Starting phenix.real_space_refine on Tue Nov 18 20:14:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x5i_38070/11_2025/8x5i_38070.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x5i_38070/11_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_38070/11_2025/8x5i_38070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x5i_38070/11_2025/8x5i_38070.map" model { file = "/net/cci-nas-00/data/ceres_data/8x5i_38070/11_2025/8x5i_38070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x5i_38070/11_2025/8x5i_38070.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 55 5.16 5 C 10851 2.51 5 N 2808 2.21 5 O 3276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17006 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3904 Classifications: {'peptide': 477} Link IDs: {'PTRANS': 8, 'TRANS': 468} Chain breaks: 1 Chain: "B" Number of atoms: 4537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4537 Classifications: {'peptide': 555} Link IDs: {'PTRANS': 8, 'TRANS': 546} Chain breaks: 1 Chain: "C" Number of atoms: 3888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3888 Classifications: {'peptide': 474} Link IDs: {'PTRANS': 8, 'TRANS': 465} Chain breaks: 1 Chain: "D" Number of atoms: 4549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4549 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 10, 'TRANS': 546} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.84, per 1000 atoms: 0.28 Number of scatterers: 17006 At special positions: 0 Unit cell: (87.36, 112.56, 193.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 55 16.00 P 12 15.00 Mg 4 11.99 O 3276 8.00 N 2808 7.00 C 10851 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 736.3 milliseconds 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3896 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 20 sheets defined 45.2% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 34 through 46 removed outlier: 3.573A pdb=" N LEU A 39 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 removed outlier: 3.529A pdb=" N ARG A 51 " --> pdb=" O ASP A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 64 removed outlier: 3.635A pdb=" N HIS A 63 " --> pdb=" O TYR A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 94 removed outlier: 4.102A pdb=" N LYS A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 98 through 102 Processing helix chain 'A' and resid 143 through 147 removed outlier: 3.525A pdb=" N ASN A 147 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 277 Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.533A pdb=" N GLN A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.920A pdb=" N TYR A 326 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 370 removed outlier: 3.674A pdb=" N SER A 368 " --> pdb=" O LYS A 364 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 394 removed outlier: 3.604A pdb=" N LYS A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 423 removed outlier: 3.643A pdb=" N LEU A 423 " --> pdb=" O THR A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 458 Processing helix chain 'A' and resid 475 through 493 removed outlier: 3.943A pdb=" N LYS A 479 " --> pdb=" O GLY A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 503 removed outlier: 3.610A pdb=" N GLU A 503 " --> pdb=" O GLU A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 529 removed outlier: 3.933A pdb=" N ASP A 515 " --> pdb=" O ASP A 511 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A 519 " --> pdb=" O ASP A 515 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLU A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N SER A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 538 removed outlier: 3.755A pdb=" N GLN A 538 " --> pdb=" O VAL A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 550 removed outlier: 3.507A pdb=" N MET A 545 " --> pdb=" O LYS A 541 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 562 Processing helix chain 'A' and resid 566 through 574 removed outlier: 4.186A pdb=" N LYS A 570 " --> pdb=" O PHE A 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 47 removed outlier: 3.835A pdb=" N LEU B 42 " --> pdb=" O PHE B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 52 Processing helix chain 'B' and resid 60 through 64 removed outlier: 3.651A pdb=" N HIS B 63 " --> pdb=" O TYR B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 91 removed outlier: 4.121A pdb=" N LYS B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 97 removed outlier: 4.287A pdb=" N ARG B 97 " --> pdb=" O LYS B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 177 removed outlier: 4.394A pdb=" N LEU B 163 " --> pdb=" O ASP B 159 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN B 166 " --> pdb=" O LYS B 162 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS B 169 " --> pdb=" O ALA B 165 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N PHE B 172 " --> pdb=" O LYS B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 194 Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.824A pdb=" N PHE B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THR B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 277 removed outlier: 3.628A pdb=" N SER B 268 " --> pdb=" O MET B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 281 removed outlier: 3.529A pdb=" N LYS B 281 " --> pdb=" O TYR B 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 278 through 281' Processing helix chain 'B' and resid 295 through 308 Processing helix chain 'B' and resid 321 through 326 removed outlier: 3.699A pdb=" N LEU B 324 " --> pdb=" O SER B 321 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR B 326 " --> pdb=" O GLU B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 357 No H-bonds generated for 'chain 'B' and resid 355 through 357' Processing helix chain 'B' and resid 358 through 370 removed outlier: 4.610A pdb=" N SER B 368 " --> pdb=" O LYS B 364 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA B 369 " --> pdb=" O ALA B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 394 removed outlier: 3.612A pdb=" N LYS B 384 " --> pdb=" O GLY B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 402 removed outlier: 3.548A pdb=" N ASN B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY B 402 " --> pdb=" O TYR B 398 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 397 through 402' Processing helix chain 'B' and resid 412 through 423 removed outlier: 4.027A pdb=" N TYR B 416 " --> pdb=" O TYR B 412 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 423 " --> pdb=" O THR B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 457 removed outlier: 3.719A pdb=" N LEU B 457 " --> pdb=" O CYS B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 493 removed outlier: 3.639A pdb=" N GLU B 480 " --> pdb=" O LYS B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 503 Processing helix chain 'B' and resid 511 through 529 removed outlier: 3.884A pdb=" N ASP B 515 " --> pdb=" O ASP B 511 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N GLU B 522 " --> pdb=" O SER B 518 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N SER B 523 " --> pdb=" O ALA B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 538 removed outlier: 3.599A pdb=" N TYR B 536 " --> pdb=" O ASP B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 550 removed outlier: 3.518A pdb=" N GLU B 547 " --> pdb=" O PHE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 562 removed outlier: 3.595A pdb=" N CYS B 557 " --> pdb=" O SER B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 574 removed outlier: 4.165A pdb=" N LYS B 570 " --> pdb=" O PHE B 566 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY B 574 " --> pdb=" O LYS B 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 47 removed outlier: 3.519A pdb=" N LEU C 42 " --> pdb=" O PHE C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 52 Processing helix chain 'C' and resid 60 through 64 removed outlier: 3.684A pdb=" N HIS C 63 " --> pdb=" O TYR C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 94 removed outlier: 4.305A pdb=" N LYS C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 278 removed outlier: 3.661A pdb=" N TYR C 270 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR C 278 " --> pdb=" O ALA C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 308 Processing helix chain 'C' and resid 321 through 326 removed outlier: 3.767A pdb=" N LEU C 324 " --> pdb=" O SER C 321 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR C 326 " --> pdb=" O GLU C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 370 removed outlier: 4.695A pdb=" N SER C 368 " --> pdb=" O LYS C 364 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA C 369 " --> pdb=" O ALA C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 394 removed outlier: 3.695A pdb=" N LYS C 384 " --> pdb=" O GLY C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 424 removed outlier: 3.555A pdb=" N VAL C 417 " --> pdb=" O PHE C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 458 removed outlier: 4.274A pdb=" N LEU C 456 " --> pdb=" O ARG C 452 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU C 457 " --> pdb=" O CYS C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 493 removed outlier: 3.688A pdb=" N GLU C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 503 Processing helix chain 'C' and resid 511 through 520 removed outlier: 3.681A pdb=" N ASP C 515 " --> pdb=" O ASP C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 529 removed outlier: 3.644A pdb=" N LYS C 525 " --> pdb=" O GLY C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 538 removed outlier: 3.802A pdb=" N TYR C 536 " --> pdb=" O ASP C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 551 removed outlier: 3.617A pdb=" N MET C 545 " --> pdb=" O LYS C 541 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL C 546 " --> pdb=" O LEU C 542 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN C 551 " --> pdb=" O GLU C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 562 Processing helix chain 'C' and resid 563 through 565 No H-bonds generated for 'chain 'C' and resid 563 through 565' Processing helix chain 'C' and resid 566 through 574 removed outlier: 4.172A pdb=" N LYS C 570 " --> pdb=" O PHE C 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 47 removed outlier: 3.746A pdb=" N LEU D 42 " --> pdb=" O PHE D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 52 removed outlier: 3.554A pdb=" N ARG D 51 " --> pdb=" O ASP D 47 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS D 52 " --> pdb=" O LYS D 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 47 through 52' Processing helix chain 'D' and resid 60 through 64 removed outlier: 3.953A pdb=" N ASP D 64 " --> pdb=" O HIS D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 91 removed outlier: 4.256A pdb=" N LYS D 87 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 147 No H-bonds generated for 'chain 'D' and resid 145 through 147' Processing helix chain 'D' and resid 159 through 168 Processing helix chain 'D' and resid 181 through 192 Processing helix chain 'D' and resid 205 through 211 Processing helix chain 'D' and resid 260 through 277 removed outlier: 3.608A pdb=" N MET D 264 " --> pdb=" O GLY D 260 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER D 266 " --> pdb=" O ARG D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 308 Processing helix chain 'D' and resid 321 through 326 removed outlier: 3.742A pdb=" N LEU D 324 " --> pdb=" O SER D 321 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR D 326 " --> pdb=" O GLU D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 370 removed outlier: 4.637A pdb=" N SER D 368 " --> pdb=" O LYS D 364 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA D 369 " --> pdb=" O ALA D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 394 removed outlier: 3.638A pdb=" N LYS D 384 " --> pdb=" O GLY D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 423 removed outlier: 3.895A pdb=" N TYR D 416 " --> pdb=" O TYR D 412 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL D 417 " --> pdb=" O PHE D 413 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU D 423 " --> pdb=" O THR D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 457 removed outlier: 3.519A pdb=" N LEU D 457 " --> pdb=" O CYS D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 493 Processing helix chain 'D' and resid 493 through 503 removed outlier: 3.796A pdb=" N GLU D 503 " --> pdb=" O GLU D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 529 removed outlier: 3.989A pdb=" N ASP D 515 " --> pdb=" O ASP D 511 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA D 519 " --> pdb=" O ASP D 515 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N GLU D 522 " --> pdb=" O SER D 518 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER D 523 " --> pdb=" O ALA D 519 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU D 529 " --> pdb=" O LYS D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 540 removed outlier: 4.163A pdb=" N SER D 540 " --> pdb=" O TYR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 550 removed outlier: 3.579A pdb=" N VAL D 546 " --> pdb=" O LEU D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 562 Processing helix chain 'D' and resid 566 through 574 removed outlier: 4.226A pdb=" N LYS D 570 " --> pdb=" O PHE D 566 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY D 574 " --> pdb=" O LYS D 570 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 20 removed outlier: 3.746A pdb=" N ASN A 5 " --> pdb=" O THR A 74 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLU A 70 " --> pdb=" O LYS A 9 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS A 112 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN A 121 " --> pdb=" O LYS A 112 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 154 removed outlier: 8.321A pdb=" N PHE A 316 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TYR A 285 " --> pdb=" O PHE A 316 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N SER A 318 " --> pdb=" O TYR A 285 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE A 287 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ASN A 25 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL A 26 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL A 336 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N PHE A 28 " --> pdb=" O VAL A 336 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 403 through 407 removed outlier: 8.429A pdb=" N TYR A 506 " --> pdb=" O HIS A 427 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE A 429 " --> pdb=" O TYR A 506 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 435 through 437 Processing sheet with id=AA5, first strand: chain 'B' and resid 14 through 20 removed outlier: 6.622A pdb=" N LYS B 16 " --> pdb=" O LYS B 9 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LYS B 9 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN B 18 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR B 7 " --> pdb=" O ASN B 18 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASN B 20 " --> pdb=" O ASN B 5 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ASN B 5 " --> pdb=" O ASN B 20 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR B 74 " --> pdb=" O SER B 4 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE B 6 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE B 72 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE B 8 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N GLU B 70 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS B 112 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN B 121 " --> pdb=" O LYS B 112 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 154 removed outlier: 8.256A pdb=" N PHE B 316 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N TYR B 285 " --> pdb=" O PHE B 316 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N SER B 318 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE B 287 " --> pdb=" O SER B 318 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS B 24 " --> pdb=" O ARG B 332 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ILE B 334 " --> pdb=" O LYS B 24 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL B 26 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N VAL B 336 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N PHE B 28 " --> pdb=" O VAL B 336 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N SER B 338 " --> pdb=" O PHE B 28 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 138 through 139 removed outlier: 3.717A pdb=" N ILE B 142 " --> pdb=" O ARG B 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 224 through 229 Processing sheet with id=AA9, first strand: chain 'B' and resid 403 through 407 removed outlier: 6.659A pdb=" N ARG B 374 " --> pdb=" O PHE B 404 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N LEU B 406 " --> pdb=" O ARG B 374 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU B 376 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 430 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N TYR B 506 " --> pdb=" O HIS B 427 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE B 429 " --> pdb=" O TYR B 506 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 435 through 437 Processing sheet with id=AB2, first strand: chain 'C' and resid 17 through 20 removed outlier: 6.805A pdb=" N THR C 74 " --> pdb=" O SER C 4 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE C 6 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE C 72 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ILE C 8 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLU C 70 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS C 112 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN C 121 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE C 134 " --> pdb=" O TRP C 126 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 149 through 154 removed outlier: 4.466A pdb=" N TYR C 314 " --> pdb=" O VAL C 283 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL C 26 " --> pdb=" O ILE C 334 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N VAL C 336 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE C 28 " --> pdb=" O VAL C 336 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 403 through 407 removed outlier: 6.659A pdb=" N ARG C 374 " --> pdb=" O PHE C 404 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LEU C 406 " --> pdb=" O ARG C 374 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU C 376 " --> pdb=" O LEU C 406 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 435 through 437 Processing sheet with id=AB6, first strand: chain 'D' and resid 14 through 20 removed outlier: 6.622A pdb=" N GLU D 15 " --> pdb=" O ASN D 10 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR D 74 " --> pdb=" O SER D 4 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE D 6 " --> pdb=" O ILE D 72 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE D 72 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ILE D 8 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLU D 70 " --> pdb=" O ILE D 8 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 149 through 154 removed outlier: 8.213A pdb=" N PHE D 316 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TYR D 285 " --> pdb=" O PHE D 316 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N SER D 318 " --> pdb=" O TYR D 285 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE D 287 " --> pdb=" O SER D 318 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS D 24 " --> pdb=" O ARG D 332 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ILE D 334 " --> pdb=" O LYS D 24 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N VAL D 26 " --> pdb=" O ILE D 334 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VAL D 336 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N PHE D 28 " --> pdb=" O VAL D 336 " (cutoff:3.500A) removed outlier: 8.932A pdb=" N SER D 338 " --> pdb=" O PHE D 28 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 113 through 114 Processing sheet with id=AB9, first strand: chain 'D' and resid 138 through 139 removed outlier: 3.832A pdb=" N ILE D 142 " --> pdb=" O ARG D 139 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 403 through 407 removed outlier: 6.596A pdb=" N ARG D 374 " --> pdb=" O PHE D 404 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N LEU D 406 " --> pdb=" O ARG D 374 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU D 376 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS D 430 " --> pdb=" O LEU D 377 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N TYR D 506 " --> pdb=" O HIS D 427 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE D 429 " --> pdb=" O TYR D 506 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 435 through 437 700 hydrogen bonds defined for protein. 1983 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.18 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4319 1.33 - 1.45: 3116 1.45 - 1.57: 9752 1.57 - 1.69: 17 1.69 - 1.81: 90 Bond restraints: 17294 Sorted by residual: bond pdb=" N VAL A 358 " pdb=" CA VAL A 358 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.25e-02 6.40e+03 1.15e+01 bond pdb=" N ILE A 467 " pdb=" CA ILE A 467 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.14e-02 7.69e+03 1.10e+01 bond pdb=" C VAL A 358 " pdb=" O VAL A 358 " ideal model delta sigma weight residual 1.236 1.274 -0.037 1.19e-02 7.06e+03 9.91e+00 bond pdb=" N VAL D 93 " pdb=" CA VAL D 93 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.59e+00 bond pdb=" N VAL B 93 " pdb=" CA VAL B 93 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.58e+00 ... (remaining 17289 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 22516 2.62 - 5.23: 606 5.23 - 7.85: 85 7.85 - 10.46: 29 10.46 - 13.08: 3 Bond angle restraints: 23239 Sorted by residual: angle pdb=" C GLU C 471 " pdb=" N ASP C 472 " pdb=" CA ASP C 472 " ideal model delta sigma weight residual 121.54 134.62 -13.08 1.91e+00 2.74e-01 4.69e+01 angle pdb=" C THR C 554 " pdb=" N LYS C 555 " pdb=" CA LYS C 555 " ideal model delta sigma weight residual 121.54 133.91 -12.37 1.91e+00 2.74e-01 4.19e+01 angle pdb=" C PHE A 528 " pdb=" N GLU A 529 " pdb=" CA GLU A 529 " ideal model delta sigma weight residual 122.08 131.48 -9.40 1.47e+00 4.63e-01 4.09e+01 angle pdb=" C ASP C 64 " pdb=" N THR C 65 " pdb=" CA THR C 65 " ideal model delta sigma weight residual 122.61 132.44 -9.83 1.56e+00 4.11e-01 3.97e+01 angle pdb=" N ASP A 32 " pdb=" CA ASP A 32 " pdb=" C ASP A 32 " ideal model delta sigma weight residual 111.52 119.96 -8.44 1.40e+00 5.10e-01 3.63e+01 ... (remaining 23234 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 9413 17.90 - 35.79: 966 35.79 - 53.69: 202 53.69 - 71.58: 35 71.58 - 89.48: 15 Dihedral angle restraints: 10631 sinusoidal: 4574 harmonic: 6057 Sorted by residual: dihedral pdb=" CA GLN B 198 " pdb=" C GLN B 198 " pdb=" N ILE B 199 " pdb=" CA ILE B 199 " ideal model delta harmonic sigma weight residual 180.00 152.10 27.90 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA GLU B 201 " pdb=" C GLU B 201 " pdb=" N MET B 202 " pdb=" CA MET B 202 " ideal model delta harmonic sigma weight residual 180.00 152.81 27.19 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA LYS C 35 " pdb=" C LYS C 35 " pdb=" N THR C 36 " pdb=" CA THR C 36 " ideal model delta harmonic sigma weight residual 180.00 154.58 25.42 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 10628 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 2358 0.114 - 0.228: 177 0.228 - 0.342: 12 0.342 - 0.456: 3 0.456 - 0.570: 1 Chirality restraints: 2551 Sorted by residual: chirality pdb=" CB VAL B 549 " pdb=" CA VAL B 549 " pdb=" CG1 VAL B 549 " pdb=" CG2 VAL B 549 " both_signs ideal model delta sigma weight residual False -2.63 -2.06 -0.57 2.00e-01 2.50e+01 8.11e+00 chirality pdb=" CB ILE D 199 " pdb=" CA ILE D 199 " pdb=" CG1 ILE D 199 " pdb=" CG2 ILE D 199 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.62e+00 chirality pdb=" CA ASP A 32 " pdb=" N ASP A 32 " pdb=" C ASP A 32 " pdb=" CB ASP A 32 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.44e+00 ... (remaining 2548 not shown) Planarity restraints: 2940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 358 " -0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C VAL C 358 " 0.061 2.00e-02 2.50e+03 pdb=" O VAL C 358 " -0.023 2.00e-02 2.50e+03 pdb=" N LYS C 359 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 90 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.88e+00 pdb=" C ILE D 90 " -0.049 2.00e-02 2.50e+03 pdb=" O ILE D 90 " 0.018 2.00e-02 2.50e+03 pdb=" N SER D 91 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 90 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.86e+00 pdb=" C ILE B 90 " 0.048 2.00e-02 2.50e+03 pdb=" O ILE B 90 " -0.018 2.00e-02 2.50e+03 pdb=" N SER B 91 " -0.016 2.00e-02 2.50e+03 ... (remaining 2937 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 188 2.67 - 3.23: 13731 3.23 - 3.79: 24175 3.79 - 4.34: 36253 4.34 - 4.90: 58753 Nonbonded interactions: 133100 Sorted by model distance: nonbonded pdb=" O1G ATP A 601 " pdb="MG MG A 602 " model vdw 2.113 2.170 nonbonded pdb=" OG1 THR D 36 " pdb="MG MG D 602 " model vdw 2.127 2.170 nonbonded pdb=" OG1 THR B 36 " pdb="MG MG B 602 " model vdw 2.130 2.170 nonbonded pdb=" OG1 THR A 36 " pdb="MG MG A 602 " model vdw 2.160 2.170 nonbonded pdb=" O2B ATP A 601 " pdb="MG MG A 602 " model vdw 2.197 2.170 ... (remaining 133095 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 156 or resid 261 through 602)) selection = (chain 'B' and (resid 1 through 156 or resid 261 through 602)) selection = chain 'C' selection = (chain 'D' and (resid 1 through 156 or resid 261 through 602)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.010 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.940 ------------------------------------------------------------------------------- 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= 0.348 Angle : 1.045 13.081 23239 Z= 0.595 Chirality : 0.064 0.570 2551 Planarity : 0.006 0.059 2940 Dihedral : 15.256 89.476 6735 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.79 % Favored : 95.16 % Rotamer: Outliers : 0.64 % Allowed : 0.95 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.57 (0.15), residues: 2047 helix: -3.88 (0.08), residues: 807 sheet: 0.41 (0.26), residues: 393 loop : -2.00 (0.18), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 51 TYR 0.021 0.002 TYR B 272 PHE 0.038 0.003 PHE C 315 TRP 0.004 0.001 TRP D 126 HIS 0.012 0.002 HIS C 320 Details of bonding type rmsd covalent geometry : bond 0.00677 (17294) covalent geometry : angle 1.04530 (23239) hydrogen bonds : bond 0.18392 ( 700) hydrogen bonds : angle 8.41163 ( 1983) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 322 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8163 (tt0) cc_final: 0.7821 (tp30) REVERT: A 143 ASN cc_start: 0.8520 (p0) cc_final: 0.8312 (p0) REVERT: A 480 GLU cc_start: 0.7159 (mp0) cc_final: 0.6626 (tp30) REVERT: A 481 ARG cc_start: 0.7940 (tpp80) cc_final: 0.7569 (tpp80) REVERT: A 511 ASP cc_start: 0.7775 (m-30) cc_final: 0.7559 (m-30) REVERT: B 132 ASN cc_start: 0.8754 (t0) cc_final: 0.8527 (t0) REVERT: B 197 GLN cc_start: 0.8395 (tm-30) cc_final: 0.7888 (tm-30) REVERT: B 210 GLN cc_start: 0.8575 (tm-30) cc_final: 0.8354 (tm-30) REVERT: B 211 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7838 (mt-10) REVERT: B 229 LYS cc_start: 0.8178 (ptpt) cc_final: 0.7944 (ptpt) REVERT: B 232 MET cc_start: 0.8234 (ppp) cc_final: 0.7987 (ptm) REVERT: B 422 ASP cc_start: 0.8446 (m-30) cc_final: 0.8093 (m-30) REVERT: B 476 LYS cc_start: 0.7322 (tttt) cc_final: 0.6949 (mptt) REVERT: B 492 GLN cc_start: 0.8152 (tt0) cc_final: 0.7929 (tt0) REVERT: C 62 LYS cc_start: 0.8370 (mttt) cc_final: 0.7661 (mmtt) REVERT: C 70 GLU cc_start: 0.7994 (tt0) cc_final: 0.7765 (tt0) REVERT: C 94 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7659 (tppt) REVERT: C 348 MET cc_start: 0.9114 (tpt) cc_final: 0.8771 (tpp) REVERT: C 464 GLU cc_start: 0.7646 (pp20) cc_final: 0.6922 (pp20) REVERT: C 465 ILE cc_start: 0.8434 (pt) cc_final: 0.7948 (tp) REVERT: C 477 LYS cc_start: 0.8652 (mmmm) cc_final: 0.7732 (pttm) REVERT: C 481 ARG cc_start: 0.7719 (mtp180) cc_final: 0.7433 (ttp-170) REVERT: D 67 LYS cc_start: 0.8110 (mmpt) cc_final: 0.7366 (mtmm) REVERT: D 87 LYS cc_start: 0.8100 (mttt) cc_final: 0.7615 (mtmt) REVERT: D 114 ASP cc_start: 0.7668 (t0) cc_final: 0.7379 (t0) REVERT: D 278 TYR cc_start: 0.8749 (m-80) cc_final: 0.8459 (m-80) REVERT: D 279 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7730 (tm-30) REVERT: D 280 ASP cc_start: 0.7533 (m-30) cc_final: 0.7267 (m-30) REVERT: D 434 ASP cc_start: 0.8406 (m-30) cc_final: 0.8134 (m-30) REVERT: D 438 LYS cc_start: 0.8255 (pttm) cc_final: 0.8008 (pttm) REVERT: D 526 ARG cc_start: 0.7863 (ttp-170) cc_final: 0.7505 (ttp-170) outliers start: 12 outliers final: 2 residues processed: 332 average time/residue: 0.1691 time to fit residues: 80.0999 Evaluate side-chains 219 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 216 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain C residue 103 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN B 178 ASN B 186 ASN B 455 ASN C 5 ASN C 13 ASN C 56 ASN C 147 ASN ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 HIS D 186 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.151883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.110036 restraints weight = 21014.404| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.55 r_work: 0.3060 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17294 Z= 0.210 Angle : 0.607 8.042 23239 Z= 0.325 Chirality : 0.046 0.174 2551 Planarity : 0.004 0.034 2940 Dihedral : 8.907 89.053 2378 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.25 % Favored : 95.70 % Rotamer: Outliers : 1.32 % Allowed : 7.57 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.17), residues: 2047 helix: -1.35 (0.15), residues: 824 sheet: 0.47 (0.26), residues: 394 loop : -1.66 (0.19), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 139 TYR 0.013 0.002 TYR B 272 PHE 0.031 0.002 PHE C 315 TRP 0.012 0.002 TRP D 126 HIS 0.012 0.002 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00506 (17294) covalent geometry : angle 0.60685 (23239) hydrogen bonds : bond 0.04701 ( 700) hydrogen bonds : angle 5.21480 ( 1983) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 222 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 511 ASP cc_start: 0.8032 (m-30) cc_final: 0.7825 (m-30) REVERT: A 530 ASN cc_start: 0.7900 (t0) cc_final: 0.7664 (t0) REVERT: B 106 TYR cc_start: 0.8780 (m-80) cc_final: 0.8371 (m-80) REVERT: B 129 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7463 (mm-30) REVERT: B 197 GLN cc_start: 0.8614 (tm-30) cc_final: 0.8091 (tm-30) REVERT: B 211 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7862 (mt-10) REVERT: B 217 ARG cc_start: 0.8377 (mtp85) cc_final: 0.8170 (mtp85) REVERT: B 232 MET cc_start: 0.8395 (ppp) cc_final: 0.8114 (ptm) REVERT: B 446 GLU cc_start: 0.8331 (tt0) cc_final: 0.8125 (tt0) REVERT: B 547 GLU cc_start: 0.8535 (tt0) cc_final: 0.8298 (tt0) REVERT: C 94 LYS cc_start: 0.8655 (ttpp) cc_final: 0.7859 (tppt) REVERT: C 278 TYR cc_start: 0.7779 (m-80) cc_final: 0.7528 (m-80) REVERT: C 397 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7846 (mt-10) REVERT: C 439 LYS cc_start: 0.8110 (tttm) cc_final: 0.7781 (tttm) REVERT: C 464 GLU cc_start: 0.8134 (pp20) cc_final: 0.7327 (pp20) REVERT: C 465 ILE cc_start: 0.8305 (pt) cc_final: 0.8102 (tt) REVERT: C 480 GLU cc_start: 0.7556 (pm20) cc_final: 0.7150 (pm20) REVERT: C 481 ARG cc_start: 0.8196 (mtp180) cc_final: 0.7981 (ttp-170) REVERT: D 30 MET cc_start: 0.8511 (mmt) cc_final: 0.8264 (tpt) REVERT: D 67 LYS cc_start: 0.8088 (mmpt) cc_final: 0.7392 (mtmm) REVERT: D 87 LYS cc_start: 0.8453 (mttt) cc_final: 0.8247 (mtmt) REVERT: D 246 LYS cc_start: 0.8335 (mtpt) cc_final: 0.7968 (mtmt) REVERT: D 279 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8257 (tm-30) REVERT: D 379 GLU cc_start: 0.8089 (tp30) cc_final: 0.7871 (tp30) REVERT: D 526 ARG cc_start: 0.8156 (ttp-170) cc_final: 0.7579 (ttt-90) outliers start: 25 outliers final: 19 residues processed: 242 average time/residue: 0.1713 time to fit residues: 58.9148 Evaluate side-chains 207 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 188 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain D residue 455 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.891 > 50: distance: 79 - 96: 14.114 distance: 92 - 96: 12.781 distance: 93 - 119: 12.681 distance: 96 - 97: 7.776 distance: 97 - 98: 7.903 distance: 97 - 100: 12.730 distance: 98 - 99: 12.814 distance: 98 - 104: 10.258 distance: 99 - 128: 9.828 distance: 100 - 101: 6.520 distance: 101 - 102: 7.496 distance: 101 - 103: 20.191 distance: 104 - 105: 15.630 distance: 105 - 106: 13.633 distance: 105 - 108: 8.545 distance: 106 - 107: 18.952 distance: 106 - 112: 20.246 distance: 107 - 136: 20.027 distance: 108 - 109: 11.734 distance: 109 - 110: 19.086 distance: 110 - 111: 21.092 distance: 112 - 113: 15.547 distance: 113 - 114: 21.605 distance: 113 - 116: 16.845 distance: 114 - 115: 16.744 distance: 114 - 119: 14.409 distance: 115 - 143: 23.008 distance: 116 - 117: 21.412 distance: 116 - 118: 21.165 distance: 119 - 120: 10.255 distance: 120 - 121: 10.865 distance: 120 - 123: 8.574 distance: 121 - 122: 17.884 distance: 121 - 128: 15.275 distance: 123 - 124: 14.863 distance: 124 - 125: 13.138 distance: 125 - 126: 6.417 distance: 125 - 127: 16.858 distance: 128 - 129: 21.839 distance: 129 - 130: 19.206 distance: 129 - 132: 16.874 distance: 130 - 131: 23.814 distance: 130 - 136: 41.307 distance: 132 - 133: 12.755 distance: 133 - 134: 9.308 distance: 133 - 135: 11.529 distance: 136 - 137: 18.154 distance: 137 - 138: 33.420 distance: 137 - 140: 28.018 distance: 138 - 139: 21.523 distance: 138 - 143: 11.768 distance: 140 - 141: 9.529 distance: 140 - 142: 16.579 distance: 143 - 144: 14.830 distance: 144 - 145: 9.410 distance: 144 - 147: 17.166 distance: 145 - 146: 15.094 distance: 145 - 151: 9.840 distance: 147 - 148: 10.018 distance: 148 - 149: 10.192 distance: 148 - 150: 23.086 distance: 152 - 153: 10.972 distance: 152 - 155: 15.200 distance: 153 - 154: 10.889 distance: 153 - 159: 5.826 distance: 155 - 156: 14.151 distance: 156 - 157: 15.044 distance: 156 - 158: 35.197 distance: 159 - 160: 6.663 distance: 160 - 161: 20.730 distance: 160 - 163: 7.656 distance: 161 - 162: 25.767 distance: 161 - 167: 10.189 distance: 163 - 164: 6.562 distance: 164 - 165: 20.161 distance: 164 - 166: 19.210 distance: 167 - 168: 14.867 distance: 168 - 169: 21.067 distance: 168 - 171: 18.274 distance: 169 - 170: 11.022 distance: 169 - 173: 7.775 distance: 171 - 172: 8.516