Starting phenix.real_space_refine on Tue Jan 21 15:23:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x5i_38070/01_2025/8x5i_38070.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x5i_38070/01_2025/8x5i_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8x5i_38070/01_2025/8x5i_38070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x5i_38070/01_2025/8x5i_38070.map" model { file = "/net/cci-nas-00/data/ceres_data/8x5i_38070/01_2025/8x5i_38070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x5i_38070/01_2025/8x5i_38070.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 10.38, per 1000 atoms: 0.61 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: 3.95 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.11 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: 6.19 Time building geometry restraints manager: 4.63 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 578 or resid 601 throug \ h 602)) selection = (chain 'B' and (resid 1 through 156 or resid 261 through 578 or resid 601 throug \ h 602)) selection = chain 'C' selection = (chain 'D' and (resid 1 through 156 or resid 261 through 578 or resid 601 throug \ h 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: 2.940 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: 0.640 Check model and map are aligned: 0.130 Set scattering table: 0.140 Process input model: 38.970 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.090 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 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= 0.431 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.004 0.001 TRP D 126 HIS 0.012 0.002 HIS C 320 PHE 0.038 0.003 PHE C 315 TYR 0.021 0.002 TYR B 272 ARG 0.007 0.001 ARG C 51 *********************** 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 : 2.045 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 211 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7600 (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 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: 0.7733 (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: 0.7377 (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: 0.7266 (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: 0.3661 time to fit residues: 172.5811 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 : 2.202 ------------------------------------------------------------------------------- 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 172 optimal weight: 0.9990 chunk 154 optimal weight: 0.8980 chunk 85 optimal weight: 0.0170 chunk 52 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 159 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 119 optimal weight: 0.6980 chunk 185 optimal weight: 0.6980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN B 186 ASN B 455 ASN C 5 ASN C 13 ASN C 56 ASN C 320 HIS C 563 HIS D 186 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.157698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.114669 restraints weight = 20960.041| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.37 r_work: 0.3139 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1728 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= 0.157 Angle : 0.508 8.289 23239 Z= 0.279 Chirality : 0.043 0.162 2551 Planarity : 0.003 0.038 2940 Dihedral : 8.608 85.050 2378 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.52 % Favored : 96.43 % Rotamer: Outliers : 1.01 % Allowed : 6.88 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.16), residues: 2047 helix: -1.27 (0.15), residues: 814 sheet: 0.65 (0.26), residues: 386 loop : -1.67 (0.19), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 126 HIS 0.012 0.001 HIS A 535 PHE 0.021 0.001 PHE C 315 TYR 0.014 0.001 TYR B 272 ARG 0.005 0.000 ARG D 139 *********************** 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 261 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 242 time to evaluate : 2.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8390 (mtpt) REVERT: A 530 ASN cc_start: 0.7832 (t0) cc_final: 0.7609 (t0) REVERT: B 197 GLN cc_start: 0.8528 (tm-30) cc_final: 0.8026 (tm-30) REVERT: B 211 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7761 (mt-10) REVERT: B 221 LYS cc_start: 0.8954 (mtmm) cc_final: 0.8553 (mppt) REVERT: B 232 MET cc_start: 0.8329 (ppp) cc_final: 0.8072 (ptm) REVERT: B 446 GLU cc_start: 0.8229 (tt0) cc_final: 0.8012 (tt0) REVERT: C 94 LYS cc_start: 0.8472 (ttpp) cc_final: 0.7684 (tppt) REVERT: C 278 TYR cc_start: 0.7714 (m-80) cc_final: 0.7465 (m-80) REVERT: C 464 GLU cc_start: 0.8103 (pp20) cc_final: 0.7382 (pp20) REVERT: C 480 GLU cc_start: 0.7588 (pm20) cc_final: 0.7192 (pm20) REVERT: D 30 MET cc_start: 0.8416 (mmt) cc_final: 0.8145 (tpt) REVERT: D 67 LYS cc_start: 0.8192 (mmpt) cc_final: 0.7457 (mtmm) REVERT: D 87 LYS cc_start: 0.8474 (mttt) cc_final: 0.8217 (mtmt) REVERT: D 279 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8181 (tm-30) REVERT: D 280 ASP cc_start: 0.7855 (m-30) cc_final: 0.7610 (m-30) REVERT: D 526 ARG cc_start: 0.8114 (ttp-170) cc_final: 0.7649 (ttp-170) REVERT: D 545 MET cc_start: 0.8592 (tpp) cc_final: 0.8300 (tpp) REVERT: D 564 GLU cc_start: 0.8003 (tp30) cc_final: 0.7803 (tp30) outliers start: 19 outliers final: 11 residues processed: 256 average time/residue: 0.3699 time to fit residues: 134.7592 Evaluate side-chains 207 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 195 time to evaluate : 2.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS 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 B residue 148 VAL Chi-restraints excluded: chain B residue 186 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 148 VAL 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 16 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 135 optimal weight: 0.3980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 147 ASN B 178 ASN B 209 GLN C 56 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.154162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.111495 restraints weight = 21017.156| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.33 r_work: 0.3101 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2141 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= 0.195 Angle : 0.504 6.767 23239 Z= 0.274 Chirality : 0.043 0.163 2551 Planarity : 0.003 0.029 2940 Dihedral : 8.016 83.892 2372 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.71 % Favored : 96.24 % Rotamer: Outliers : 1.32 % Allowed : 9.37 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.18), residues: 2047 helix: 0.02 (0.18), residues: 822 sheet: 0.66 (0.26), residues: 392 loop : -1.40 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 126 HIS 0.006 0.001 HIS A 535 PHE 0.024 0.001 PHE C 315 TYR 0.012 0.001 TYR B 272 ARG 0.003 0.000 ARG A 481 *********************** 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 234 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 209 time to evaluate : 2.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 530 ASN cc_start: 0.7874 (t0) cc_final: 0.7122 (t0) REVERT: B 129 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7541 (mp0) REVERT: B 197 GLN cc_start: 0.8620 (tm-30) cc_final: 0.8045 (tm-30) REVERT: B 211 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7900 (mt-10) REVERT: B 221 LYS cc_start: 0.8935 (mtmm) cc_final: 0.8722 (mppt) REVERT: B 232 MET cc_start: 0.8381 (ppp) cc_final: 0.8074 (ptm) REVERT: C 94 LYS cc_start: 0.8642 (ttpp) cc_final: 0.7810 (tppt) REVERT: C 278 TYR cc_start: 0.7763 (m-80) cc_final: 0.7542 (m-80) REVERT: C 464 GLU cc_start: 0.8166 (pp20) cc_final: 0.7486 (pp20) REVERT: D 30 MET cc_start: 0.8481 (mmt) cc_final: 0.8224 (tpt) REVERT: D 67 LYS cc_start: 0.8261 (mmpt) cc_final: 0.7424 (mtmm) REVERT: D 87 LYS cc_start: 0.8476 (mttt) cc_final: 0.8181 (mtmt) REVERT: D 526 ARG cc_start: 0.8186 (ttp-170) cc_final: 0.7612 (ttt-90) REVERT: D 564 GLU cc_start: 0.8023 (tp30) cc_final: 0.7752 (tp30) outliers start: 25 outliers final: 18 residues processed: 227 average time/residue: 0.3724 time to fit residues: 120.1863 Evaluate side-chains 217 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 199 time to evaluate : 2.019 ------------------------------------------------------------------------------- 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 548 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue 77 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 66 SER Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 161 ASP 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 6 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 192 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 163 optimal weight: 0.6980 chunk 175 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 153 optimal weight: 0.1980 chunk 195 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.154617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.114371 restraints weight = 20888.136| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.30 r_work: 0.3123 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17294 Z= 0.157 Angle : 0.467 6.796 23239 Z= 0.256 Chirality : 0.043 0.157 2551 Planarity : 0.002 0.028 2940 Dihedral : 7.536 89.509 2372 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.52 % Favored : 96.43 % Rotamer: Outliers : 1.43 % Allowed : 10.69 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.18), residues: 2047 helix: 0.69 (0.18), residues: 817 sheet: 0.69 (0.27), residues: 391 loop : -1.17 (0.20), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 126 HIS 0.007 0.001 HIS A 535 PHE 0.021 0.001 PHE C 315 TYR 0.011 0.001 TYR B 272 ARG 0.004 0.000 ARG C 526 *********************** 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 238 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 211 time to evaluate : 2.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 LYS cc_start: 0.7478 (pptt) cc_final: 0.7112 (ptpp) REVERT: A 530 ASN cc_start: 0.7939 (t0) cc_final: 0.7212 (t0) REVERT: B 197 GLN cc_start: 0.8696 (tm-30) cc_final: 0.8277 (tm-30) REVERT: B 209 GLN cc_start: 0.7937 (mm110) cc_final: 0.7734 (mm110) REVERT: B 211 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7913 (mt-10) REVERT: B 217 ARG cc_start: 0.8299 (mtp85) cc_final: 0.7978 (mtp85) REVERT: B 221 LYS cc_start: 0.8961 (mtmm) cc_final: 0.8686 (mppt) REVERT: B 227 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7827 (mm-30) REVERT: B 232 MET cc_start: 0.8357 (ppp) cc_final: 0.8054 (ptm) REVERT: C 94 LYS cc_start: 0.8744 (ttpp) cc_final: 0.7931 (tppt) REVERT: C 464 GLU cc_start: 0.8130 (pp20) cc_final: 0.7460 (pp20) REVERT: C 485 ARG cc_start: 0.8430 (tpp80) cc_final: 0.8120 (tpt170) REVERT: C 491 LYS cc_start: 0.8328 (ttmm) cc_final: 0.7911 (mtpp) REVERT: D 30 MET cc_start: 0.8465 (mmt) cc_final: 0.8209 (tpt) REVERT: D 67 LYS cc_start: 0.8262 (mmpt) cc_final: 0.7567 (mtmt) REVERT: D 87 LYS cc_start: 0.8440 (mttt) cc_final: 0.8165 (mtmt) REVERT: D 246 LYS cc_start: 0.8247 (mtpt) cc_final: 0.7818 (mtmt) REVERT: D 526 ARG cc_start: 0.8196 (ttp-170) cc_final: 0.7631 (ttt-90) REVERT: D 564 GLU cc_start: 0.8007 (tp30) cc_final: 0.7723 (tp30) outliers start: 27 outliers final: 21 residues processed: 231 average time/residue: 0.3620 time to fit residues: 119.0516 Evaluate side-chains 217 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 195 time to evaluate : 1.909 ------------------------------------------------------------------------------- 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 548 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 148 VAL 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 549 VAL Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 77 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 418 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 46 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 56 optimal weight: 0.0070 chunk 59 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 201 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 ASN C 551 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.154293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.113045 restraints weight = 21185.079| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.56 r_work: 0.3104 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17294 Z= 0.160 Angle : 0.469 6.947 23239 Z= 0.256 Chirality : 0.042 0.154 2551 Planarity : 0.002 0.028 2940 Dihedral : 7.315 86.922 2372 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.91 % Favored : 96.04 % Rotamer: Outliers : 1.80 % Allowed : 11.75 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.19), residues: 2047 helix: 1.01 (0.19), residues: 818 sheet: 0.73 (0.26), residues: 390 loop : -1.08 (0.20), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 126 HIS 0.007 0.001 HIS A 535 PHE 0.019 0.001 PHE C 315 TYR 0.010 0.001 TYR B 272 ARG 0.004 0.000 ARG C 526 *********************** 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 246 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 212 time to evaluate : 1.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 ASN cc_start: 0.7952 (t0) cc_final: 0.7189 (t0) REVERT: B 197 GLN cc_start: 0.8820 (tm-30) cc_final: 0.8444 (tm-30) REVERT: B 206 LYS cc_start: 0.8374 (mmtt) cc_final: 0.8144 (mmtt) REVERT: B 211 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7823 (mt-10) REVERT: B 217 ARG cc_start: 0.8291 (mtp85) cc_final: 0.8022 (mtp85) REVERT: B 221 LYS cc_start: 0.8934 (mtmm) cc_final: 0.8648 (mppt) REVERT: B 227 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7876 (mm-30) REVERT: B 232 MET cc_start: 0.8393 (ppp) cc_final: 0.8030 (ptm) REVERT: B 494 LYS cc_start: 0.8192 (ttpp) cc_final: 0.7819 (pttm) REVERT: C 77 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7240 (mt) REVERT: C 464 GLU cc_start: 0.8147 (pp20) cc_final: 0.7498 (pp20) REVERT: C 491 LYS cc_start: 0.8314 (ttmm) cc_final: 0.7921 (mtpp) REVERT: D 30 MET cc_start: 0.8499 (mmt) cc_final: 0.8234 (tpt) REVERT: D 67 LYS cc_start: 0.8268 (mmpt) cc_final: 0.7570 (mtmt) REVERT: D 87 LYS cc_start: 0.8474 (mttt) cc_final: 0.8210 (mtmt) REVERT: D 246 LYS cc_start: 0.8229 (mtpt) cc_final: 0.7760 (mtmt) REVERT: D 526 ARG cc_start: 0.8222 (ttp-170) cc_final: 0.7657 (ttt-90) REVERT: D 564 GLU cc_start: 0.8085 (tp30) cc_final: 0.7798 (tp30) outliers start: 34 outliers final: 23 residues processed: 236 average time/residue: 0.3590 time to fit residues: 120.4900 Evaluate side-chains 214 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 2.237 ------------------------------------------------------------------------------- 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 343 VAL 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 211 GLU 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 66 SER Chi-restraints excluded: chain C residue 77 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 23 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 166 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 189 optimal weight: 0.9990 chunk 197 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 5 ASN C 56 ASN D 198 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.149505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.108574 restraints weight = 21201.571| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.58 r_work: 0.3039 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2757 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= 0.362 Angle : 0.600 7.245 23239 Z= 0.316 Chirality : 0.046 0.166 2551 Planarity : 0.003 0.035 2940 Dihedral : 7.910 82.298 2372 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.93 % Favored : 95.02 % Rotamer: Outliers : 2.01 % Allowed : 13.08 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.19), residues: 2047 helix: 0.95 (0.19), residues: 809 sheet: 0.52 (0.26), residues: 394 loop : -1.05 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 126 HIS 0.005 0.001 HIS C 415 PHE 0.028 0.002 PHE C 315 TYR 0.012 0.002 TYR A 517 ARG 0.004 0.000 ARG C 526 *********************** 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 232 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 194 time to evaluate : 2.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 ASN cc_start: 0.8050 (t0) cc_final: 0.7230 (t0) REVERT: B 106 TYR cc_start: 0.8815 (m-80) cc_final: 0.8332 (m-80) REVERT: B 197 GLN cc_start: 0.8819 (tm-30) cc_final: 0.8460 (tm-30) REVERT: B 211 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7788 (mt-10) REVERT: B 217 ARG cc_start: 0.8331 (mtp85) cc_final: 0.8071 (mtp85) REVERT: B 221 LYS cc_start: 0.8929 (mtmm) cc_final: 0.8630 (mppt) REVERT: B 232 MET cc_start: 0.8359 (ppp) cc_final: 0.8046 (ptm) REVERT: B 379 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8210 (tp30) REVERT: B 494 LYS cc_start: 0.8386 (ttpp) cc_final: 0.7979 (pttm) REVERT: C 464 GLU cc_start: 0.8233 (pp20) cc_final: 0.7568 (pp20) REVERT: C 491 LYS cc_start: 0.8325 (ttmm) cc_final: 0.7936 (mtpp) REVERT: D 67 LYS cc_start: 0.8265 (mmpt) cc_final: 0.7522 (mtmt) REVERT: D 198 GLN cc_start: 0.7137 (OUTLIER) cc_final: 0.6215 (pm20) REVERT: D 526 ARG cc_start: 0.8220 (ttp-170) cc_final: 0.7521 (ttt-90) REVERT: D 545 MET cc_start: 0.8707 (tpp) cc_final: 0.8472 (tpp) REVERT: D 564 GLU cc_start: 0.8114 (tp30) cc_final: 0.7810 (tp30) outliers start: 38 outliers final: 26 residues processed: 222 average time/residue: 0.3520 time to fit residues: 112.8753 Evaluate side-chains 217 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 189 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE 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 555 LYS 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 549 VAL Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 311 THR 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 418 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 134 optimal weight: 2.9990 chunk 192 optimal weight: 0.3980 chunk 177 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 92 optimal weight: 5.9990 chunk 176 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN C 5 ASN C 56 ASN D 198 GLN D 538 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.152370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.112276 restraints weight = 21007.528| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.57 r_work: 0.3093 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2797 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= 0.181 Angle : 0.496 7.191 23239 Z= 0.268 Chirality : 0.043 0.153 2551 Planarity : 0.003 0.033 2940 Dihedral : 7.448 88.341 2372 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.96 % Favored : 95.99 % Rotamer: Outliers : 1.91 % Allowed : 13.34 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.19), residues: 2047 helix: 1.16 (0.19), residues: 813 sheet: 0.50 (0.26), residues: 397 loop : -1.00 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 126 HIS 0.004 0.001 HIS C 415 PHE 0.020 0.001 PHE C 315 TYR 0.008 0.001 TYR A 517 ARG 0.004 0.000 ARG C 526 *********************** 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 237 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 201 time to evaluate : 2.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 LYS cc_start: 0.7430 (OUTLIER) cc_final: 0.6964 (ptpp) REVERT: A 530 ASN cc_start: 0.8039 (t0) cc_final: 0.7310 (t0) REVERT: B 106 TYR cc_start: 0.8784 (m-80) cc_final: 0.8361 (m-80) REVERT: B 197 GLN cc_start: 0.8840 (tm-30) cc_final: 0.8504 (tm-30) REVERT: B 211 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7794 (mt-10) REVERT: B 217 ARG cc_start: 0.8304 (mtp85) cc_final: 0.8075 (mtp85) REVERT: B 221 LYS cc_start: 0.8923 (mtmm) cc_final: 0.8637 (mppt) REVERT: B 232 MET cc_start: 0.8353 (ppp) cc_final: 0.8037 (ptm) REVERT: B 379 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8115 (tp30) REVERT: B 494 LYS cc_start: 0.8205 (ttpp) cc_final: 0.7822 (pttm) REVERT: C 464 GLU cc_start: 0.8239 (pp20) cc_final: 0.7601 (pp20) REVERT: C 485 ARG cc_start: 0.8425 (tpp80) cc_final: 0.8075 (tpt170) REVERT: C 491 LYS cc_start: 0.8280 (ttmm) cc_final: 0.7911 (mtpp) REVERT: D 30 MET cc_start: 0.8490 (mmt) cc_final: 0.8203 (tpt) REVERT: D 67 LYS cc_start: 0.8236 (mmpt) cc_final: 0.7492 (mtmt) REVERT: D 87 LYS cc_start: 0.8431 (mttt) cc_final: 0.8229 (mttp) REVERT: D 198 GLN cc_start: 0.6902 (OUTLIER) cc_final: 0.6420 (pm20) REVERT: D 526 ARG cc_start: 0.8207 (ttp-170) cc_final: 0.7505 (ttt-90) REVERT: D 545 MET cc_start: 0.8616 (tpp) cc_final: 0.8389 (tpp) REVERT: D 564 GLU cc_start: 0.8072 (tp30) cc_final: 0.7771 (tp30) outliers start: 36 outliers final: 28 residues processed: 226 average time/residue: 0.3560 time to fit residues: 114.2337 Evaluate side-chains 221 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE 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 477 LYS Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 198 GLN Chi-restraints excluded: chain B residue 209 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 287 ILE Chi-restraints excluded: chain C residue 311 THR 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 418 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 13 optimal weight: 0.0570 chunk 4 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 154 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 5 ASN C 56 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.150929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.109956 restraints weight = 20913.186| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.62 r_work: 0.3066 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17294 Z= 0.241 Angle : 0.534 7.366 23239 Z= 0.285 Chirality : 0.044 0.159 2551 Planarity : 0.003 0.032 2940 Dihedral : 7.495 89.383 2372 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.64 % Favored : 95.31 % Rotamer: Outliers : 1.85 % Allowed : 14.13 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.19), residues: 2047 helix: 1.19 (0.19), residues: 811 sheet: 0.44 (0.26), residues: 399 loop : -1.01 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 126 HIS 0.005 0.001 HIS D 415 PHE 0.023 0.001 PHE C 315 TYR 0.028 0.001 TYR D 253 ARG 0.005 0.000 ARG C 526 *********************** 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 230 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 195 time to evaluate : 1.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.6951 (pptt) REVERT: A 530 ASN cc_start: 0.8170 (t0) cc_final: 0.7290 (t0) REVERT: B 106 TYR cc_start: 0.8799 (m-80) cc_final: 0.8348 (m-80) REVERT: B 197 GLN cc_start: 0.8859 (tm-30) cc_final: 0.8528 (tm-30) REVERT: B 206 LYS cc_start: 0.8491 (mmtt) cc_final: 0.7605 (mmtt) REVERT: B 210 GLN cc_start: 0.8249 (mt0) cc_final: 0.7920 (mp10) REVERT: B 211 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7815 (mt-10) REVERT: B 217 ARG cc_start: 0.8322 (mtp85) cc_final: 0.8113 (mtp85) REVERT: B 221 LYS cc_start: 0.8919 (mtmm) cc_final: 0.8632 (mppt) REVERT: B 232 MET cc_start: 0.8225 (ppp) cc_final: 0.7936 (ptm) REVERT: B 379 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8143 (tp30) REVERT: B 494 LYS cc_start: 0.8265 (ttpp) cc_final: 0.7851 (pttm) REVERT: C 464 GLU cc_start: 0.8262 (pp20) cc_final: 0.7553 (pp20) REVERT: C 491 LYS cc_start: 0.8307 (ttmm) cc_final: 0.7942 (mtpp) REVERT: D 67 LYS cc_start: 0.8303 (mmpt) cc_final: 0.7528 (mtmt) REVERT: D 526 ARG cc_start: 0.8200 (ttp-170) cc_final: 0.7482 (ttt-90) REVERT: D 545 MET cc_start: 0.8654 (tpp) cc_final: 0.8385 (tpp) REVERT: D 564 GLU cc_start: 0.8101 (tp30) cc_final: 0.7801 (tp30) outliers start: 35 outliers final: 30 residues processed: 221 average time/residue: 0.3527 time to fit residues: 111.8833 Evaluate side-chains 221 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 189 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE 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 477 LYS Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 198 GLN Chi-restraints excluded: chain B residue 209 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 287 ILE Chi-restraints excluded: chain C residue 311 THR 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 418 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 58 optimal weight: 0.3980 chunk 49 optimal weight: 0.9980 chunk 171 optimal weight: 7.9990 chunk 115 optimal weight: 0.0870 chunk 175 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 162 optimal weight: 0.1980 chunk 84 optimal weight: 2.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 210 GLN C 5 ASN C 56 ASN C 147 ASN D 544 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.155454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.113995 restraints weight = 21033.762| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.47 r_work: 0.3118 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17294 Z= 0.133 Angle : 0.484 8.462 23239 Z= 0.260 Chirality : 0.042 0.152 2551 Planarity : 0.002 0.034 2940 Dihedral : 7.008 78.380 2372 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.71 % Favored : 96.24 % Rotamer: Outliers : 1.69 % Allowed : 14.29 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.19), residues: 2047 helix: 1.35 (0.19), residues: 818 sheet: 0.63 (0.26), residues: 394 loop : -0.94 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 126 HIS 0.004 0.001 HIS A 535 PHE 0.018 0.001 PHE C 315 TYR 0.020 0.001 TYR D 253 ARG 0.005 0.000 ARG C 526 *********************** 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 232 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 200 time to evaluate : 1.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 LYS cc_start: 0.7327 (OUTLIER) cc_final: 0.6728 (pptt) REVERT: A 530 ASN cc_start: 0.8154 (t0) cc_final: 0.7288 (t0) REVERT: B 197 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8562 (tm-30) REVERT: B 221 LYS cc_start: 0.8917 (mtmm) cc_final: 0.8637 (mppt) REVERT: B 494 LYS cc_start: 0.8135 (ttpp) cc_final: 0.7769 (pttm) REVERT: C 464 GLU cc_start: 0.8183 (pp20) cc_final: 0.7606 (pp20) REVERT: C 485 ARG cc_start: 0.8449 (tpp80) cc_final: 0.8162 (tpp-160) REVERT: C 491 LYS cc_start: 0.8301 (ttmm) cc_final: 0.7920 (mtpp) REVERT: D 30 MET cc_start: 0.8583 (mmt) cc_final: 0.8254 (tpt) REVERT: D 67 LYS cc_start: 0.8301 (mmpt) cc_final: 0.7589 (mtmt) REVERT: D 246 LYS cc_start: 0.8125 (mtpt) cc_final: 0.7672 (mtmt) REVERT: D 526 ARG cc_start: 0.8182 (ttp-170) cc_final: 0.7520 (ttt-90) REVERT: D 564 GLU cc_start: 0.8034 (tp30) cc_final: 0.7739 (tp30) outliers start: 32 outliers final: 27 residues processed: 222 average time/residue: 0.3557 time to fit residues: 112.9755 Evaluate side-chains 213 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 2.066 ------------------------------------------------------------------------------- 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 477 LYS 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 209 GLN Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 397 GLU 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 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 428 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 198 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 159 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 210 GLN C 5 ASN C 13 ASN C 56 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.151890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.112136 restraints weight = 21157.456| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.40 r_work: 0.3048 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17294 Z= 0.275 Angle : 0.569 9.110 23239 Z= 0.300 Chirality : 0.045 0.155 2551 Planarity : 0.003 0.033 2940 Dihedral : 7.341 86.658 2372 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.08 % Favored : 94.87 % Rotamer: Outliers : 1.80 % Allowed : 14.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.19), residues: 2047 helix: 1.27 (0.19), residues: 814 sheet: 0.48 (0.26), residues: 396 loop : -0.95 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 126 HIS 0.006 0.001 HIS D 415 PHE 0.024 0.001 PHE C 315 TYR 0.028 0.001 TYR D 253 ARG 0.006 0.000 ARG C 526 ********************** 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 225 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 191 time to evaluate : 2.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.6809 (pptt) REVERT: A 530 ASN cc_start: 0.8187 (t0) cc_final: 0.7337 (t0) REVERT: B 106 TYR cc_start: 0.8784 (m-80) cc_final: 0.8351 (m-80) REVERT: B 197 GLN cc_start: 0.8848 (tm-30) cc_final: 0.8543 (tm-30) REVERT: B 221 LYS cc_start: 0.8913 (mtmm) cc_final: 0.8661 (mppt) REVERT: B 494 LYS cc_start: 0.8318 (ttpp) cc_final: 0.7906 (pttm) REVERT: C 464 GLU cc_start: 0.8115 (pp20) cc_final: 0.7645 (pp20) REVERT: C 485 ARG cc_start: 0.8506 (tpp80) cc_final: 0.8194 (tpp-160) REVERT: C 491 LYS cc_start: 0.8300 (ttmm) cc_final: 0.7933 (mtpp) REVERT: D 67 LYS cc_start: 0.8314 (mmpt) cc_final: 0.7583 (mtmt) REVERT: D 246 LYS cc_start: 0.8152 (mtpt) cc_final: 0.7700 (mtmt) REVERT: D 526 ARG cc_start: 0.8211 (ttp-170) cc_final: 0.7505 (ttt-90) REVERT: D 564 GLU cc_start: 0.8060 (tp30) cc_final: 0.7766 (tp30) outliers start: 34 outliers final: 29 residues processed: 214 average time/residue: 0.3552 time to fit residues: 109.4933 Evaluate side-chains 219 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 2.060 ------------------------------------------------------------------------------- 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 477 LYS 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 209 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 549 VAL Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 311 THR 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 40 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 95 optimal weight: 0.4980 chunk 107 optimal weight: 0.9980 chunk 195 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN C 5 ASN C 56 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.152430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.112533 restraints weight = 21163.542| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.51 r_work: 0.3105 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17294 Z= 0.191 Angle : 0.542 12.938 23239 Z= 0.285 Chirality : 0.043 0.152 2551 Planarity : 0.003 0.033 2940 Dihedral : 7.165 81.664 2372 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.25 % Favored : 95.70 % Rotamer: Outliers : 1.80 % Allowed : 14.88 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.19), residues: 2047 helix: 1.28 (0.19), residues: 818 sheet: 0.48 (0.26), residues: 397 loop : -0.93 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 126 HIS 0.005 0.001 HIS A 535 PHE 0.021 0.001 PHE C 315 TYR 0.024 0.001 TYR D 253 ARG 0.006 0.000 ARG C 526 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9895.72 seconds wall clock time: 176 minutes 22.10 seconds (10582.10 seconds total)