Starting phenix.real_space_refine on Thu Jul 2 17:36:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8cua_26997/07_2026/8cua_26997.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cua_26997/07_2026/8cua_26997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8cua_26997/07_2026/8cua_26997.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8cua_26997/07_2026/8cua_26997.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cua_26997/07_2026/8cua_26997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cua_26997/07_2026/8cua_26997.map" model { file = "/net/cci-nas-00/data/ceres_data/8cua_26997/07_2026/8cua_26997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cua_26997/07_2026/8cua_26997.cif" } resolution = 2.44 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= 0.008 sd= 0.104 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 Hg 3 10.96 5 K 3 8.98 5 S 63 5.16 5 C 6228 2.51 5 N 1512 2.21 5 O 1725 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9534 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3166 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 11, 'TRANS': 404} Chain breaks: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' HG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1605 SG CYS A 269 23.791 36.895 25.246 1.00 69.82 S ATOM 2886 SG CYS A 441 25.221 34.804 25.594 1.00 76.78 S Restraints were copied for chains: B, C Time building chain proxies: 2.60, per 1000 atoms: 0.27 Number of scatterers: 9534 At special positions: 0 Unit cell: (106.5, 103.092, 78.384, 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) Hg 3 79.96 K 3 19.00 S 63 16.00 O 1725 8.00 N 1512 7.00 C 6228 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: 0.70 Conformation dependent library (CDL) restraints added in 256.1 milliseconds 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2310 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 3 sheets defined 86.1% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 18 through 42 removed outlier: 3.691A pdb=" N LEU A 22 " --> pdb=" O ASN A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.831A pdb=" N ALA A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 66 removed outlier: 3.558A pdb=" N ILE A 66 " --> pdb=" O MET A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 81 removed outlier: 3.554A pdb=" N LEU A 70 " --> pdb=" O ILE A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 117 removed outlier: 3.629A pdb=" N ILE A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.519A pdb=" N LEU A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 158 Processing helix chain 'A' and resid 211 through 227 Processing helix chain 'A' and resid 229 through 232 removed outlier: 3.738A pdb=" N LYS A 232 " --> pdb=" O MET A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 233 through 270 removed outlier: 3.747A pdb=" N TRP A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TYR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 3.512A pdb=" N PHE A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 282 removed outlier: 3.966A pdb=" N ARG A 280 " --> pdb=" O TRP A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 299 Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 312 through 319 Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 333 through 335 No H-bonds generated for 'chain 'A' and resid 333 through 335' Processing helix chain 'A' and resid 336 through 347 Processing helix chain 'A' and resid 351 through 366 removed outlier: 3.675A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Proline residue: A 360 - end of helix removed outlier: 3.672A pdb=" N THR A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 385 removed outlier: 3.624A pdb=" N LEU A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 405 removed outlier: 3.653A pdb=" N SER A 405 " --> pdb=" O ALA A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 427 removed outlier: 4.243A pdb=" N VAL A 417 " --> pdb=" O GLN A 413 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N VAL A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 432 through 438 removed outlier: 4.001A pdb=" N ILE A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 466 removed outlier: 3.926A pdb=" N ARG A 445 " --> pdb=" O CYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 477 removed outlier: 3.716A pdb=" N ASP A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 42 removed outlier: 3.691A pdb=" N LEU B 22 " --> pdb=" O ASN B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.832A pdb=" N ALA B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 66 removed outlier: 3.558A pdb=" N ILE B 66 " --> pdb=" O MET B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 81 removed outlier: 3.554A pdb=" N LEU B 70 " --> pdb=" O ILE B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 117 removed outlier: 3.629A pdb=" N ILE B 90 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 150 removed outlier: 3.519A pdb=" N LEU B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE B 146 " --> pdb=" O MET B 142 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 158 Processing helix chain 'B' and resid 211 through 227 Processing helix chain 'B' and resid 229 through 232 removed outlier: 3.738A pdb=" N LYS B 232 " --> pdb=" O MET B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 229 through 232' Processing helix chain 'B' and resid 233 through 270 removed outlier: 3.749A pdb=" N TRP B 256 " --> pdb=" O GLN B 252 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) Proline residue: B 259 - end of helix removed outlier: 3.512A pdb=" N PHE B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 282 removed outlier: 3.967A pdb=" N ARG B 280 " --> pdb=" O TRP B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 299 Processing helix chain 'B' and resid 299 through 309 Processing helix chain 'B' and resid 312 through 319 Processing helix chain 'B' and resid 320 through 331 Processing helix chain 'B' and resid 333 through 335 No H-bonds generated for 'chain 'B' and resid 333 through 335' Processing helix chain 'B' and resid 336 through 347 Processing helix chain 'B' and resid 351 through 366 removed outlier: 3.675A pdb=" N PHE B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Proline residue: B 360 - end of helix removed outlier: 3.672A pdb=" N THR B 364 " --> pdb=" O PRO B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 385 removed outlier: 3.624A pdb=" N LEU B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA B 375 " --> pdb=" O ALA B 371 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 405 removed outlier: 3.653A pdb=" N SER B 405 " --> pdb=" O ALA B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 427 removed outlier: 4.244A pdb=" N VAL B 417 " --> pdb=" O GLN B 413 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 421 " --> pdb=" O VAL B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 432 through 438 removed outlier: 4.002A pdb=" N ILE B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA B 438 " --> pdb=" O THR B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 466 removed outlier: 3.926A pdb=" N ARG B 445 " --> pdb=" O CYS B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 477 removed outlier: 3.715A pdb=" N ASP B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER B 476 " --> pdb=" O GLN B 472 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER B 477 " --> pdb=" O MET B 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 42 removed outlier: 3.691A pdb=" N LEU C 22 " --> pdb=" O ASN C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 53 removed outlier: 3.832A pdb=" N ALA C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 66 removed outlier: 3.558A pdb=" N ILE C 66 " --> pdb=" O MET C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 81 removed outlier: 3.554A pdb=" N LEU C 70 " --> pdb=" O ILE C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 117 removed outlier: 3.629A pdb=" N ILE C 90 " --> pdb=" O VAL C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 150 removed outlier: 3.519A pdb=" N LEU C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE C 146 " --> pdb=" O MET C 142 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE C 150 " --> pdb=" O ILE C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 158 Processing helix chain 'C' and resid 211 through 227 Processing helix chain 'C' and resid 229 through 232 removed outlier: 3.738A pdb=" N LYS C 232 " --> pdb=" O MET C 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 229 through 232' Processing helix chain 'C' and resid 233 through 270 removed outlier: 3.747A pdb=" N TRP C 256 " --> pdb=" O GLN C 252 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TYR C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) Proline residue: C 259 - end of helix removed outlier: 3.513A pdb=" N PHE C 264 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 282 removed outlier: 3.966A pdb=" N ARG C 280 " --> pdb=" O TRP C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 299 Processing helix chain 'C' and resid 299 through 309 Processing helix chain 'C' and resid 312 through 319 Processing helix chain 'C' and resid 320 through 331 Processing helix chain 'C' and resid 333 through 335 No H-bonds generated for 'chain 'C' and resid 333 through 335' Processing helix chain 'C' and resid 336 through 347 Processing helix chain 'C' and resid 351 through 366 removed outlier: 3.676A pdb=" N PHE C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Proline residue: C 360 - end of helix removed outlier: 3.671A pdb=" N THR C 364 " --> pdb=" O PRO C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 385 removed outlier: 3.624A pdb=" N LEU C 372 " --> pdb=" O ASP C 368 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA C 375 " --> pdb=" O ALA C 371 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL C 376 " --> pdb=" O LEU C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 405 removed outlier: 3.653A pdb=" N SER C 405 " --> pdb=" O ALA C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 427 removed outlier: 4.243A pdb=" N VAL C 417 " --> pdb=" O GLN C 413 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N VAL C 420 " --> pdb=" O LEU C 416 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE C 421 " --> pdb=" O VAL C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 431 No H-bonds generated for 'chain 'C' and resid 429 through 431' Processing helix chain 'C' and resid 432 through 438 removed outlier: 4.002A pdb=" N ILE C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA C 438 " --> pdb=" O THR C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 466 removed outlier: 3.926A pdb=" N ARG C 445 " --> pdb=" O CYS C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 477 removed outlier: 3.716A pdb=" N ASP C 474 " --> pdb=" O LEU C 470 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER C 476 " --> pdb=" O GLN C 472 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER C 477 " --> pdb=" O MET C 473 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167 Processing sheet with id=AA2, first strand: chain 'B' and resid 160 through 167 Processing sheet with id=AA3, first strand: chain 'C' and resid 160 through 167 708 hydrogen bonds defined for protein. 2106 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: 1.57 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2259 1.33 - 1.45: 1629 1.45 - 1.57: 5634 1.57 - 1.69: 0 1.69 - 1.81: 117 Bond restraints: 9639 Sorted by residual: bond pdb=" N ILE A 406 " pdb=" CA ILE A 406 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.87e+00 bond pdb=" N ILE C 406 " pdb=" CA ILE C 406 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.82e+00 bond pdb=" N ILE B 406 " pdb=" CA ILE B 406 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.80e+00 bond pdb=" N CYS C 441 " pdb=" CA CYS C 441 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.30e-02 5.92e+03 7.01e+00 bond pdb=" N CYS A 441 " pdb=" CA CYS A 441 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.30e-02 5.92e+03 6.99e+00 ... (remaining 9634 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 12867 1.88 - 3.76: 168 3.76 - 5.63: 36 5.63 - 7.51: 3 7.51 - 9.39: 6 Bond angle restraints: 13080 Sorted by residual: angle pdb=" CB MET C 75 " pdb=" CG MET C 75 " pdb=" SD MET C 75 " ideal model delta sigma weight residual 112.70 103.31 9.39 3.00e+00 1.11e-01 9.79e+00 angle pdb=" CB MET B 75 " pdb=" CG MET B 75 " pdb=" SD MET B 75 " ideal model delta sigma weight residual 112.70 103.33 9.37 3.00e+00 1.11e-01 9.75e+00 angle pdb=" CB MET A 75 " pdb=" CG MET A 75 " pdb=" SD MET A 75 " ideal model delta sigma weight residual 112.70 103.33 9.37 3.00e+00 1.11e-01 9.75e+00 angle pdb=" N MET C 258 " pdb=" CA MET C 258 " pdb=" C MET C 258 " ideal model delta sigma weight residual 109.81 116.17 -6.36 2.21e+00 2.05e-01 8.29e+00 angle pdb=" N MET A 258 " pdb=" CA MET A 258 " pdb=" C MET A 258 " ideal model delta sigma weight residual 109.81 116.16 -6.35 2.21e+00 2.05e-01 8.24e+00 ... (remaining 13075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.67: 5029 15.67 - 31.34: 495 31.34 - 47.01: 164 47.01 - 62.69: 66 62.69 - 78.36: 9 Dihedral angle restraints: 5763 sinusoidal: 2184 harmonic: 3579 Sorted by residual: dihedral pdb=" CG ARG B 315 " pdb=" CD ARG B 315 " pdb=" NE ARG B 315 " pdb=" CZ ARG B 315 " ideal model delta sinusoidal sigma weight residual -90.00 -39.98 -50.02 2 1.50e+01 4.44e-03 1.25e+01 dihedral pdb=" CG ARG C 315 " pdb=" CD ARG C 315 " pdb=" NE ARG C 315 " pdb=" CZ ARG C 315 " ideal model delta sinusoidal sigma weight residual -90.00 -40.02 -49.98 2 1.50e+01 4.44e-03 1.25e+01 dihedral pdb=" CG ARG A 315 " pdb=" CD ARG A 315 " pdb=" NE ARG A 315 " pdb=" CZ ARG A 315 " ideal model delta sinusoidal sigma weight residual -90.00 -40.02 -49.98 2 1.50e+01 4.44e-03 1.25e+01 ... (remaining 5760 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1105 0.031 - 0.063: 352 0.063 - 0.094: 148 0.094 - 0.125: 40 0.125 - 0.157: 14 Chirality restraints: 1659 Sorted by residual: chirality pdb=" CA LEU B 443 " pdb=" N LEU B 443 " pdb=" C LEU B 443 " pdb=" CB LEU B 443 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.15e-01 chirality pdb=" CA LEU A 443 " pdb=" N LEU A 443 " pdb=" C LEU A 443 " pdb=" CB LEU A 443 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CA LEU C 443 " pdb=" N LEU C 443 " pdb=" C LEU C 443 " pdb=" CB LEU C 443 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.91e-01 ... (remaining 1656 not shown) Planarity restraints: 1593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 295 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.29e+00 pdb=" C ILE A 295 " -0.031 2.00e-02 2.50e+03 pdb=" O ILE A 295 " 0.012 2.00e-02 2.50e+03 pdb=" N HIS A 296 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 295 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.24e+00 pdb=" C ILE C 295 " 0.031 2.00e-02 2.50e+03 pdb=" O ILE C 295 " -0.012 2.00e-02 2.50e+03 pdb=" N HIS C 296 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 295 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.23e+00 pdb=" C ILE B 295 " -0.031 2.00e-02 2.50e+03 pdb=" O ILE B 295 " 0.012 2.00e-02 2.50e+03 pdb=" N HIS B 296 " 0.010 2.00e-02 2.50e+03 ... (remaining 1590 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.59: 57 2.59 - 3.23: 9248 3.23 - 3.87: 18958 3.87 - 4.50: 25091 4.50 - 5.14: 40074 Nonbonded interactions: 93428 Sorted by model distance: nonbonded pdb=" SG CYS B 441 " pdb="HG HG B 601 " model vdw 1.957 2.880 nonbonded pdb=" SG CYS C 441 " pdb="HG HG C 601 " model vdw 1.957 2.880 nonbonded pdb=" SG CYS A 441 " pdb="HG HG A 601 " model vdw 1.957 2.880 nonbonded pdb=" OD2 ASP A 368 " pdb=" O HOH A 701 " model vdw 2.226 3.040 nonbonded pdb=" OD2 ASP C 368 " pdb=" O HOH C 701 " model vdw 2.226 3.040 ... (remaining 93423 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.260 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.070 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 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 : 0.003 0.035 9639 Z= 0.226 Angle : 0.575 9.388 13080 Z= 0.345 Chirality : 0.039 0.157 1659 Planarity : 0.004 0.027 1593 Dihedral : 15.571 78.357 3453 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 21.61 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.24), residues: 1230 helix: 1.92 (0.17), residues: 963 sheet: 0.89 (0.66), residues: 48 loop : -1.20 (0.36), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 315 TYR 0.009 0.001 TYR B 285 PHE 0.007 0.001 PHE A 218 TRP 0.007 0.001 TRP B 256 HIS 0.001 0.000 HIS C 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.23 ( 9639) covalent geometry : angle 0.57550 / 0.35 (13080) hydrogen bonds : bond 0.12930 / 8.56 ( 708) hydrogen bonds : angle 5.13416 / 3.70 ( 2106) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.212 Fit side-chains REVERT: A 205 MET cc_start: 0.8426 (ptm) cc_final: 0.8177 (ptt) REVERT: A 385 ASN cc_start: 0.7509 (m-40) cc_final: 0.7298 (m110) REVERT: A 475 VAL cc_start: 0.7494 (p) cc_final: 0.7276 (m) REVERT: B 205 MET cc_start: 0.8250 (ptm) cc_final: 0.7960 (ptt) REVERT: B 315 ARG cc_start: 0.6984 (ttm-80) cc_final: 0.6409 (ttp80) REVERT: B 322 GLN cc_start: 0.7710 (mt0) cc_final: 0.7448 (tt0) REVERT: C 205 MET cc_start: 0.8319 (ptm) cc_final: 0.8055 (ptt) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.5603 time to fit residues: 81.2943 Evaluate side-chains 121 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.0570 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 252 GLN A 366 ASN A 413 GLN B 252 GLN B 413 GLN C 252 GLN C 413 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.173112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.127860 restraints weight = 3527.476| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 0.94 r_work: 0.3395 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9639 Z= 0.131 Angle : 0.485 6.821 13080 Z= 0.254 Chirality : 0.037 0.142 1659 Planarity : 0.004 0.028 1593 Dihedral : 3.380 15.979 1308 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.92 % Allowed : 19.40 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.24), residues: 1230 helix: 2.03 (0.17), residues: 972 sheet: -0.00 (0.71), residues: 54 loop : -0.73 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 315 TYR 0.010 0.001 TYR C 285 PHE 0.013 0.001 PHE C 99 TRP 0.003 0.000 TRP C 19 HIS 0.001 0.000 HIS C 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.13 ( 9639) covalent geometry : angle 0.48466 / 0.25 (13080) hydrogen bonds : bond 0.05553 / 3.78 ( 708) hydrogen bonds : angle 4.07749 / 2.95 ( 2106) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: B 205 MET cc_start: 0.8732 (ptm) cc_final: 0.8487 (ptm) outliers start: 20 outliers final: 6 residues processed: 147 average time/residue: 0.5054 time to fit residues: 79.5402 Evaluate side-chains 132 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 474 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 0.0020 chunk 34 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 252 GLN B 252 GLN B 385 ASN C 252 GLN C 451 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.173569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.128964 restraints weight = 3528.608| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 0.93 r_work: 0.3411 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9639 Z= 0.119 Angle : 0.464 6.765 13080 Z= 0.241 Chirality : 0.036 0.139 1659 Planarity : 0.003 0.032 1593 Dihedral : 3.313 15.123 1308 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.02 % Allowed : 20.85 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.24), residues: 1230 helix: 2.12 (0.17), residues: 975 sheet: 0.05 (0.74), residues: 54 loop : -0.84 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 315 TYR 0.009 0.001 TYR C 285 PHE 0.014 0.001 PHE C 99 TRP 0.003 0.000 TRP C 19 HIS 0.000 0.000 HIS B 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.12 ( 9639) covalent geometry : angle 0.46405 / 0.24 (13080) hydrogen bonds : bond 0.05090 / 3.46 ( 708) hydrogen bonds : angle 3.94425 / 2.85 ( 2106) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.283 Fit side-chains REVERT: A 39 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.7164 (mtp-110) REVERT: A 116 ILE cc_start: 0.7006 (mt) cc_final: 0.6803 (mt) REVERT: A 231 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7082 (mm-30) REVERT: A 346 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7479 (mm-30) REVERT: A 471 GLU cc_start: 0.8089 (pt0) cc_final: 0.7871 (pt0) REVERT: B 205 MET cc_start: 0.8681 (ptm) cc_final: 0.8423 (ptm) REVERT: C 346 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7450 (mm-30) outliers start: 21 outliers final: 7 residues processed: 150 average time/residue: 0.5360 time to fit residues: 85.6433 Evaluate side-chains 133 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 364 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 6.9990 chunk 59 optimal weight: 0.2980 chunk 110 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 81 optimal weight: 0.2980 chunk 97 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 252 GLN A 451 ASN B 252 GLN B 385 ASN B 451 ASN C 252 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.173008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.128644 restraints weight = 3360.960| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 0.91 r_work: 0.3408 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9639 Z= 0.121 Angle : 0.463 6.834 13080 Z= 0.242 Chirality : 0.036 0.138 1659 Planarity : 0.003 0.033 1593 Dihedral : 3.319 14.984 1308 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.31 % Allowed : 19.79 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.41 (0.24), residues: 1230 helix: 2.12 (0.17), residues: 981 sheet: -0.02 (0.74), residues: 54 loop : -0.64 (0.40), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 315 TYR 0.010 0.001 TYR C 285 PHE 0.016 0.001 PHE B 99 TRP 0.002 0.000 TRP A 19 HIS 0.001 0.000 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.12 ( 9639) covalent geometry : angle 0.46280 / 0.24 (13080) hydrogen bonds : bond 0.05240 / 3.55 ( 708) hydrogen bonds : angle 3.87508 / 2.80 ( 2106) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.280 Fit side-chains REVERT: A 39 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.7184 (mtp-110) REVERT: A 116 ILE cc_start: 0.6799 (mt) cc_final: 0.6589 (mt) REVERT: A 231 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7095 (mm-30) REVERT: A 346 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7473 (mm-30) REVERT: B 241 ASN cc_start: 0.8808 (OUTLIER) cc_final: 0.8468 (m-40) REVERT: C 346 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7386 (mm-30) outliers start: 24 outliers final: 8 residues processed: 150 average time/residue: 0.5178 time to fit residues: 82.9232 Evaluate side-chains 139 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 472 GLN Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 346 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 93 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 77 optimal weight: 0.0570 chunk 58 optimal weight: 2.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 252 GLN B 252 GLN B 385 ASN C 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.163709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.115739 restraints weight = 2990.284| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 0.90 r_work: 0.3190 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9639 Z= 0.193 Angle : 0.567 7.759 13080 Z= 0.299 Chirality : 0.040 0.150 1659 Planarity : 0.004 0.038 1593 Dihedral : 3.677 15.568 1308 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.50 % Allowed : 19.88 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.24), residues: 1230 helix: 1.71 (0.17), residues: 981 sheet: 1.14 (0.68), residues: 48 loop : -0.99 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 315 TYR 0.011 0.002 TYR A 285 PHE 0.016 0.002 PHE B 99 TRP 0.005 0.001 TRP B 256 HIS 0.002 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 ( 9639) covalent geometry : angle 0.56689 / 0.30 (13080) hydrogen bonds : bond 0.07555 / 5.14 ( 708) hydrogen bonds : angle 4.18585 / 3.02 ( 2106) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.265 Fit side-chains REVERT: A 21 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6236 (mp) REVERT: A 39 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.7182 (mtp-110) REVERT: A 231 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7439 (mm-30) REVERT: A 241 ASN cc_start: 0.8951 (OUTLIER) cc_final: 0.8492 (t0) REVERT: A 396 THR cc_start: 0.7542 (m) cc_final: 0.7333 (m) REVERT: B 115 SER cc_start: 0.7734 (t) cc_final: 0.7207 (m) REVERT: B 205 MET cc_start: 0.8698 (ptm) cc_final: 0.8377 (ptm) REVERT: C 115 SER cc_start: 0.7718 (t) cc_final: 0.7127 (m) REVERT: C 346 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7324 (mm-30) outliers start: 26 outliers final: 6 residues processed: 154 average time/residue: 0.5223 time to fit residues: 85.5441 Evaluate side-chains 137 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 346 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 61 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 78 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 252 GLN B 252 GLN C 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.167579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.120833 restraints weight = 2755.733| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 0.90 r_work: 0.3273 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9639 Z= 0.136 Angle : 0.496 7.281 13080 Z= 0.258 Chirality : 0.037 0.140 1659 Planarity : 0.004 0.038 1593 Dihedral : 3.504 15.244 1308 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.92 % Allowed : 19.98 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.24), residues: 1230 helix: 1.99 (0.17), residues: 969 sheet: 0.14 (0.73), residues: 54 loop : -0.48 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 315 TYR 0.010 0.001 TYR C 285 PHE 0.017 0.001 PHE B 99 TRP 0.004 0.000 TRP B 19 HIS 0.001 0.000 HIS C 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 ( 9639) covalent geometry : angle 0.49606 / 0.26 (13080) hydrogen bonds : bond 0.05886 / 4.00 ( 708) hydrogen bonds : angle 3.96722 / 2.86 ( 2106) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.259 Fit side-chains REVERT: A 39 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.7106 (mtp-110) REVERT: A 231 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7280 (mm-30) REVERT: A 241 ASN cc_start: 0.8817 (OUTLIER) cc_final: 0.8474 (t0) REVERT: A 346 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7235 (mt-10) REVERT: A 396 THR cc_start: 0.7536 (m) cc_final: 0.7322 (m) REVERT: B 39 ARG cc_start: 0.7516 (ttp80) cc_final: 0.6896 (ttp80) REVERT: B 205 MET cc_start: 0.8594 (ptm) cc_final: 0.8236 (ptm) REVERT: C 115 SER cc_start: 0.7528 (t) cc_final: 0.6908 (m) REVERT: C 346 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7339 (mm-30) outliers start: 20 outliers final: 5 residues processed: 147 average time/residue: 0.5108 time to fit residues: 80.2038 Evaluate side-chains 136 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 346 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 50 optimal weight: 0.7980 chunk 103 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 0.1980 chunk 115 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 252 GLN B 252 GLN C 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.163812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.116909 restraints weight = 2975.116| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 0.86 r_work: 0.3210 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9639 Z= 0.182 Angle : 0.560 7.725 13080 Z= 0.293 Chirality : 0.039 0.146 1659 Planarity : 0.004 0.043 1593 Dihedral : 3.673 15.412 1308 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.73 % Allowed : 19.98 % Favored : 78.29 % 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: 1.83 (0.24), residues: 1230 helix: 1.67 (0.17), residues: 981 sheet: 1.17 (0.67), residues: 48 loop : -0.98 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 315 TYR 0.011 0.002 TYR B 285 PHE 0.017 0.002 PHE B 99 TRP 0.003 0.001 TRP C 19 HIS 0.002 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 ( 9639) covalent geometry : angle 0.55951 / 0.29 (13080) hydrogen bonds : bond 0.07229 / 4.92 ( 708) hydrogen bonds : angle 4.13718 / 2.98 ( 2106) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.338 Fit side-chains REVERT: A 39 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.7180 (mtp-110) REVERT: A 231 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7424 (mm-30) REVERT: A 241 ASN cc_start: 0.8930 (OUTLIER) cc_final: 0.8483 (t0) REVERT: A 396 THR cc_start: 0.7582 (m) cc_final: 0.7381 (m) REVERT: B 115 SER cc_start: 0.7777 (t) cc_final: 0.7271 (m) REVERT: B 205 MET cc_start: 0.8707 (ptm) cc_final: 0.8345 (ptm) REVERT: C 115 SER cc_start: 0.7698 (t) cc_final: 0.7102 (m) REVERT: C 272 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6972 (mt-10) outliers start: 18 outliers final: 8 residues processed: 145 average time/residue: 0.5748 time to fit residues: 88.7686 Evaluate side-chains 138 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 340 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 92 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 252 GLN B 252 GLN C 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.163697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.116684 restraints weight = 3010.469| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 0.87 r_work: 0.3207 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9639 Z= 0.182 Angle : 0.563 7.705 13080 Z= 0.294 Chirality : 0.039 0.146 1659 Planarity : 0.004 0.043 1593 Dihedral : 3.707 15.429 1308 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.83 % Allowed : 20.17 % Favored : 78.00 % 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: 1.73 (0.24), residues: 1230 helix: 1.60 (0.17), residues: 981 sheet: 1.10 (0.65), residues: 48 loop : -0.99 (0.41), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 315 TYR 0.010 0.002 TYR A 285 PHE 0.018 0.002 PHE B 99 TRP 0.004 0.001 TRP A 19 HIS 0.002 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 ( 9639) covalent geometry : angle 0.56343 / 0.29 (13080) hydrogen bonds : bond 0.07221 / 4.91 ( 708) hydrogen bonds : angle 4.14367 / 2.99 ( 2106) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.380 Fit side-chains REVERT: A 39 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.7176 (mtp-110) REVERT: A 231 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7456 (mm-30) REVERT: A 241 ASN cc_start: 0.8940 (OUTLIER) cc_final: 0.8513 (t0) REVERT: A 396 THR cc_start: 0.7630 (m) cc_final: 0.7430 (m) REVERT: B 115 SER cc_start: 0.7763 (t) cc_final: 0.7279 (m) REVERT: B 205 MET cc_start: 0.8698 (ptm) cc_final: 0.8342 (ptm) REVERT: C 115 SER cc_start: 0.7703 (t) cc_final: 0.7105 (m) REVERT: C 272 GLU cc_start: 0.7302 (mm-30) cc_final: 0.7022 (mt-10) REVERT: C 346 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7069 (mt-10) outliers start: 19 outliers final: 9 residues processed: 143 average time/residue: 0.5998 time to fit residues: 91.1981 Evaluate side-chains 139 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 346 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 102 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 87 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 252 GLN B 252 GLN C 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.164322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.117383 restraints weight = 3059.249| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 0.88 r_work: 0.3218 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9639 Z= 0.166 Angle : 0.546 7.604 13080 Z= 0.284 Chirality : 0.039 0.144 1659 Planarity : 0.004 0.044 1593 Dihedral : 3.664 15.341 1308 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.54 % Allowed : 20.37 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.24), residues: 1230 helix: 1.67 (0.17), residues: 981 sheet: 1.12 (0.65), residues: 48 loop : -0.97 (0.41), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 315 TYR 0.010 0.002 TYR B 285 PHE 0.019 0.002 PHE B 99 TRP 0.004 0.001 TRP C 19 HIS 0.002 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 ( 9639) covalent geometry : angle 0.54640 / 0.28 (13080) hydrogen bonds : bond 0.06826 / 4.64 ( 708) hydrogen bonds : angle 4.09411 / 2.95 ( 2106) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.239 Fit side-chains REVERT: A 39 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.7160 (mtp-110) REVERT: A 231 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7445 (mm-30) REVERT: A 241 ASN cc_start: 0.8887 (OUTLIER) cc_final: 0.8476 (t0) REVERT: A 346 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7274 (mt-10) REVERT: B 115 SER cc_start: 0.7748 (t) cc_final: 0.7269 (m) REVERT: B 205 MET cc_start: 0.8687 (ptm) cc_final: 0.8329 (ptm) REVERT: B 385 ASN cc_start: 0.7022 (m-40) cc_final: 0.6794 (m110) REVERT: C 115 SER cc_start: 0.7693 (t) cc_final: 0.7095 (m) REVERT: C 272 GLU cc_start: 0.7278 (mm-30) cc_final: 0.6972 (mt-10) REVERT: C 346 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7090 (mt-10) outliers start: 16 outliers final: 8 residues processed: 142 average time/residue: 0.5672 time to fit residues: 85.6357 Evaluate side-chains 139 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 346 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 37 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 27 optimal weight: 0.0770 chunk 54 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 252 GLN B 252 GLN C 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.169673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.123595 restraints weight = 2773.364| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 0.90 r_work: 0.3311 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9639 Z= 0.121 Angle : 0.483 7.026 13080 Z= 0.248 Chirality : 0.037 0.135 1659 Planarity : 0.004 0.046 1593 Dihedral : 3.434 14.995 1308 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.25 % Allowed : 20.75 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.25), residues: 1230 helix: 2.10 (0.17), residues: 969 sheet: 0.17 (0.72), residues: 54 loop : -0.52 (0.43), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 315 TYR 0.009 0.001 TYR B 285 PHE 0.020 0.001 PHE B 99 TRP 0.004 0.001 TRP B 256 HIS 0.000 0.000 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.12 ( 9639) covalent geometry : angle 0.48301 / 0.25 (13080) hydrogen bonds : bond 0.05045 / 3.41 ( 708) hydrogen bonds : angle 3.85326 / 2.77 ( 2106) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.327 Fit side-chains REVERT: A 39 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.7076 (mtp-110) REVERT: A 241 ASN cc_start: 0.8758 (OUTLIER) cc_final: 0.8509 (t0) REVERT: A 346 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7224 (mt-10) REVERT: A 396 THR cc_start: 0.7591 (m) cc_final: 0.7383 (m) REVERT: B 205 MET cc_start: 0.8570 (ptm) cc_final: 0.8201 (ptm) REVERT: B 241 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8471 (m-40) REVERT: C 115 SER cc_start: 0.7527 (t) cc_final: 0.6908 (m) REVERT: C 272 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6846 (mt-10) REVERT: C 346 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7263 (mm-30) outliers start: 13 outliers final: 5 residues processed: 139 average time/residue: 0.5840 time to fit residues: 86.6260 Evaluate side-chains 132 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 346 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 252 GLN B 252 GLN C 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.167169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.120233 restraints weight = 2755.479| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 0.90 r_work: 0.3264 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9639 Z= 0.146 Angle : 0.522 7.247 13080 Z= 0.268 Chirality : 0.038 0.139 1659 Planarity : 0.004 0.045 1593 Dihedral : 3.515 15.221 1308 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.06 % Allowed : 20.94 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.24), residues: 1230 helix: 1.98 (0.17), residues: 969 sheet: 0.19 (0.72), residues: 54 loop : -0.49 (0.43), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 315 TYR 0.011 0.001 TYR B 285 PHE 0.019 0.001 PHE B 99 TRP 0.004 0.000 TRP C 19 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 ( 9639) covalent geometry : angle 0.52181 / 0.27 (13080) hydrogen bonds : bond 0.06110 / 4.15 ( 708) hydrogen bonds : angle 3.97158 / 2.85 ( 2106) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3370.86 seconds wall clock time: 57 minutes 57.74 seconds (3477.74 seconds total)