Starting phenix.real_space_refine on Thu Oct 22 22:28:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wdr_65900/10_2026/9wdr_65900.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wdr_65900/10_2026/9wdr_65900.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wdr_65900/10_2026/9wdr_65900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wdr_65900/10_2026/9wdr_65900.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wdr_65900/10_2026/9wdr_65900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wdr_65900/10_2026/9wdr_65900.map" } resolution = 2.92 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= -0.000 sd= 0.027 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: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 4016 2.51 5 N 1160 2.21 5 O 1189 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6400 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3183 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 399} Chain breaks: 1 Chain: "C" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3183 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 399} Chain breaks: 1 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'WV2': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.73, per 1000 atoms: 0.27 Number of scatterers: 6400 At special positions: 0 Unit cell: (71.4, 85.85, 116.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 1189 8.00 N 1160 7.00 C 4016 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: 0.50 Conformation dependent library (CDL) restraints added in 333.9 milliseconds 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1552 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 4 sheets defined 51.1% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 68 through 75 removed outlier: 3.583A pdb=" N CYS A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 111 Processing helix chain 'A' and resid 123 through 140 Processing helix chain 'A' and resid 144 through 148 removed outlier: 3.761A pdb=" N TYR A 148 " --> pdb=" O PRO A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 279 removed outlier: 3.918A pdb=" N ARG A 270 " --> pdb=" O GLU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 302 removed outlier: 3.971A pdb=" N VAL A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY A 302 " --> pdb=" O ARG A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 322 removed outlier: 3.809A pdb=" N VAL A 320 " --> pdb=" O ASN A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 330 removed outlier: 3.576A pdb=" N GLU A 328 " --> pdb=" O ASP A 324 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 364 removed outlier: 3.509A pdb=" N ALA A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 384 through 398 removed outlier: 3.840A pdb=" N GLY A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 429 removed outlier: 3.566A pdb=" N ALA A 417 " --> pdb=" O PHE A 413 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 418 " --> pdb=" O PRO A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 444 removed outlier: 3.574A pdb=" N LEU A 437 " --> pdb=" O TYR A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 467 removed outlier: 3.513A pdb=" N VAL A 454 " --> pdb=" O ASP A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 486 Processing helix chain 'A' and resid 499 through 506 Processing helix chain 'A' and resid 507 through 509 No H-bonds generated for 'chain 'A' and resid 507 through 509' Processing helix chain 'A' and resid 524 through 543 removed outlier: 3.568A pdb=" N ASP A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 75 removed outlier: 3.534A pdb=" N CYS C 74 " --> pdb=" O LEU C 70 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU C 75 " --> pdb=" O GLU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 111 Processing helix chain 'C' and resid 123 through 140 Processing helix chain 'C' and resid 144 through 148 removed outlier: 3.759A pdb=" N TYR C 148 " --> pdb=" O PRO C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 279 removed outlier: 4.170A pdb=" N ARG C 270 " --> pdb=" O GLU C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 302 removed outlier: 3.885A pdb=" N VAL C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY C 302 " --> pdb=" O ARG C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 306 removed outlier: 3.663A pdb=" N HIS C 306 " --> pdb=" O PRO C 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 303 through 306' Processing helix chain 'C' and resid 316 through 322 removed outlier: 3.535A pdb=" N VAL C 320 " --> pdb=" O ASN C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 330 removed outlier: 3.544A pdb=" N ILE C 326 " --> pdb=" O ARG C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 347 No H-bonds generated for 'chain 'C' and resid 345 through 347' Processing helix chain 'C' and resid 348 through 364 Processing helix chain 'C' and resid 374 through 379 removed outlier: 3.533A pdb=" N ILE C 378 " --> pdb=" O GLU C 375 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR C 379 " --> pdb=" O SER C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 398 removed outlier: 3.939A pdb=" N GLY C 398 " --> pdb=" O ALA C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 429 removed outlier: 3.613A pdb=" N ALA C 417 " --> pdb=" O PHE C 413 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 418 " --> pdb=" O PRO C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 444 removed outlier: 3.701A pdb=" N LEU C 437 " --> pdb=" O TYR C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 467 Processing helix chain 'C' and resid 478 through 487 removed outlier: 4.481A pdb=" N TYR C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 506 Processing helix chain 'C' and resid 507 through 509 No H-bonds generated for 'chain 'C' and resid 507 through 509' Processing helix chain 'C' and resid 524 through 543 removed outlier: 3.745A pdb=" N ASP C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 93 removed outlier: 6.436A pdb=" N ALA A 115 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ASP A 156 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU A 117 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE A 153 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N PHE A 284 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU A 155 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY A 332 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET A 403 " --> pdb=" O CYS A 369 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N SER A 89 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N LEU A 404 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE A 91 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 512 through 516 removed outlier: 6.874A pdb=" N VAL A 493 " --> pdb=" O PHE A 513 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N LEU A 515 " --> pdb=" O VAL A 493 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA A 495 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE A 471 " --> pdb=" O ILE A 494 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL A 496 " --> pdb=" O ILE A 471 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL A 473 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA A 470 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 567 " --> pdb=" O THR A 556 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 89 through 94 removed outlier: 5.019A pdb=" N ASN C 118 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ALA C 115 " --> pdb=" O ALA C 154 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ASP C 156 " --> pdb=" O ALA C 115 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU C 117 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE C 153 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N PHE C 284 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU C 155 " --> pdb=" O PHE C 284 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY C 332 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS C 401 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET C 403 " --> pdb=" O CYS C 369 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N SER C 89 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N LEU C 404 " --> pdb=" O SER C 89 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE C 91 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 512 through 516 removed outlier: 6.915A pdb=" N VAL C 493 " --> pdb=" O PHE C 513 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU C 515 " --> pdb=" O VAL C 493 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA C 495 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE C 471 " --> pdb=" O ILE C 494 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N VAL C 496 " --> pdb=" O ILE C 471 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL C 473 " --> pdb=" O VAL C 496 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA C 470 " --> pdb=" O LEU C 551 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C 567 " --> pdb=" O THR C 556 " (cutoff:3.500A) 296 hydrogen bonds defined for protein. 864 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: 0.84 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1087 1.28 - 1.42: 1535 1.42 - 1.56: 3825 1.56 - 1.69: 3 1.69 - 1.83: 56 Bond restraints: 6506 Sorted by residual: bond pdb=" C20 WV2 C 601 " pdb=" N3 WV2 C 601 " ideal model delta sigma weight residual 1.451 1.140 0.311 2.00e-02 2.50e+03 2.42e+02 bond pdb=" C15 WV2 C 601 " pdb=" N3 WV2 C 601 " ideal model delta sigma weight residual 1.450 1.143 0.307 2.00e-02 2.50e+03 2.36e+02 bond pdb=" C14 WV2 C 601 " pdb=" C15 WV2 C 601 " ideal model delta sigma weight residual 1.521 1.370 0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" C20 WV2 C 601 " pdb=" C21 WV2 C 601 " ideal model delta sigma weight residual 1.520 1.376 0.144 2.00e-02 2.50e+03 5.15e+01 bond pdb=" C13 WV2 C 601 " pdb=" N2 WV2 C 601 " ideal model delta sigma weight residual 1.351 1.479 -0.128 2.00e-02 2.50e+03 4.12e+01 ... (remaining 6501 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.62: 8767 3.62 - 7.24: 39 7.24 - 10.87: 0 10.87 - 14.49: 2 14.49 - 18.11: 2 Bond angle restraints: 8810 Sorted by residual: angle pdb=" O WV2 C 601 " pdb=" S WV2 C 601 " pdb=" O2 WV2 C 601 " ideal model delta sigma weight residual 118.67 100.56 18.11 3.00e+00 1.11e-01 3.64e+01 angle pdb=" C15 WV2 C 601 " pdb=" N3 WV2 C 601 " pdb=" C20 WV2 C 601 " ideal model delta sigma weight residual 110.57 127.52 -16.95 3.00e+00 1.11e-01 3.19e+01 angle pdb=" C14 WV2 C 601 " pdb=" C15 WV2 C 601 " pdb=" N3 WV2 C 601 " ideal model delta sigma weight residual 111.19 124.89 -13.70 3.00e+00 1.11e-01 2.09e+01 angle pdb=" C21 WV2 C 601 " pdb=" C20 WV2 C 601 " pdb=" N3 WV2 C 601 " ideal model delta sigma weight residual 110.75 124.39 -13.64 3.00e+00 1.11e-01 2.07e+01 angle pdb=" C THR A 565 " pdb=" N ASN A 566 " pdb=" CA ASN A 566 " ideal model delta sigma weight residual 122.08 127.77 -5.69 1.47e+00 4.63e-01 1.50e+01 ... (remaining 8805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.21: 3600 27.21 - 54.42: 335 54.42 - 81.63: 51 81.63 - 108.84: 2 108.84 - 136.04: 4 Dihedral angle restraints: 3992 sinusoidal: 1592 harmonic: 2400 Sorted by residual: dihedral pdb=" C15 WV2 C 601 " pdb=" C16 WV2 C 601 " pdb=" N3 WV2 C 601 " pdb=" C17 WV2 C 601 " ideal model delta sinusoidal sigma weight residual 65.11 -70.93 136.04 1 3.00e+01 1.11e-03 1.83e+01 dihedral pdb=" C9 WV2 C 601 " pdb=" N1 WV2 C 601 " pdb=" S WV2 C 601 " pdb=" O2 WV2 C 601 " ideal model delta sinusoidal sigma weight residual 72.13 -154.56 -133.31 1 3.00e+01 1.11e-03 1.80e+01 dihedral pdb=" C WV2 C 601 " pdb=" N1 WV2 C 601 " pdb=" S WV2 C 601 " pdb=" C9 WV2 C 601 " ideal model delta sinusoidal sigma weight residual 42.25 -84.41 126.66 1 3.00e+01 1.11e-03 1.70e+01 ... (remaining 3989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 906 0.072 - 0.143: 107 0.143 - 0.215: 1 0.215 - 0.286: 0 0.286 - 0.358: 1 Chirality restraints: 1015 Sorted by residual: chirality pdb=" C17 WV2 C 601 " pdb=" C16 WV2 C 601 " pdb=" C18 WV2 C 601 " pdb=" C19 WV2 C 601 " both_signs ideal model delta sigma weight residual True 2.39 2.75 -0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" CA ASN C 566 " pdb=" N ASN C 566 " pdb=" C ASN C 566 " pdb=" CB ASN C 566 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.53e-01 chirality pdb=" CA ILE A 471 " pdb=" N ILE A 471 " pdb=" C ILE A 471 " pdb=" CB ILE A 471 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 1012 not shown) Planarity restraints: 1153 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 344 " -0.038 5.00e-02 4.00e+02 5.74e-02 5.28e+00 pdb=" N PRO C 345 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 345 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 345 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 486 " -0.175 9.50e-02 1.11e+02 7.92e-02 4.81e+00 pdb=" NE ARG A 486 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 486 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG A 486 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 486 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 486 " -0.171 9.50e-02 1.11e+02 7.73e-02 4.61e+00 pdb=" NE ARG C 486 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG C 486 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG C 486 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG C 486 " -0.001 2.00e-02 2.50e+03 ... (remaining 1150 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 856 2.76 - 3.30: 5481 3.30 - 3.83: 10130 3.83 - 4.37: 11146 4.37 - 4.90: 20488 Nonbonded interactions: 48101 Sorted by model distance: nonbonded pdb=" OE1 GLU A 440 " pdb=" OG1 THR C 68 " model vdw 2.225 3.040 nonbonded pdb=" OG SER C 100 " pdb=" OE1 GLU C 102 " model vdw 2.283 3.040 nonbonded pdb=" OG SER A 144 " pdb=" OG SER A 147 " model vdw 2.385 3.040 nonbonded pdb=" OG1 THR A 68 " pdb=" OE2 GLU C 440 " model vdw 2.394 3.040 nonbonded pdb=" OG1 THR A 68 " pdb=" N PHE A 69 " model vdw 2.410 3.120 ... (remaining 48096 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 'C' and resid 66 through 574) } 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: 1.620 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.860 Find NCS groups from input model: 0.110 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:6.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.311 6506 Z= 0.358 Angle : 0.705 18.112 8810 Z= 0.336 Chirality : 0.046 0.358 1015 Planarity : 0.007 0.079 1153 Dihedral : 20.098 136.044 2440 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.00 % Allowed : 32.93 % Favored : 67.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.28), residues: 832 helix: 0.66 (0.24), residues: 382 sheet: 1.30 (0.41), residues: 166 loop : -1.07 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 486 TYR 0.012 0.002 TYR A 517 PHE 0.012 0.001 PHE A 274 TRP 0.009 0.001 TRP C 525 HIS 0.004 0.001 HIS A 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00725 / 0.36 ( 6506) covalent geometry : angle 0.70535 / 0.34 ( 8810) hydrogen bonds : bond 0.17200 / 11.39 ( 296) hydrogen bonds : angle 5.04714 / 3.57 ( 864) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.191 Fit side-chains REVERT: C 158 LYS cc_start: 0.6987 (ttpt) cc_final: 0.6577 (ttpp) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.6902 time to fit residues: 49.5513 Evaluate side-chains 65 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 HIS C 118 ASN C 133 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.190073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.147890 restraints weight = 6734.680| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.49 r_work: 0.3371 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6506 Z= 0.161 Angle : 0.539 6.228 8810 Z= 0.277 Chirality : 0.045 0.156 1015 Planarity : 0.005 0.042 1153 Dihedral : 10.521 125.599 946 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.34 % Allowed : 25.90 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.29), residues: 832 helix: 1.50 (0.25), residues: 390 sheet: 0.69 (0.40), residues: 170 loop : -0.81 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 486 TYR 0.010 0.001 TYR A 517 PHE 0.012 0.001 PHE C 274 TRP 0.007 0.001 TRP C 525 HIS 0.005 0.001 HIS C 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.16 ( 6506) covalent geometry : angle 0.53943 / 0.28 ( 8810) hydrogen bonds : bond 0.05761 / 3.96 ( 296) hydrogen bonds : angle 3.56378 / 2.50 ( 864) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 65 time to evaluate : 0.241 Fit side-chains REVERT: A 277 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6886 (tm-30) REVERT: A 373 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.7917 (mtt) REVERT: A 464 PHE cc_start: 0.7494 (OUTLIER) cc_final: 0.6861 (t80) REVERT: C 136 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7602 (tt0) REVERT: C 158 LYS cc_start: 0.6968 (ttpt) cc_final: 0.6560 (ttpp) REVERT: C 373 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.7587 (mtt) REVERT: C 380 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7508 (mttp) REVERT: C 531 ARG cc_start: 0.6847 (mtp180) cc_final: 0.6443 (mmt-90) outliers start: 29 outliers final: 7 residues processed: 85 average time/residue: 0.6585 time to fit residues: 58.2858 Evaluate side-chains 76 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 373 MET Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 548 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: [20, 40, 27, 53, 59, 31, 35, 66, 46, 50, 8] chunk 20 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 566 ASN C 118 ASN C 133 ASN C 317 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.185159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.142761 restraints weight = 6536.238| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.39 r_work: 0.3379 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6506 Z= 0.213 Angle : 0.585 6.393 8810 Z= 0.302 Chirality : 0.046 0.162 1015 Planarity : 0.005 0.037 1153 Dihedral : 10.543 126.730 946 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.49 % Allowed : 23.35 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.28), residues: 832 helix: 1.57 (0.26), residues: 386 sheet: 0.50 (0.39), residues: 164 loop : -0.95 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 337 TYR 0.009 0.002 TYR A 126 PHE 0.014 0.002 PHE C 274 TRP 0.006 0.001 TRP C 525 HIS 0.006 0.001 HIS C 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.21 ( 6506) covalent geometry : angle 0.58519 / 0.30 ( 8810) hydrogen bonds : bond 0.06466 / 4.45 ( 296) hydrogen bonds : angle 3.59870 / 2.52 ( 864) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 68 time to evaluate : 0.254 Fit side-chains REVERT: A 158 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7556 (ttpp) REVERT: A 380 LYS cc_start: 0.8316 (mtmt) cc_final: 0.8000 (mttp) REVERT: A 464 PHE cc_start: 0.7610 (OUTLIER) cc_final: 0.6905 (t80) REVERT: A 568 MET cc_start: 0.2427 (mtm) cc_final: 0.1942 (tmm) REVERT: C 136 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7603 (tt0) REVERT: C 158 LYS cc_start: 0.6810 (ttpt) cc_final: 0.6331 (ttpp) REVERT: C 347 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.7017 (pt0) REVERT: C 373 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.7674 (mtt) REVERT: C 380 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7545 (mttp) REVERT: C 382 ARG cc_start: 0.7879 (mtp-110) cc_final: 0.7558 (mtp85) REVERT: C 429 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7736 (mt-10) REVERT: C 439 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6699 (mt-10) REVERT: C 531 ARG cc_start: 0.7032 (mtp180) cc_final: 0.6592 (mmt-90) REVERT: C 547 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6307 (mtt180) outliers start: 30 outliers final: 14 residues processed: 89 average time/residue: 0.6023 time to fit residues: 56.1154 Evaluate side-chains 89 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 66 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 373 MET Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 439 GLU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 547 ARG Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 572 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: [49, 52, 50, 5, 58, 74, 38, 48, 13, 22, 26] chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 0.0870 chunk 50 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 13 optimal weight: 0.0970 chunk 22 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 118 ASN C 133 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.188549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.141838 restraints weight = 6537.882| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 3.05 r_work: 0.3381 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6506 Z= 0.096 Angle : 0.450 4.412 8810 Z= 0.231 Chirality : 0.042 0.139 1015 Planarity : 0.003 0.034 1153 Dihedral : 9.873 123.073 946 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.14 % Allowed : 25.15 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.13 (0.29), residues: 832 helix: 2.01 (0.26), residues: 388 sheet: 0.27 (0.39), residues: 170 loop : -0.74 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 382 TYR 0.012 0.001 TYR A 517 PHE 0.012 0.001 PHE C 274 TRP 0.007 0.001 TRP C 525 HIS 0.003 0.001 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 ( 6506) covalent geometry : angle 0.44963 / 0.23 ( 8810) hydrogen bonds : bond 0.03734 / 2.59 ( 296) hydrogen bonds : angle 3.30602 / 2.31 ( 864) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.256 Fit side-chains REVERT: A 380 LYS cc_start: 0.8158 (mtmt) cc_final: 0.7818 (mttp) REVERT: A 464 PHE cc_start: 0.7441 (OUTLIER) cc_final: 0.6898 (t80) REVERT: C 136 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7555 (tt0) REVERT: C 158 LYS cc_start: 0.6906 (ttpt) cc_final: 0.6484 (ttpp) REVERT: C 380 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7410 (mttp) REVERT: C 531 ARG cc_start: 0.6867 (mtp180) cc_final: 0.6428 (mmt-90) outliers start: 21 outliers final: 8 residues processed: 91 average time/residue: 0.6271 time to fit residues: 59.6199 Evaluate side-chains 84 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 564 TYR Chi-restraints excluded: chain C residue 572 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: [64, 82, 8, 44, 33, 15, 20, 21, 38, 30, 79] chunk 64 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 118 ASN C 133 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.190079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.147196 restraints weight = 6757.865| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.42 r_work: 0.3433 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6506 Z= 0.098 Angle : 0.444 4.659 8810 Z= 0.228 Chirality : 0.042 0.139 1015 Planarity : 0.003 0.034 1153 Dihedral : 9.693 122.117 946 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.59 % Allowed : 25.15 % Favored : 71.26 % 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: 1.32 (0.30), residues: 832 helix: 2.22 (0.27), residues: 388 sheet: 0.25 (0.39), residues: 170 loop : -0.65 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 486 TYR 0.009 0.001 TYR A 517 PHE 0.011 0.001 PHE C 274 TRP 0.006 0.001 TRP C 525 HIS 0.003 0.001 HIS C 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 ( 6506) covalent geometry : angle 0.44442 / 0.23 ( 8810) hydrogen bonds : bond 0.03842 / 2.67 ( 296) hydrogen bonds : angle 3.22958 / 2.25 ( 864) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.208 Fit side-chains REVERT: A 139 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7407 (mm-30) REVERT: A 287 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.7465 (t80) REVERT: A 380 LYS cc_start: 0.8158 (mtmt) cc_final: 0.7850 (mttp) REVERT: A 464 PHE cc_start: 0.7577 (OUTLIER) cc_final: 0.6928 (t80) REVERT: C 136 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7622 (tt0) REVERT: C 158 LYS cc_start: 0.6931 (ttpt) cc_final: 0.6493 (ttpp) REVERT: C 373 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.7525 (mtt) REVERT: C 380 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7486 (mttp) REVERT: C 439 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6681 (mt-10) REVERT: C 531 ARG cc_start: 0.6924 (mtp180) cc_final: 0.6489 (mmt-90) REVERT: C 547 ARG cc_start: 0.6999 (OUTLIER) cc_final: 0.6211 (mtt180) outliers start: 24 outliers final: 9 residues processed: 85 average time/residue: 0.6300 time to fit residues: 55.9769 Evaluate side-chains 90 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 373 MET Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 439 GLU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 547 ARG Chi-restraints excluded: chain C residue 572 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: [45, 19, 40, 81, 25, 24, 42, 51, 29, 35, 5] chunk 45 optimal weight: 3.9990 chunk 19 optimal weight: 0.0870 chunk 40 optimal weight: 7.9990 chunk 81 optimal weight: 0.1980 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 chunk 29 optimal weight: 0.0270 chunk 35 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 overall best weight: 0.9818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 118 ASN C 133 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.190828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.142950 restraints weight = 6618.930| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 3.29 r_work: 0.3410 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6506 Z= 0.105 Angle : 0.447 4.225 8810 Z= 0.230 Chirality : 0.042 0.140 1015 Planarity : 0.004 0.040 1153 Dihedral : 9.656 122.399 946 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.74 % Allowed : 24.85 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.30), residues: 832 helix: 2.24 (0.26), residues: 388 sheet: 0.22 (0.39), residues: 170 loop : -0.62 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 486 TYR 0.009 0.001 TYR A 517 PHE 0.011 0.001 PHE C 274 TRP 0.006 0.001 TRP C 525 HIS 0.003 0.001 HIS C 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 6506) covalent geometry : angle 0.44675 / 0.23 ( 8810) hydrogen bonds : bond 0.03961 / 2.75 ( 296) hydrogen bonds : angle 3.22827 / 2.25 ( 864) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 78 time to evaluate : 0.185 Fit side-chains REVERT: A 158 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7458 (ttpp) REVERT: A 277 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6876 (tm-30) REVERT: A 287 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.7411 (t80) REVERT: A 373 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.7742 (mtt) REVERT: A 380 LYS cc_start: 0.8053 (mtmt) cc_final: 0.7726 (mttp) REVERT: A 464 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.6860 (t80) REVERT: A 568 MET cc_start: 0.2250 (mtm) cc_final: 0.1859 (tmm) REVERT: C 136 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7495 (tt0) REVERT: C 158 LYS cc_start: 0.6854 (ttpt) cc_final: 0.6409 (ttpp) REVERT: C 373 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.7454 (mtt) REVERT: C 380 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7325 (mttp) REVERT: C 439 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6554 (mt-10) REVERT: C 531 ARG cc_start: 0.6746 (mtp180) cc_final: 0.6307 (mmt-90) REVERT: C 547 ARG cc_start: 0.6975 (OUTLIER) cc_final: 0.6124 (mtt180) outliers start: 25 outliers final: 10 residues processed: 94 average time/residue: 0.6011 time to fit residues: 59.0753 Evaluate side-chains 97 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 373 MET Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 439 GLU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 547 ARG Chi-restraints excluded: chain C residue 564 TYR Chi-restraints excluded: chain C residue 572 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: [1, 47, 50, 38, 22, 81, 59, 15, 10, 24, 51] chunk 1 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 22 optimal weight: 0.0050 chunk 81 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 overall best weight: 1.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 118 ASN C 133 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.180219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.137633 restraints weight = 6766.023| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.51 r_work: 0.3436 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6506 Z= 0.141 Angle : 0.491 4.588 8810 Z= 0.253 Chirality : 0.043 0.148 1015 Planarity : 0.004 0.042 1153 Dihedral : 9.706 123.635 946 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.04 % Allowed : 24.55 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.30), residues: 832 helix: 2.10 (0.26), residues: 388 sheet: 0.25 (0.39), residues: 166 loop : -0.65 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 486 TYR 0.009 0.001 TYR A 517 PHE 0.011 0.001 PHE C 274 TRP 0.005 0.001 TRP C 525 HIS 0.005 0.001 HIS C 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.14 ( 6506) covalent geometry : angle 0.49106 / 0.25 ( 8810) hydrogen bonds : bond 0.04883 / 3.38 ( 296) hydrogen bonds : angle 3.30441 / 2.31 ( 864) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 75 time to evaluate : 0.239 Fit side-chains REVERT: A 158 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7553 (ttpp) REVERT: A 277 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7008 (tm-30) REVERT: A 287 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.7471 (t80) REVERT: A 380 LYS cc_start: 0.8230 (mtmt) cc_final: 0.7891 (mttp) REVERT: A 464 PHE cc_start: 0.7671 (OUTLIER) cc_final: 0.6953 (t80) REVERT: A 568 MET cc_start: 0.2607 (mtm) cc_final: 0.2075 (tmm) REVERT: C 136 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7625 (tt0) REVERT: C 158 LYS cc_start: 0.6818 (ttpt) cc_final: 0.6331 (ttpp) REVERT: C 373 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.7621 (mtt) REVERT: C 380 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7520 (mttp) REVERT: C 429 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7552 (mt-10) REVERT: C 439 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6766 (mt-10) REVERT: C 531 ARG cc_start: 0.7035 (mtp180) cc_final: 0.6597 (mmt-90) REVERT: C 547 ARG cc_start: 0.7027 (OUTLIER) cc_final: 0.6241 (mtt180) outliers start: 27 outliers final: 10 residues processed: 93 average time/residue: 0.6014 time to fit residues: 58.4837 Evaluate side-chains 93 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 373 MET Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 439 GLU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 547 ARG Chi-restraints excluded: chain C residue 564 TYR Chi-restraints excluded: chain C residue 572 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: [72, 7, 8, 83, 80, 29, 25, 58, 22, 0, 32] chunk 72 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 22 optimal weight: 0.0370 chunk 0 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 278 HIS C 118 ASN C 133 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.188324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.142299 restraints weight = 6559.198| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.96 r_work: 0.3412 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6506 Z= 0.171 Angle : 0.532 5.225 8810 Z= 0.275 Chirality : 0.044 0.154 1015 Planarity : 0.004 0.040 1153 Dihedral : 9.764 125.600 946 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.59 % Allowed : 24.85 % Favored : 71.56 % 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: 1.02 (0.29), residues: 832 helix: 1.95 (0.26), residues: 386 sheet: 0.14 (0.39), residues: 166 loop : -0.76 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 486 TYR 0.010 0.002 TYR A 517 PHE 0.012 0.002 PHE C 274 TRP 0.004 0.001 TRP C 525 HIS 0.005 0.001 HIS C 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.17 ( 6506) covalent geometry : angle 0.53195 / 0.28 ( 8810) hydrogen bonds : bond 0.05522 / 3.82 ( 296) hydrogen bonds : angle 3.40392 / 2.38 ( 864) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.250 Fit side-chains REVERT: A 158 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7498 (ttpp) REVERT: A 277 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6995 (tm-30) REVERT: A 287 PHE cc_start: 0.7867 (OUTLIER) cc_final: 0.7251 (t80) REVERT: A 380 LYS cc_start: 0.8234 (mtmt) cc_final: 0.7863 (mttp) REVERT: A 464 PHE cc_start: 0.7744 (OUTLIER) cc_final: 0.6998 (t80) REVERT: A 568 MET cc_start: 0.2720 (mtm) cc_final: 0.2244 (tmm) REVERT: C 136 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7529 (tt0) REVERT: C 158 LYS cc_start: 0.6825 (ttpt) cc_final: 0.6353 (ttpp) REVERT: C 380 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7488 (mttp) REVERT: C 429 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7758 (mt-10) REVERT: C 439 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6579 (mt-10) REVERT: C 531 ARG cc_start: 0.6956 (mtp180) cc_final: 0.6507 (mmt-90) REVERT: C 547 ARG cc_start: 0.7106 (OUTLIER) cc_final: 0.6192 (mpt180) outliers start: 24 outliers final: 9 residues processed: 91 average time/residue: 0.6192 time to fit residues: 58.8322 Evaluate side-chains 91 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 439 GLU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 547 ARG Chi-restraints excluded: chain C residue 564 TYR Chi-restraints excluded: chain C residue 572 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: [16, 40, 57, 65, 83, 32, 67, 78, 52, 76, 63] chunk 16 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 67 optimal weight: 7.9990 chunk 78 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 HIS C 118 ASN C 133 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.189683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.143342 restraints weight = 6627.716| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 3.14 r_work: 0.3426 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6506 Z= 0.127 Angle : 0.487 5.310 8810 Z= 0.251 Chirality : 0.043 0.146 1015 Planarity : 0.004 0.036 1153 Dihedral : 9.725 125.106 946 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.29 % Allowed : 25.30 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.30), residues: 832 helix: 2.08 (0.26), residues: 386 sheet: 0.16 (0.39), residues: 166 loop : -0.68 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 486 TYR 0.013 0.001 TYR A 517 PHE 0.011 0.001 PHE C 274 TRP 0.006 0.001 TRP C 525 HIS 0.004 0.001 HIS C 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 6506) covalent geometry : angle 0.48721 / 0.25 ( 8810) hydrogen bonds : bond 0.04539 / 3.14 ( 296) hydrogen bonds : angle 3.31693 / 2.33 ( 864) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.149 Fit side-chains REVERT: A 158 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7432 (ttpp) REVERT: A 277 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6922 (tm-30) REVERT: A 287 PHE cc_start: 0.7840 (OUTLIER) cc_final: 0.7395 (t80) REVERT: A 373 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.7796 (mtt) REVERT: A 380 LYS cc_start: 0.8142 (mtmt) cc_final: 0.7751 (mttp) REVERT: A 453 GLU cc_start: 0.6709 (mp0) cc_final: 0.5914 (mp0) REVERT: A 464 PHE cc_start: 0.7660 (OUTLIER) cc_final: 0.6948 (t80) REVERT: A 568 MET cc_start: 0.2635 (mtm) cc_final: 0.2196 (tmm) REVERT: C 136 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7466 (tt0) REVERT: C 158 LYS cc_start: 0.6662 (ttpt) cc_final: 0.6230 (ttpp) REVERT: C 380 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7356 (mttp) REVERT: C 429 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7514 (mt-10) REVERT: C 439 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6485 (mt-10) REVERT: C 519 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7458 (mp0) REVERT: C 531 ARG cc_start: 0.6890 (mtp180) cc_final: 0.6434 (mmt-90) REVERT: C 547 ARG cc_start: 0.6978 (OUTLIER) cc_final: 0.6157 (mtt180) outliers start: 22 outliers final: 9 residues processed: 89 average time/residue: 0.6103 time to fit residues: 56.5918 Evaluate side-chains 92 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 439 GLU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain C residue 547 ARG Chi-restraints excluded: chain C residue 564 TYR Chi-restraints excluded: chain C residue 572 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: [72, 75, 34, 17, 81, 6, 27, 14, 77, 50, 25] chunk 72 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 HIS C 118 ASN C 133 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.189341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.146345 restraints weight = 6646.284| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.45 r_work: 0.3413 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6506 Z= 0.112 Angle : 0.468 5.499 8810 Z= 0.241 Chirality : 0.042 0.143 1015 Planarity : 0.004 0.035 1153 Dihedral : 9.667 124.401 946 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.14 % Allowed : 25.30 % Favored : 71.56 % 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: 1.29 (0.30), residues: 832 helix: 2.18 (0.26), residues: 386 sheet: 0.23 (0.40), residues: 166 loop : -0.61 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 486 TYR 0.011 0.001 TYR A 517 PHE 0.011 0.001 PHE C 274 TRP 0.007 0.001 TRP C 525 HIS 0.003 0.001 HIS A 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 ( 6506) covalent geometry : angle 0.46776 / 0.24 ( 8810) hydrogen bonds : bond 0.04125 / 2.85 ( 296) hydrogen bonds : angle 3.25728 / 2.28 ( 864) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.162 Fit side-chains REVERT: A 158 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7493 (ttpp) REVERT: A 277 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7030 (tm-30) REVERT: A 287 PHE cc_start: 0.7868 (OUTLIER) cc_final: 0.7473 (t80) REVERT: A 373 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.7783 (mtt) REVERT: A 380 LYS cc_start: 0.8230 (mtmt) cc_final: 0.7869 (mttp) REVERT: A 453 GLU cc_start: 0.6776 (mp0) cc_final: 0.6011 (mp0) REVERT: A 464 PHE cc_start: 0.7687 (OUTLIER) cc_final: 0.6994 (t80) REVERT: A 568 MET cc_start: 0.2708 (mtm) cc_final: 0.2261 (tmm) REVERT: C 136 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7608 (tt0) REVERT: C 158 LYS cc_start: 0.6769 (ttpt) cc_final: 0.6334 (ttpp) REVERT: C 380 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7415 (mttp) REVERT: C 429 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7418 (mt-10) REVERT: C 439 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6665 (mt-10) REVERT: C 519 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7525 (mp0) REVERT: C 531 ARG cc_start: 0.7026 (mtp180) cc_final: 0.6586 (mmt-90) REVERT: C 547 ARG cc_start: 0.7007 (OUTLIER) cc_final: 0.6220 (mtt180) outliers start: 21 outliers final: 9 residues processed: 86 average time/residue: 0.6350 time to fit residues: 56.9441 Evaluate side-chains 92 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 439 GLU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain C residue 547 ARG Chi-restraints excluded: chain C residue 564 TYR Chi-restraints excluded: chain C residue 572 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: [51, 13, 0, 3, 64, 2, 18, 58, 69, 46, 26] chunk 51 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 64 optimal weight: 0.0370 chunk 2 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 overall best weight: 2.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 HIS C 118 ASN C 133 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.181063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.133467 restraints weight = 6661.136| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.70 r_work: 0.3406 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6506 Z= 0.199 Angle : 0.566 6.332 8810 Z= 0.291 Chirality : 0.046 0.158 1015 Planarity : 0.004 0.037 1153 Dihedral : 9.835 125.708 946 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.29 % Allowed : 25.15 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.29), residues: 832 helix: 1.86 (0.26), residues: 386 sheet: 0.10 (0.39), residues: 166 loop : -0.82 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 486 TYR 0.014 0.002 TYR A 517 PHE 0.013 0.002 PHE C 274 TRP 0.004 0.001 TRP C 525 HIS 0.005 0.001 HIS C 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.20 ( 6506) covalent geometry : angle 0.56556 / 0.29 ( 8810) hydrogen bonds : bond 0.05955 / 4.11 ( 296) hydrogen bonds : angle 3.44240 / 2.42 ( 864) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2071.68 seconds wall clock time: 35 minutes 59.39 seconds (2159.39 seconds total)