Starting phenix.real_space_refine on Sun Dec 29 01:18:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cua_26997/12_2024/8cua_26997.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cua_26997/12_2024/8cua_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8cua_26997/12_2024/8cua_26997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cua_26997/12_2024/8cua_26997.map" model { file = "/net/cci-nas-00/data/ceres_data/8cua_26997/12_2024/8cua_26997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cua_26997/12_2024/8cua_26997.cif" } resolution = 2.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: C, B Time building chain proxies: 6.28, per 1000 atoms: 0.66 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: 2.40 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.99 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: 3.03 Time building geometry restraints manager: 2.79 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: 0.00 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: 1.640 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 25.300 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 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= 0.214 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.007 0.001 TRP B 256 HIS 0.001 0.000 HIS C 41 PHE 0.007 0.001 PHE A 218 TYR 0.009 0.001 TYR B 285 ARG 0.003 0.000 ARG A 315 *********************** 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 : 1.098 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: 1.4386 time to fit residues: 208.5905 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 : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 7.9990 chunk 93 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN A 366 ASN A 413 GLN A 451 ASN B 252 GLN B 413 GLN B 451 ASN C 252 GLN C 413 GLN C 451 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1568 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= 0.280 Angle : 0.578 7.838 13080 Z= 0.306 Chirality : 0.040 0.153 1659 Planarity : 0.004 0.030 1593 Dihedral : 3.682 16.783 1308 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.92 % Allowed : 20.37 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.24), residues: 1230 helix: 1.54 (0.17), residues: 978 sheet: 1.00 (0.65), residues: 48 loop : -1.18 (0.38), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 19 HIS 0.002 0.001 HIS A 296 PHE 0.012 0.002 PHE C 99 TYR 0.013 0.002 TYR C 285 ARG 0.007 0.001 ARG B 315 *********************** 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 154 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 1.229 Fit side-chains revert: symmetry clash REVERT: A 39 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7476 (mtp-110) REVERT: A 473 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.8018 (mtp) REVERT: B 115 SER cc_start: 0.7795 (t) cc_final: 0.7358 (m) REVERT: B 205 MET cc_start: 0.8343 (ptm) cc_final: 0.8044 (ptm) REVERT: B 329 MET cc_start: 0.7698 (mmt) cc_final: 0.7403 (mmt) outliers start: 20 outliers final: 7 residues processed: 147 average time/residue: 1.3366 time to fit residues: 209.7465 Evaluate side-chains 138 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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 364 THR Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 472 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN B 252 GLN B 385 ASN C 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9639 Z= 0.183 Angle : 0.499 7.211 13080 Z= 0.262 Chirality : 0.037 0.146 1659 Planarity : 0.004 0.033 1593 Dihedral : 3.531 15.565 1308 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.31 % Allowed : 20.37 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.24), residues: 1230 helix: 1.80 (0.17), residues: 978 sheet: 1.06 (0.65), residues: 48 loop : -0.87 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 19 HIS 0.001 0.000 HIS C 296 PHE 0.016 0.001 PHE B 99 TYR 0.010 0.001 TYR C 285 ARG 0.008 0.001 ARG C 315 *********************** 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 155 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 1.047 Fit side-chains REVERT: A 39 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7319 (mtp-110) REVERT: A 241 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.8317 (t0) REVERT: A 473 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.8046 (mtp) REVERT: B 205 MET cc_start: 0.8314 (ptm) cc_final: 0.8034 (ptm) REVERT: B 329 MET cc_start: 0.7688 (mmt) cc_final: 0.7425 (mmt) REVERT: C 346 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7401 (mm-30) outliers start: 24 outliers final: 11 residues processed: 149 average time/residue: 1.3293 time to fit residues: 211.4483 Evaluate side-chains 144 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 1.113 ------------------------------------------------------------------------------- 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 265 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 472 GLN Chi-restraints excluded: chain C residue 474 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 58 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 75 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 118 optimal weight: 0.0870 chunk 106 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 99 optimal weight: 0.3980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN A 383 GLN B 252 GLN B 385 ASN C 252 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1593 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= 0.137 Angle : 0.459 6.924 13080 Z= 0.239 Chirality : 0.036 0.138 1659 Planarity : 0.003 0.033 1593 Dihedral : 3.384 15.152 1308 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.79 % Allowed : 19.98 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.24), residues: 1230 helix: 2.11 (0.17), residues: 966 sheet: 0.05 (0.72), residues: 54 loop : -0.61 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 19 HIS 0.001 0.000 HIS A 41 PHE 0.016 0.001 PHE B 99 TYR 0.009 0.001 TYR A 285 ARG 0.008 0.000 ARG B 315 *********************** 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 157 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 1.106 Fit side-chains REVERT: A 39 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7284 (mtp-110) REVERT: A 116 ILE cc_start: 0.7063 (mt) cc_final: 0.6852 (mt) REVERT: B 205 MET cc_start: 0.8302 (ptm) cc_final: 0.8047 (ptm) REVERT: B 241 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.8291 (m-40) REVERT: C 346 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7367 (mm-30) outliers start: 29 outliers final: 6 residues processed: 152 average time/residue: 1.2841 time to fit residues: 208.6858 Evaluate side-chains 132 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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 265 LEU 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 Chi-restraints excluded: chain C residue 364 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 60 optimal weight: 0.5980 chunk 106 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN B 252 GLN B 385 ASN C 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9639 Z= 0.204 Angle : 0.509 7.291 13080 Z= 0.266 Chirality : 0.038 0.141 1659 Planarity : 0.004 0.038 1593 Dihedral : 3.514 15.337 1308 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.50 % Allowed : 20.08 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.24), residues: 1230 helix: 1.86 (0.17), residues: 981 sheet: 1.11 (0.67), residues: 48 loop : -0.97 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 19 HIS 0.001 0.001 HIS C 296 PHE 0.017 0.002 PHE B 99 TYR 0.011 0.002 TYR C 285 ARG 0.008 0.001 ARG B 315 *********************** 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 157 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 1.157 Fit side-chains REVERT: A 39 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7354 (mtp-110) REVERT: A 241 ASN cc_start: 0.8729 (OUTLIER) cc_final: 0.8280 (t0) REVERT: A 396 THR cc_start: 0.7899 (m) cc_final: 0.7697 (m) REVERT: A 469 GLU cc_start: 0.8101 (mp0) cc_final: 0.7397 (mp0) REVERT: B 39 ARG cc_start: 0.7772 (ttp80) cc_final: 0.7371 (ttt-90) REVERT: B 115 SER cc_start: 0.7826 (t) cc_final: 0.7409 (m) REVERT: B 205 MET cc_start: 0.8277 (ptm) cc_final: 0.8040 (ptm) REVERT: C 346 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7417 (mm-30) outliers start: 26 outliers final: 9 residues processed: 151 average time/residue: 1.3017 time to fit residues: 210.4894 Evaluate side-chains 140 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 1.157 ------------------------------------------------------------------------------- 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 241 ASN Chi-restraints excluded: chain A residue 265 LEU 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 472 GLN Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 472 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 69 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 62 optimal weight: 0.3980 chunk 114 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN B 252 GLN B 385 ASN C 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1722 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= 0.155 Angle : 0.475 7.121 13080 Z= 0.247 Chirality : 0.037 0.138 1659 Planarity : 0.004 0.037 1593 Dihedral : 3.426 15.192 1308 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.24), residues: 1230 helix: 2.08 (0.17), residues: 969 sheet: 0.12 (0.73), residues: 54 loop : -0.47 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 19 HIS 0.001 0.000 HIS A 41 PHE 0.018 0.001 PHE B 99 TYR 0.009 0.001 TYR B 285 ARG 0.009 0.000 ARG C 315 *********************** 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 149 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 1.303 Fit side-chains REVERT: A 39 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7257 (mtp-110) REVERT: A 241 ASN cc_start: 0.8671 (OUTLIER) cc_final: 0.8339 (t0) REVERT: A 396 THR cc_start: 0.7955 (m) cc_final: 0.7751 (m) REVERT: A 469 GLU cc_start: 0.8063 (mp0) cc_final: 0.7455 (mp0) REVERT: B 39 ARG cc_start: 0.7738 (ttp80) cc_final: 0.7331 (ttt-90) REVERT: B 205 MET cc_start: 0.8306 (ptm) cc_final: 0.8054 (ptm) REVERT: B 396 THR cc_start: 0.7906 (m) cc_final: 0.7630 (t) REVERT: C 346 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7362 (mm-30) outliers start: 19 outliers final: 9 residues processed: 145 average time/residue: 1.2807 time to fit residues: 198.6551 Evaluate side-chains 135 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 241 ASN Chi-restraints excluded: chain A residue 265 LEU 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 271 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 0.9990 chunk 67 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN B 252 GLN B 385 ASN C 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9639 Z= 0.171 Angle : 0.492 7.147 13080 Z= 0.254 Chirality : 0.037 0.137 1659 Planarity : 0.004 0.040 1593 Dihedral : 3.449 15.173 1308 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.11 % Allowed : 19.69 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.24), residues: 1230 helix: 2.05 (0.17), residues: 969 sheet: 0.16 (0.73), residues: 54 loop : -0.50 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 19 HIS 0.001 0.000 HIS C 296 PHE 0.017 0.001 PHE B 99 TYR 0.010 0.001 TYR A 285 ARG 0.009 0.001 ARG B 315 *********************** 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 148 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 1.150 Fit side-chains REVERT: A 39 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.7247 (mtp-110) REVERT: A 231 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6965 (mm-30) REVERT: A 241 ASN cc_start: 0.8699 (OUTLIER) cc_final: 0.8327 (t0) REVERT: A 469 GLU cc_start: 0.8104 (mp0) cc_final: 0.7491 (mp0) REVERT: B 39 ARG cc_start: 0.7759 (ttp80) cc_final: 0.7195 (ttp80) REVERT: B 205 MET cc_start: 0.8283 (ptm) cc_final: 0.8050 (ptm) REVERT: B 396 THR cc_start: 0.7932 (m) cc_final: 0.7683 (t) REVERT: C 115 SER cc_start: 0.7756 (t) cc_final: 0.7238 (m) REVERT: C 272 GLU cc_start: 0.7322 (mm-30) cc_final: 0.7095 (mt-10) REVERT: C 346 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7376 (mm-30) outliers start: 22 outliers final: 10 residues processed: 146 average time/residue: 1.3611 time to fit residues: 212.1689 Evaluate side-chains 137 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 1.072 ------------------------------------------------------------------------------- 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 265 LEU 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 472 GLN Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 346 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN B 252 GLN B 385 ASN C 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1795 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= 0.177 Angle : 0.497 7.153 13080 Z= 0.257 Chirality : 0.037 0.138 1659 Planarity : 0.004 0.042 1593 Dihedral : 3.465 15.219 1308 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.63 % Allowed : 20.17 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.24), residues: 1230 helix: 2.02 (0.17), residues: 969 sheet: 0.15 (0.73), residues: 54 loop : -0.49 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 19 HIS 0.001 0.000 HIS A 296 PHE 0.018 0.001 PHE B 99 TYR 0.010 0.001 TYR A 285 ARG 0.009 0.001 ARG B 315 *********************** 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 145 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 1.142 Fit side-chains REVERT: A 39 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7290 (mtp-110) REVERT: A 231 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6974 (mm-30) REVERT: A 241 ASN cc_start: 0.8697 (OUTLIER) cc_final: 0.8334 (t0) REVERT: A 469 GLU cc_start: 0.8140 (mp0) cc_final: 0.7544 (mp0) REVERT: B 39 ARG cc_start: 0.7810 (ttp80) cc_final: 0.7234 (ttp80) REVERT: B 205 MET cc_start: 0.8265 (ptm) cc_final: 0.8030 (ptm) REVERT: B 396 THR cc_start: 0.7929 (m) cc_final: 0.7684 (t) REVERT: C 115 SER cc_start: 0.7753 (t) cc_final: 0.7234 (m) REVERT: C 272 GLU cc_start: 0.7294 (mm-30) cc_final: 0.7060 (mt-10) REVERT: C 346 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7360 (mm-30) outliers start: 17 outliers final: 11 residues processed: 143 average time/residue: 1.2593 time to fit residues: 192.6959 Evaluate side-chains 141 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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 265 LEU 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 271 ILE Chi-restraints excluded: chain B residue 472 GLN Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 271 ILE 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 103 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN B 252 GLN C 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1839 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= 0.197 Angle : 0.515 7.287 13080 Z= 0.267 Chirality : 0.038 0.139 1659 Planarity : 0.004 0.044 1593 Dihedral : 3.529 15.349 1308 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.63 % Allowed : 19.88 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.24), residues: 1230 helix: 1.91 (0.17), residues: 978 sheet: 0.17 (0.72), residues: 54 loop : -0.67 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 19 HIS 0.001 0.000 HIS A 296 PHE 0.018 0.002 PHE B 99 TYR 0.010 0.001 TYR A 285 ARG 0.009 0.001 ARG B 315 *********************** 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 143 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 1.122 Fit side-chains REVERT: A 39 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7331 (mtp-110) REVERT: A 231 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7089 (mm-30) REVERT: A 241 ASN cc_start: 0.8719 (OUTLIER) cc_final: 0.8314 (t0) REVERT: A 469 GLU cc_start: 0.8157 (mp0) cc_final: 0.7546 (mp0) REVERT: B 205 MET cc_start: 0.8283 (ptm) cc_final: 0.7990 (ptm) REVERT: C 115 SER cc_start: 0.7753 (t) cc_final: 0.7255 (m) REVERT: C 272 GLU cc_start: 0.7286 (mm-30) cc_final: 0.6983 (mt-10) REVERT: C 346 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7367 (mm-30) outliers start: 17 outliers final: 9 residues processed: 142 average time/residue: 1.2980 time to fit residues: 197.1276 Evaluate side-chains 137 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 1.113 ------------------------------------------------------------------------------- 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 265 LEU 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 472 GLN 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 71 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 122 optimal weight: 0.2980 chunk 112 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 103 optimal weight: 0.0870 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN B 252 GLN B 385 ASN C 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9639 Z= 0.137 Angle : 0.469 6.898 13080 Z= 0.241 Chirality : 0.037 0.134 1659 Planarity : 0.004 0.044 1593 Dihedral : 3.365 14.940 1308 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.63 % Allowed : 19.88 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.24), residues: 1230 helix: 2.20 (0.17), residues: 969 sheet: 0.16 (0.74), residues: 54 loop : -0.55 (0.43), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 256 HIS 0.000 0.000 HIS B 296 PHE 0.020 0.001 PHE B 99 TYR 0.009 0.001 TYR A 285 ARG 0.010 0.000 ARG A 315 ********************** 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 143 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 1.053 Fit side-chains REVERT: A 39 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7241 (mtp-110) REVERT: A 231 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6844 (mm-30) REVERT: A 469 GLU cc_start: 0.8076 (mp0) cc_final: 0.7562 (mp0) REVERT: B 205 MET cc_start: 0.8302 (ptm) cc_final: 0.8052 (ptm) REVERT: B 241 ASN cc_start: 0.8605 (OUTLIER) cc_final: 0.8310 (m-40) REVERT: C 115 SER cc_start: 0.7699 (t) cc_final: 0.7175 (m) REVERT: C 272 GLU cc_start: 0.7280 (mm-30) cc_final: 0.6958 (mt-10) REVERT: C 346 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7240 (mm-30) outliers start: 17 outliers final: 7 residues processed: 140 average time/residue: 1.3220 time to fit residues: 197.7942 Evaluate side-chains 134 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 1.162 ------------------------------------------------------------------------------- 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 231 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 472 GLN Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 271 ILE 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 29 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3969 r_free = 0.3969 target = 0.168708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.122091 restraints weight = 2738.642| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 0.90 r_work: 0.3288 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9639 Z= 0.171 Angle : 0.500 7.031 13080 Z= 0.256 Chirality : 0.037 0.135 1659 Planarity : 0.004 0.044 1593 Dihedral : 3.425 15.086 1308 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.06 % Allowed : 20.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.24), residues: 1230 helix: 2.09 (0.17), residues: 972 sheet: 0.12 (0.73), residues: 54 loop : -0.45 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 19 HIS 0.001 0.000 HIS A 296 PHE 0.019 0.001 PHE B 99 TYR 0.010 0.001 TYR A 285 ARG 0.010 0.001 ARG A 315 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3656.87 seconds wall clock time: 66 minutes 11.21 seconds (3971.21 seconds total)