 % Rotamer: Outliers : 2.12 % Allowed : 14.29 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.19), residues: 2047 helix: 1.06 (0.19), residues: 819 sheet: 0.48 (0.26), residues: 394 loop : -1.03 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 526 TYR 0.008 0.001 TYR A 314 PHE 0.022 0.001 PHE C 315 TRP 0.004 0.001 TRP A 126 HIS 0.006 0.001 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (17294) covalent geometry : angle 0.51543 / 0.28 (23239) hydrogen bonds : bond 0.03506 / 2.26 ( 700) hydrogen bonds : angle 4.55899 / 3.11 ( 1983) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 196 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 LYS cc_start: 0.6799 (mptt) cc_final: 0.6291 (ttpt) REVERT: A 511 ASP cc_start: 0.8046 (m-30) cc_final: 0.7813 (m-30) REVERT: A 530 ASN cc_start: 0.8191 (t0) cc_final: 0.7320 (t0) REVERT: B 106 TYR cc_start: 0.8799 (m-80) cc_final: 0.8353 (m-80) REVERT: B 197 GLN cc_start: 0.8767 (tm-30) cc_final: 0.8304 (tm-30) REVERT: B 211 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7751 (mt-10) REVERT: B 221 LYS cc_start: 0.8977 (mtmm) cc_final: 0.8658 (mppt) REVERT: B 232 MET cc_start: 0.8390 (ppp) cc_final: 0.7859 (ptm) REVERT: B 379 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8158 (tp30) REVERT: C 147 ASN cc_start: 0.8781 (t0) cc_final: 0.8471 (t0) REVERT: C 278 TYR cc_start: 0.7752 (m-80) cc_final: 0.7514 (m-80) REVERT: C 464 GLU cc_start: 0.8213 (pp20) cc_final: 0.7629 (pp20) REVERT: C 465 ILE cc_start: 0.8019 (tp) cc_final: 0.7414 (tp) REVERT: C 476 LYS cc_start: 0.7947 (mmmm) cc_final: 0.7465 (mptt) REVERT: C 491 LYS cc_start: 0.8303 (ttmm) cc_final: 0.7925 (mtpp) REVERT: D 67 LYS cc_start: 0.8211 (mmpt) cc_final: 0.7492 (mtmt) REVERT: D 198 GLN cc_start: 0.7040 (OUTLIER) cc_final: 0.6352 (pm20) REVERT: D 460 GLU cc_start: 0.8195 (tp30) cc_final: 0.7920 (tp30) REVERT: D 526 ARG cc_start: 0.8155 (ttp-170) cc_final: 0.7558 (ttt-90) REVERT: D 564 GLU cc_start: 0.8047 (tp30) cc_final: 0.7770 (tp30) outliers start: 40 outliers final: 35 residues processed: 228 average time/residue: 0.1260 time to fit residues: 41.7327 Evaluate side-chains 229 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 192 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 198 GLN Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 198 GLN Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain D residue 428 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 135 optimal weight: 8.9990 chunk 29 optimal weight: 0.0980 chunk 172 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 190 optimal weight: 0.9980 chunk 187 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 196 ASN C 5 ASN C 56 ASN ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.151652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.111346 restraints weight = 21141.877| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.44 r_work: 0.3076 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17294 Z= 0.122 Angle : 0.507 8.567 23239 Z= 0.271 Chirality : 0.043 0.153 2551 Planarity : 0.003 0.031 2940 Dihedral : 7.307 84.001 2372 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.30 % Favored : 95.65 % Rotamer: Outliers : 1.91 % Allowed : 14.66 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.19), residues: 2047 helix: 1.20 (0.19), residues: 817 sheet: 0.45 (0.26), residues: 401 loop : -1.02 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 485 TYR 0.011 0.001 TYR D 253 PHE 0.020 0.001 PHE C 315 TRP 0.004 0.001 TRP A 126 HIS 0.005 0.001 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (17294) covalent geometry : angle 0.50731 / 0.27 (23239) hydrogen bonds : bond 0.03366 / 2.18 ( 700) hydrogen bonds : angle 4.48189 / 3.06 ( 1983) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 197 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 LYS cc_start: 0.6718 (mptt) cc_final: 0.6202 (ttpt) REVERT: A 511 ASP cc_start: 0.8037 (m-30) cc_final: 0.7809 (m-30) REVERT: A 530 ASN cc_start: 0.8233 (t0) cc_final: 0.7387 (t0) REVERT: B 106 TYR cc_start: 0.8797 (m-80) cc_final: 0.8352 (m-80) REVERT: B 197 GLN cc_start: 0.8803 (tm-30) cc_final: 0.8354 (tm-30) REVERT: B 206 LYS cc_start: 0.8529 (mmtt) cc_final: 0.7442 (mmtt) REVERT: B 208 PHE cc_start: 0.8750 (t80) cc_final: 0.8461 (t80) REVERT: B 210 GLN cc_start: 0.8251 (mt0) cc_final: 0.7850 (mp10) REVERT: B 211 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7743 (mt-10) REVERT: B 221 LYS cc_start: 0.8969 (mtmm) cc_final: 0.8667 (mppt) REVERT: B 232 MET cc_start: 0.8406 (ppp) cc_final: 0.7852 (ptm) REVERT: B 379 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8163 (tp30) REVERT: C 147 ASN cc_start: 0.8789 (t0) cc_final: 0.8499 (t0) REVERT: C 278 TYR cc_start: 0.7768 (m-80) cc_final: 0.7523 (m-80) REVERT: C 464 GLU cc_start: 0.8199 (pp20) cc_final: 0.7603 (pp20) REVERT: C 465 ILE cc_start: 0.7898 (tp) cc_final: 0.7431 (tt) REVERT: C 485 ARG cc_start: 0.8369 (tpp80) cc_final: 0.8125 (tpt170) REVERT: C 491 LYS cc_start: 0.8297 (ttmm) cc_final: 0.7928 (mtpp) REVERT: D 67 LYS cc_start: 0.8218 (mmpt) cc_final: 0.7522 (mtmt) REVERT: D 198 GLN cc_start: 0.6948 (OUTLIER) cc_final: 0.6371 (pm20) REVERT: D 460 GLU cc_start: 0.8221 (tp30) cc_final: 0.7941 (tp30) REVERT: D 526 ARG cc_start: 0.8157 (ttp-170) cc_final: 0.7553 (ttt-90) REVERT: D 564 GLU cc_start: 0.8065 (tp30) cc_final: 0.7790 (tp30) outliers start: 36 outliers final: 32 residues processed: 225 average time/residue: 0.1201 time to fit residues: 39.9997 Evaluate side-chains 226 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 192 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 198 GLN Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 198 GLN Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain D residue 428 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 111 optimal weight: 0.3980 chunk 24 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 193 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 133 optimal weight: 0.4980 chunk 107 optimal weight: 0.0470 chunk 99 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 ASN C 56 ASN ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.153069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.113368 restraints weight = 21038.664| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.32 r_work: 0.3103 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17294 Z= 0.101 Angle : 0.495 8.084 23239 Z= 0.266 Chirality : 0.043 0.174 2551 Planarity : 0.002 0.031 2940 Dihedral : 7.076 81.244 2372 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.91 % Favored : 96.04 % Rotamer: Outliers : 1.64 % Allowed : 15.19 % Favored : 83.17 % 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 are not related in a simple way. whole: 0.36 (0.19), residues: 2047 helix: 1.29 (0.19), residues: 820 sheet: 0.55 (0.26), residues: 398 loop : -0.96 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 526 TYR 0.009 0.001 TYR C 416 PHE 0.018 0.001 PHE C 315 TRP 0.004 0.001 TRP A 126 HIS 0.005 0.001 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (17294) covalent geometry : angle 0.49469 / 0.27 (23239) hydrogen bonds : bond 0.03080 / 1.98 ( 700) hydrogen bonds : angle 4.37874 / 2.99 ( 1983) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 200 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 LYS cc_start: 0.6674 (mptt) cc_final: 0.6197 (ttpt) REVERT: A 511 ASP cc_start: 0.7969 (m-30) cc_final: 0.7739 (m-30) REVERT: A 530 ASN cc_start: 0.8258 (t0) cc_final: 0.7413 (t0) REVERT: B 106 TYR cc_start: 0.8796 (m-80) cc_final: 0.8375 (m-80) REVERT: B 197 GLN cc_start: 0.8795 (tm-30) cc_final: 0.8340 (tm-30) REVERT: B 206 LYS cc_start: 0.8500 (mmtt) cc_final: 0.7432 (mmtt) REVERT: B 208 PHE cc_start: 0.8625 (t80) cc_final: 0.8302 (t80) REVERT: B 210 GLN cc_start: 0.8278 (mt0) cc_final: 0.7850 (mp10) REVERT: B 211 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7721 (mt-10) REVERT: B 221 LYS cc_start: 0.8969 (mtmm) cc_final: 0.8670 (mppt) REVERT: B 232 MET cc_start: 0.8404 (ppp) cc_final: 0.7899 (ptm) REVERT: C 147 ASN cc_start: 0.8773 (t0) cc_final: 0.8493 (t0) REVERT: C 278 TYR cc_start: 0.7739 (m-80) cc_final: 0.7519 (m-80) REVERT: C 464 GLU cc_start: 0.8139 (pp20) cc_final: 0.7539 (pp20) REVERT: C 465 ILE cc_start: 0.7878 (tp) cc_final: 0.7357 (tt) REVERT: C 485 ARG cc_start: 0.8345 (tpp80) cc_final: 0.8078 (tpt170) REVERT: C 491 LYS cc_start: 0.8289 (ttmm) cc_final: 0.7920 (mtpp) REVERT: D 67 LYS cc_start: 0.8224 (mmpt) cc_final: 0.7522 (mtmt) REVERT: D 460 GLU cc_start: 0.8228 (tp30) cc_final: 0.7958 (tp30) REVERT: D 526 ARG cc_start: 0.8172 (ttp-170) cc_final: 0.7461 (ttt-90) REVERT: D 564 GLU cc_start: 0.8017 (tp30) cc_final: 0.7753 (tp30) outliers start: 31 outliers final: 29 residues processed: 223 average time/residue: 0.1367 time to fit residues: 44.3067 Evaluate side-chains 221 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 198 GLN Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain D residue 428 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 133 optimal weight: 2.9990 chunk 29 optimal weight: 0.0000 chunk 134 optimal weight: 0.9980 chunk 179 optimal weight: 0.0170 chunk 83 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 156 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 overall best weight: 0.5022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 ASN C 56 ASN ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.153412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.113663 restraints weight = 21049.825| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.49 r_work: 0.3104 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17294 Z= 0.102 Angle : 0.496 8.498 23239 Z= 0.265 Chirality : 0.043 0.150 2551 Planarity : 0.002 0.032 2940 Dihedral : 6.939 81.004 2372 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.20 % Favored : 95.75 % Rotamer: Outliers : 1.69 % Allowed : 15.25 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.19), residues: 2047 helix: 1.41 (0.19), residues: 819 sheet: 0.59 (0.26), residues: 398 loop : -0.95 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 526 TYR 0.009 0.001 TYR A 267 PHE 0.018 0.001 PHE C 315 TRP 0.004 0.001 TRP A 126 HIS 0.005 0.001 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (17294) covalent geometry : angle 0.49624 / 0.27 (23239) hydrogen bonds : bond 0.03050 / 1.96 ( 700) hydrogen bonds : angle 4.32649 / 2.95 ( 1983) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4336.59 seconds wall clock time: 74 minutes 58.32 seconds (4498.32 seconds total)