Starting phenix.real_space_refine on Sun May 3 17:04:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v9c_64869/05_2026/9v9c_64869.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v9c_64869/05_2026/9v9c_64869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v9c_64869/05_2026/9v9c_64869.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v9c_64869/05_2026/9v9c_64869.map" model { file = "/net/cci-nas-00/data/ceres_data/9v9c_64869/05_2026/9v9c_64869.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v9c_64869/05_2026/9v9c_64869.cif" } resolution = 2.62 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= 0.004 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 80 5.16 5 C 8960 2.51 5 N 2700 2.21 5 O 2620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14360 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 718 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 4, 'TRANS': 82} Restraints were copied for chains: B, C, D, E, F, I, L, O, R, G, J, M, P, S, H, K, N, Q, T Time building chain proxies: 1.53, per 1000 atoms: 0.11 Number of scatterers: 14360 At special positions: 0 Unit cell: (85.49, 85.49, 144.42, 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 80 16.00 O 2620 8.00 N 2700 7.00 C 8960 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 721.7 milliseconds 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 0 sheets defined 93.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 355 through 365 removed outlier: 3.780A pdb=" N LEU A 359 " --> pdb=" O ASP A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 370 through 379 Processing helix chain 'A' and resid 381 through 392 Processing helix chain 'A' and resid 395 through 411 Processing helix chain 'A' and resid 412 through 416 Processing helix chain 'A' and resid 417 through 428 removed outlier: 3.859A pdb=" N LEU A 421 " --> pdb=" O THR A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 441 removed outlier: 3.502A pdb=" N ALA A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 365 Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'B' and resid 370 through 379 Processing helix chain 'B' and resid 381 through 392 Processing helix chain 'B' and resid 395 through 411 Processing helix chain 'B' and resid 412 through 416 Processing helix chain 'B' and resid 417 through 428 removed outlier: 3.859A pdb=" N LEU B 421 " --> pdb=" O THR B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 441 removed outlier: 3.501A pdb=" N ALA B 440 " --> pdb=" O ASP B 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 365 Processing helix chain 'C' and resid 367 through 369 No H-bonds generated for 'chain 'C' and resid 367 through 369' Processing helix chain 'C' and resid 370 through 379 Processing helix chain 'C' and resid 381 through 392 Processing helix chain 'C' and resid 395 through 411 Processing helix chain 'C' and resid 412 through 416 Processing helix chain 'C' and resid 417 through 428 removed outlier: 3.859A pdb=" N LEU C 421 " --> pdb=" O THR C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 441 removed outlier: 3.501A pdb=" N ALA C 440 " --> pdb=" O ASP C 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 365 Processing helix chain 'D' and resid 367 through 369 No H-bonds generated for 'chain 'D' and resid 367 through 369' Processing helix chain 'D' and resid 370 through 379 Processing helix chain 'D' and resid 381 through 392 Processing helix chain 'D' and resid 395 through 411 Processing helix chain 'D' and resid 412 through 416 Processing helix chain 'D' and resid 417 through 428 removed outlier: 3.859A pdb=" N LEU D 421 " --> pdb=" O THR D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 441 removed outlier: 3.501A pdb=" N ALA D 440 " --> pdb=" O ASP D 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 365 Processing helix chain 'E' and resid 367 through 369 No H-bonds generated for 'chain 'E' and resid 367 through 369' Processing helix chain 'E' and resid 370 through 379 Processing helix chain 'E' and resid 381 through 392 Processing helix chain 'E' and resid 395 through 411 Processing helix chain 'E' and resid 412 through 416 Processing helix chain 'E' and resid 417 through 428 removed outlier: 3.859A pdb=" N LEU E 421 " --> pdb=" O THR E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 441 removed outlier: 3.501A pdb=" N ALA E 440 " --> pdb=" O ASP E 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 356 through 365 Processing helix chain 'F' and resid 367 through 369 No H-bonds generated for 'chain 'F' and resid 367 through 369' Processing helix chain 'F' and resid 370 through 379 Processing helix chain 'F' and resid 381 through 392 Processing helix chain 'F' and resid 395 through 411 Processing helix chain 'F' and resid 412 through 416 Processing helix chain 'F' and resid 417 through 428 removed outlier: 3.859A pdb=" N LEU F 421 " --> pdb=" O THR F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 430 through 441 removed outlier: 3.502A pdb=" N ALA F 440 " --> pdb=" O ASP F 436 " (cutoff:3.500A) Processing helix chain 'I' and resid 356 through 365 Processing helix chain 'I' and resid 367 through 369 No H-bonds generated for 'chain 'I' and resid 367 through 369' Processing helix chain 'I' and resid 370 through 379 Processing helix chain 'I' and resid 381 through 392 Processing helix chain 'I' and resid 395 through 411 Processing helix chain 'I' and resid 412 through 416 Processing helix chain 'I' and resid 417 through 428 removed outlier: 3.859A pdb=" N LEU I 421 " --> pdb=" O THR I 417 " (cutoff:3.500A) Processing helix chain 'I' and resid 430 through 441 removed outlier: 3.502A pdb=" N ALA I 440 " --> pdb=" O ASP I 436 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 365 Processing helix chain 'L' and resid 367 through 369 No H-bonds generated for 'chain 'L' and resid 367 through 369' Processing helix chain 'L' and resid 370 through 379 Processing helix chain 'L' and resid 381 through 392 Processing helix chain 'L' and resid 395 through 411 Processing helix chain 'L' and resid 412 through 416 Processing helix chain 'L' and resid 417 through 428 removed outlier: 3.859A pdb=" N LEU L 421 " --> pdb=" O THR L 417 " (cutoff:3.500A) Processing helix chain 'L' and resid 430 through 441 removed outlier: 3.502A pdb=" N ALA L 440 " --> pdb=" O ASP L 436 " (cutoff:3.500A) Processing helix chain 'O' and resid 356 through 365 Processing helix chain 'O' and resid 367 through 369 No H-bonds generated for 'chain 'O' and resid 367 through 369' Processing helix chain 'O' and resid 370 through 379 Processing helix chain 'O' and resid 381 through 392 Processing helix chain 'O' and resid 395 through 411 Processing helix chain 'O' and resid 412 through 416 Processing helix chain 'O' and resid 417 through 428 removed outlier: 3.859A pdb=" N LEU O 421 " --> pdb=" O THR O 417 " (cutoff:3.500A) Processing helix chain 'O' and resid 430 through 441 removed outlier: 3.502A pdb=" N ALA O 440 " --> pdb=" O ASP O 436 " (cutoff:3.500A) Processing helix chain 'R' and resid 356 through 365 Processing helix chain 'R' and resid 367 through 369 No H-bonds generated for 'chain 'R' and resid 367 through 369' Processing helix chain 'R' and resid 370 through 379 Processing helix chain 'R' and resid 381 through 392 Processing helix chain 'R' and resid 395 through 411 Processing helix chain 'R' and resid 412 through 416 Processing helix chain 'R' and resid 417 through 428 removed outlier: 3.859A pdb=" N LEU R 421 " --> pdb=" O THR R 417 " (cutoff:3.500A) Processing helix chain 'R' and resid 430 through 441 removed outlier: 3.501A pdb=" N ALA R 440 " --> pdb=" O ASP R 436 " (cutoff:3.500A) Processing helix chain 'G' and resid 356 through 365 Processing helix chain 'G' and resid 367 through 369 No H-bonds generated for 'chain 'G' and resid 367 through 369' Processing helix chain 'G' and resid 370 through 379 Processing helix chain 'G' and resid 381 through 392 Processing helix chain 'G' and resid 395 through 411 Processing helix chain 'G' and resid 412 through 416 Processing helix chain 'G' and resid 417 through 428 removed outlier: 3.859A pdb=" N LEU G 421 " --> pdb=" O THR G 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 430 through 441 removed outlier: 3.502A pdb=" N ALA G 440 " --> pdb=" O ASP G 436 " (cutoff:3.500A) Processing helix chain 'J' and resid 356 through 365 Processing helix chain 'J' and resid 367 through 369 No H-bonds generated for 'chain 'J' and resid 367 through 369' Processing helix chain 'J' and resid 370 through 379 Processing helix chain 'J' and resid 381 through 392 Processing helix chain 'J' and resid 395 through 411 Processing helix chain 'J' and resid 412 through 416 Processing helix chain 'J' and resid 417 through 428 removed outlier: 3.860A pdb=" N LEU J 421 " --> pdb=" O THR J 417 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 441 removed outlier: 3.501A pdb=" N ALA J 440 " --> pdb=" O ASP J 436 " (cutoff:3.500A) Processing helix chain 'M' and resid 356 through 365 Processing helix chain 'M' and resid 367 through 369 No H-bonds generated for 'chain 'M' and resid 367 through 369' Processing helix chain 'M' and resid 370 through 379 Processing helix chain 'M' and resid 381 through 392 Processing helix chain 'M' and resid 395 through 411 Processing helix chain 'M' and resid 412 through 416 Processing helix chain 'M' and resid 417 through 428 removed outlier: 3.859A pdb=" N LEU M 421 " --> pdb=" O THR M 417 " (cutoff:3.500A) Processing helix chain 'M' and resid 430 through 441 removed outlier: 3.501A pdb=" N ALA M 440 " --> pdb=" O ASP M 436 " (cutoff:3.500A) Processing helix chain 'P' and resid 356 through 365 Processing helix chain 'P' and resid 367 through 369 No H-bonds generated for 'chain 'P' and resid 367 through 369' Processing helix chain 'P' and resid 370 through 379 Processing helix chain 'P' and resid 381 through 392 Processing helix chain 'P' and resid 395 through 411 Processing helix chain 'P' and resid 412 through 416 Processing helix chain 'P' and resid 417 through 428 removed outlier: 3.859A pdb=" N LEU P 421 " --> pdb=" O THR P 417 " (cutoff:3.500A) Processing helix chain 'P' and resid 430 through 441 removed outlier: 3.502A pdb=" N ALA P 440 " --> pdb=" O ASP P 436 " (cutoff:3.500A) Processing helix chain 'S' and resid 356 through 365 Processing helix chain 'S' and resid 367 through 369 No H-bonds generated for 'chain 'S' and resid 367 through 369' Processing helix chain 'S' and resid 370 through 379 Processing helix chain 'S' and resid 381 through 392 Processing helix chain 'S' and resid 395 through 411 Processing helix chain 'S' and resid 412 through 416 Processing helix chain 'S' and resid 417 through 428 removed outlier: 3.859A pdb=" N LEU S 421 " --> pdb=" O THR S 417 " (cutoff:3.500A) Processing helix chain 'S' and resid 430 through 441 removed outlier: 3.502A pdb=" N ALA S 440 " --> pdb=" O ASP S 436 " (cutoff:3.500A) Processing helix chain 'H' and resid 356 through 365 Processing helix chain 'H' and resid 367 through 369 No H-bonds generated for 'chain 'H' and resid 367 through 369' Processing helix chain 'H' and resid 370 through 379 Processing helix chain 'H' and resid 381 through 392 Processing helix chain 'H' and resid 395 through 411 Processing helix chain 'H' and resid 412 through 416 Processing helix chain 'H' and resid 417 through 428 removed outlier: 3.859A pdb=" N LEU H 421 " --> pdb=" O THR H 417 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 441 removed outlier: 3.501A pdb=" N ALA H 440 " --> pdb=" O ASP H 436 " (cutoff:3.500A) Processing helix chain 'K' and resid 356 through 365 Processing helix chain 'K' and resid 367 through 369 No H-bonds generated for 'chain 'K' and resid 367 through 369' Processing helix chain 'K' and resid 370 through 379 Processing helix chain 'K' and resid 381 through 392 Processing helix chain 'K' and resid 395 through 411 Processing helix chain 'K' and resid 412 through 416 Processing helix chain 'K' and resid 417 through 428 removed outlier: 3.859A pdb=" N LEU K 421 " --> pdb=" O THR K 417 " (cutoff:3.500A) Processing helix chain 'K' and resid 430 through 441 removed outlier: 3.501A pdb=" N ALA K 440 " --> pdb=" O ASP K 436 " (cutoff:3.500A) Processing helix chain 'N' and resid 356 through 365 Processing helix chain 'N' and resid 367 through 369 No H-bonds generated for 'chain 'N' and resid 367 through 369' Processing helix chain 'N' and resid 370 through 379 Processing helix chain 'N' and resid 381 through 392 Processing helix chain 'N' and resid 395 through 411 Processing helix chain 'N' and resid 412 through 416 Processing helix chain 'N' and resid 417 through 428 removed outlier: 3.859A pdb=" N LEU N 421 " --> pdb=" O THR N 417 " (cutoff:3.500A) Processing helix chain 'N' and resid 430 through 441 removed outlier: 3.502A pdb=" N ALA N 440 " --> pdb=" O ASP N 436 " (cutoff:3.500A) Processing helix chain 'Q' and resid 356 through 365 Processing helix chain 'Q' and resid 367 through 369 No H-bonds generated for 'chain 'Q' and resid 367 through 369' Processing helix chain 'Q' and resid 370 through 379 Processing helix chain 'Q' and resid 381 through 392 Processing helix chain 'Q' and resid 395 through 411 Processing helix chain 'Q' and resid 412 through 416 Processing helix chain 'Q' and resid 417 through 428 removed outlier: 3.860A pdb=" N LEU Q 421 " --> pdb=" O THR Q 417 " (cutoff:3.500A) Processing helix chain 'Q' and resid 430 through 441 removed outlier: 3.501A pdb=" N ALA Q 440 " --> pdb=" O ASP Q 436 " (cutoff:3.500A) Processing helix chain 'T' and resid 356 through 365 Processing helix chain 'T' and resid 367 through 369 No H-bonds generated for 'chain 'T' and resid 367 through 369' Processing helix chain 'T' and resid 370 through 379 Processing helix chain 'T' and resid 381 through 392 Processing helix chain 'T' and resid 395 through 411 Processing helix chain 'T' and resid 412 through 416 Processing helix chain 'T' and resid 417 through 428 removed outlier: 3.859A pdb=" N LEU T 421 " --> pdb=" O THR T 417 " (cutoff:3.500A) Processing helix chain 'T' and resid 430 through 441 removed outlier: 3.502A pdb=" N ALA T 440 " --> pdb=" O ASP T 436 " (cutoff:3.500A) 980 hydrogen bonds defined for protein. 2820 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: 2.08 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5035 1.34 - 1.45: 1149 1.45 - 1.57: 8276 1.57 - 1.68: 0 1.68 - 1.80: 120 Bond restraints: 14580 Sorted by residual: bond pdb=" CB ARG P 376 " pdb=" CG ARG P 376 " ideal model delta sigma weight residual 1.520 1.461 0.059 3.00e-02 1.11e+03 3.80e+00 bond pdb=" CB ARG B 376 " pdb=" CG ARG B 376 " ideal model delta sigma weight residual 1.520 1.462 0.058 3.00e-02 1.11e+03 3.79e+00 bond pdb=" CB ARG T 376 " pdb=" CG ARG T 376 " ideal model delta sigma weight residual 1.520 1.462 0.058 3.00e-02 1.11e+03 3.76e+00 bond pdb=" CB ARG R 376 " pdb=" CG ARG R 376 " ideal model delta sigma weight residual 1.520 1.462 0.058 3.00e-02 1.11e+03 3.76e+00 bond pdb=" CB ARG H 376 " pdb=" CG ARG H 376 " ideal model delta sigma weight residual 1.520 1.462 0.058 3.00e-02 1.11e+03 3.74e+00 ... (remaining 14575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 17424 1.04 - 2.08: 1776 2.08 - 3.12: 322 3.12 - 4.17: 138 4.17 - 5.21: 40 Bond angle restraints: 19700 Sorted by residual: angle pdb=" C ARG T 413 " pdb=" N ARG T 414 " pdb=" CA ARG T 414 " ideal model delta sigma weight residual 121.94 116.73 5.21 2.00e+00 2.50e-01 6.78e+00 angle pdb=" C ARG R 413 " pdb=" N ARG R 414 " pdb=" CA ARG R 414 " ideal model delta sigma weight residual 121.94 116.74 5.20 2.00e+00 2.50e-01 6.76e+00 angle pdb=" C ARG K 413 " pdb=" N ARG K 414 " pdb=" CA ARG K 414 " ideal model delta sigma weight residual 121.94 116.75 5.19 2.00e+00 2.50e-01 6.74e+00 angle pdb=" C ARG J 413 " pdb=" N ARG J 414 " pdb=" CA ARG J 414 " ideal model delta sigma weight residual 121.94 116.76 5.18 2.00e+00 2.50e-01 6.72e+00 angle pdb=" C ARG D 413 " pdb=" N ARG D 414 " pdb=" CA ARG D 414 " ideal model delta sigma weight residual 121.94 116.76 5.18 2.00e+00 2.50e-01 6.72e+00 ... (remaining 19695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 8260 17.73 - 35.46: 640 35.46 - 53.19: 100 53.19 - 70.92: 20 70.92 - 88.65: 60 Dihedral angle restraints: 9080 sinusoidal: 4000 harmonic: 5080 Sorted by residual: dihedral pdb=" CG ARG B 414 " pdb=" CD ARG B 414 " pdb=" NE ARG B 414 " pdb=" CZ ARG B 414 " ideal model delta sinusoidal sigma weight residual -90.00 -133.13 43.13 2 1.50e+01 4.44e-03 9.97e+00 dihedral pdb=" CG ARG E 414 " pdb=" CD ARG E 414 " pdb=" NE ARG E 414 " pdb=" CZ ARG E 414 " ideal model delta sinusoidal sigma weight residual -90.00 -133.12 43.12 2 1.50e+01 4.44e-03 9.97e+00 dihedral pdb=" CG ARG S 414 " pdb=" CD ARG S 414 " pdb=" NE ARG S 414 " pdb=" CZ ARG S 414 " ideal model delta sinusoidal sigma weight residual -90.00 -133.11 43.11 2 1.50e+01 4.44e-03 9.96e+00 ... (remaining 9077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 800 0.029 - 0.058: 881 0.058 - 0.086: 319 0.086 - 0.115: 178 0.115 - 0.144: 22 Chirality restraints: 2200 Sorted by residual: chirality pdb=" CA PRO J 368 " pdb=" N PRO J 368 " pdb=" C PRO J 368 " pdb=" CB PRO J 368 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA PRO M 368 " pdb=" N PRO M 368 " pdb=" C PRO M 368 " pdb=" CB PRO M 368 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA PRO D 368 " pdb=" N PRO D 368 " pdb=" C PRO D 368 " pdb=" CB PRO D 368 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 2197 not shown) Planarity restraints: 2580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO O 367 " -0.028 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO O 368 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO O 368 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO O 368 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 367 " -0.028 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO A 368 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 368 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 368 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO M 367 " -0.028 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO M 368 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO M 368 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO M 368 " -0.024 5.00e-02 4.00e+02 ... (remaining 2577 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3640 2.81 - 3.33: 13037 3.33 - 3.85: 24170 3.85 - 4.38: 29178 4.38 - 4.90: 48051 Nonbonded interactions: 118076 Sorted by model distance: nonbonded pdb=" OE2 GLU L 364 " pdb=" NH1 ARG L 397 " model vdw 2.287 3.120 nonbonded pdb=" OE2 GLU F 364 " pdb=" NH1 ARG F 397 " model vdw 2.287 3.120 nonbonded pdb=" OE2 GLU O 364 " pdb=" NH1 ARG O 397 " model vdw 2.287 3.120 nonbonded pdb=" OE2 GLU N 364 " pdb=" NH1 ARG N 397 " model vdw 2.287 3.120 nonbonded pdb=" OE2 GLU J 364 " pdb=" NH1 ARG J 397 " model vdw 2.287 3.120 ... (remaining 118071 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' selection = chain 'R' selection = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'S' selection = chain 'H' selection = chain 'K' selection = chain 'N' selection = chain 'Q' selection = chain 'T' } 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: 4.720 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: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.580 Find NCS groups from input model: 0.140 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:6.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 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 : 0.008 0.059 14580 Z= 0.340 Angle : 0.763 5.207 19700 Z= 0.433 Chirality : 0.051 0.144 2200 Planarity : 0.006 0.043 2580 Dihedral : 15.089 88.649 5760 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % 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: -1.48 (0.18), residues: 1700 helix: -0.93 (0.12), residues: 1480 sheet: None (None), residues: 0 loop : 0.19 (0.33), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 414 TYR 0.014 0.005 TYR R 401 PHE 0.005 0.001 PHE B 374 TRP 0.013 0.003 TRP C 371 HIS 0.001 0.000 HIS P 383 Details of bonding type rmsd covalent geometry : bond 0.00818 (14580) covalent geometry : angle 0.76304 (19700) hydrogen bonds : bond 0.19552 ( 980) hydrogen bonds : angle 5.10003 ( 2820) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 442 time to evaluate : 0.562 Fit side-chains revert: symmetry clash REVERT: A 384 GLU cc_start: 0.7630 (tp30) cc_final: 0.7348 (mm-30) REVERT: A 394 ARG cc_start: 0.7388 (mmm160) cc_final: 0.7164 (mmp-170) REVERT: B 436 ASP cc_start: 0.7962 (m-30) cc_final: 0.7672 (m-30) REVERT: E 384 GLU cc_start: 0.7613 (tp30) cc_final: 0.7236 (mm-30) REVERT: F 398 GLU cc_start: 0.8403 (tp30) cc_final: 0.8195 (tp30) REVERT: F 410 ARG cc_start: 0.8183 (mtp-110) cc_final: 0.7753 (mtp180) REVERT: F 417 THR cc_start: 0.8853 (p) cc_final: 0.8485 (p) REVERT: F 423 ARG cc_start: 0.7504 (ttm170) cc_final: 0.7209 (ttm110) REVERT: F 435 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7320 (mt-10) REVERT: I 394 ARG cc_start: 0.7620 (mmm160) cc_final: 0.7197 (mmm160) REVERT: I 413 ARG cc_start: 0.7701 (ttm170) cc_final: 0.7389 (ttm110) REVERT: I 435 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7343 (mt-10) REVERT: L 384 GLU cc_start: 0.7570 (tp30) cc_final: 0.7299 (tp30) REVERT: L 410 ARG cc_start: 0.8060 (mtp-110) cc_final: 0.7636 (mtp180) REVERT: L 413 ARG cc_start: 0.7643 (ttm170) cc_final: 0.7400 (ttm-80) REVERT: O 435 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7333 (mt-10) REVERT: R 384 GLU cc_start: 0.7662 (tp30) cc_final: 0.7201 (mm-30) REVERT: R 394 ARG cc_start: 0.7403 (mmm160) cc_final: 0.6990 (mmm160) REVERT: G 384 GLU cc_start: 0.7567 (tp30) cc_final: 0.7130 (tp30) REVERT: G 398 GLU cc_start: 0.8339 (tp30) cc_final: 0.8139 (tp30) REVERT: G 410 ARG cc_start: 0.7913 (mtp-110) cc_final: 0.7566 (mtp180) REVERT: G 418 LEU cc_start: 0.7880 (mp) cc_final: 0.7663 (tt) REVERT: G 435 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7310 (mt-10) REVERT: J 355 ASP cc_start: 0.7548 (t70) cc_final: 0.7326 (t70) REVERT: J 384 GLU cc_start: 0.7531 (tp30) cc_final: 0.7184 (tp30) REVERT: J 410 ARG cc_start: 0.7995 (mtp-110) cc_final: 0.7652 (mtp180) REVERT: J 420 LEU cc_start: 0.8532 (tp) cc_final: 0.8330 (tt) REVERT: J 435 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7313 (mt-10) REVERT: M 355 ASP cc_start: 0.7764 (t70) cc_final: 0.7531 (t70) REVERT: M 384 GLU cc_start: 0.7683 (tp30) cc_final: 0.7482 (tp30) REVERT: M 418 LEU cc_start: 0.7786 (mp) cc_final: 0.7517 (tt) REVERT: M 420 LEU cc_start: 0.8361 (tp) cc_final: 0.8155 (tt) REVERT: M 435 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7479 (mt-10) REVERT: P 384 GLU cc_start: 0.7504 (tp30) cc_final: 0.7262 (tp30) REVERT: P 427 ASP cc_start: 0.7822 (m-30) cc_final: 0.7567 (m-30) REVERT: S 384 GLU cc_start: 0.7541 (tp30) cc_final: 0.7221 (tp30) REVERT: S 413 ARG cc_start: 0.7691 (ttm170) cc_final: 0.7453 (ttp-170) REVERT: H 389 GLU cc_start: 0.7568 (tt0) cc_final: 0.7358 (tt0) REVERT: H 410 ARG cc_start: 0.7830 (mtp-110) cc_final: 0.6963 (mmm160) REVERT: H 435 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7351 (mt-10) REVERT: H 436 ASP cc_start: 0.7970 (m-30) cc_final: 0.7589 (m-30) REVERT: K 410 ARG cc_start: 0.7985 (mtp-110) cc_final: 0.6976 (mmm160) REVERT: K 423 ARG cc_start: 0.7431 (ttm170) cc_final: 0.7136 (ttm110) REVERT: K 435 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7324 (mt-10) REVERT: N 384 GLU cc_start: 0.7478 (tp30) cc_final: 0.7162 (mm-30) REVERT: N 397 ARG cc_start: 0.8468 (ttm-80) cc_final: 0.8149 (ttp-170) REVERT: N 410 ARG cc_start: 0.7857 (mtp-110) cc_final: 0.7007 (mmm160) REVERT: N 435 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7428 (mt-10) REVERT: Q 410 ARG cc_start: 0.7827 (mtp-110) cc_final: 0.7025 (mmm160) REVERT: Q 413 ARG cc_start: 0.7678 (ttm170) cc_final: 0.7420 (ttm-80) REVERT: Q 426 ARG cc_start: 0.7660 (mtt90) cc_final: 0.7390 (mtm110) REVERT: Q 427 ASP cc_start: 0.7897 (m-30) cc_final: 0.7658 (m-30) REVERT: Q 435 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7361 (mt-10) REVERT: T 410 ARG cc_start: 0.7920 (mtp-110) cc_final: 0.7338 (mmm160) REVERT: T 435 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7468 (mt-10) outliers start: 0 outliers final: 0 residues processed: 442 average time/residue: 0.9755 time to fit residues: 456.1343 Evaluate side-chains 391 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 391 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 GLN B 400 GLN C 400 GLN F 400 GLN I 400 GLN L 400 GLN O 400 GLN R 400 GLN G 400 GLN J 400 GLN M 400 GLN P 400 GLN S 400 GLN H 400 GLN K 400 GLN N 400 GLN Q 400 GLN T 400 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.128118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.105352 restraints weight = 14442.403| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.25 r_work: 0.2892 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 14580 Z= 0.103 Angle : 0.450 5.544 19700 Z= 0.235 Chirality : 0.034 0.117 2200 Planarity : 0.005 0.039 2580 Dihedral : 4.141 15.241 2020 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.51 % Allowed : 7.21 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.20), residues: 1700 helix: 1.17 (0.14), residues: 1480 sheet: None (None), residues: 0 loop : 0.79 (0.35), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 410 TYR 0.009 0.002 TYR C 360 PHE 0.006 0.001 PHE P 374 TRP 0.006 0.001 TRP K 371 HIS 0.001 0.000 HIS E 383 Details of bonding type rmsd covalent geometry : bond 0.00232 (14580) covalent geometry : angle 0.44990 (19700) hydrogen bonds : bond 0.03815 ( 980) hydrogen bonds : angle 3.28368 ( 2820) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 432 time to evaluate : 0.663 Fit side-chains REVERT: A 394 ARG cc_start: 0.7467 (mmm160) cc_final: 0.7168 (mmp-170) REVERT: A 418 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7450 (tt) REVERT: B 394 ARG cc_start: 0.7339 (mmm160) cc_final: 0.6882 (mmm160) REVERT: B 418 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7493 (tt) REVERT: B 423 ARG cc_start: 0.8186 (ttm110) cc_final: 0.7726 (ttm170) REVERT: B 436 ASP cc_start: 0.8172 (m-30) cc_final: 0.7869 (m-30) REVERT: C 410 ARG cc_start: 0.7902 (mtp-110) cc_final: 0.7239 (mtt-85) REVERT: D 364 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7833 (mt-10) REVERT: E 384 GLU cc_start: 0.8201 (tp30) cc_final: 0.7824 (mm-30) REVERT: F 410 ARG cc_start: 0.8004 (mtp-110) cc_final: 0.7739 (mtp180) REVERT: I 394 ARG cc_start: 0.7857 (mmm160) cc_final: 0.7562 (mmm160) REVERT: I 410 ARG cc_start: 0.8087 (mtp-110) cc_final: 0.7835 (mtp180) REVERT: I 423 ARG cc_start: 0.8102 (ttm110) cc_final: 0.7856 (ttm110) REVERT: I 435 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7853 (mt-10) REVERT: L 384 GLU cc_start: 0.8123 (tp30) cc_final: 0.7897 (tp30) REVERT: L 410 ARG cc_start: 0.7929 (mtp-110) cc_final: 0.7574 (mtp180) REVERT: O 435 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7574 (mt-10) REVERT: R 394 ARG cc_start: 0.7452 (mmm160) cc_final: 0.7233 (mmm160) REVERT: G 384 GLU cc_start: 0.8005 (tp30) cc_final: 0.7628 (tp30) REVERT: G 398 GLU cc_start: 0.8514 (tp30) cc_final: 0.8300 (tp30) REVERT: G 410 ARG cc_start: 0.7791 (mtp-110) cc_final: 0.7487 (mtp180) REVERT: G 418 LEU cc_start: 0.7824 (mp) cc_final: 0.7580 (tt) REVERT: G 435 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7866 (mt-10) REVERT: J 384 GLU cc_start: 0.8123 (tp30) cc_final: 0.7848 (tp30) REVERT: J 410 ARG cc_start: 0.8046 (mtp-110) cc_final: 0.7783 (mtp180) REVERT: J 413 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.6927 (ttp-170) REVERT: J 435 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7748 (mt-10) REVERT: M 364 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7328 (mp0) REVERT: M 418 LEU cc_start: 0.7700 (mp) cc_final: 0.7439 (tt) REVERT: S 364 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: S 384 GLU cc_start: 0.8037 (tp30) cc_final: 0.7783 (tp30) REVERT: S 391 GLN cc_start: 0.8234 (mt0) cc_final: 0.7990 (mt0) REVERT: S 398 GLU cc_start: 0.8652 (tp30) cc_final: 0.8320 (mm-30) REVERT: H 389 GLU cc_start: 0.8196 (tt0) cc_final: 0.7965 (tt0) REVERT: H 410 ARG cc_start: 0.7784 (mtp-110) cc_final: 0.6728 (mmm160) REVERT: H 435 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7694 (mt-10) REVERT: K 391 GLN cc_start: 0.8298 (mt0) cc_final: 0.7992 (mt0) REVERT: K 410 ARG cc_start: 0.8062 (mtp-110) cc_final: 0.6797 (mmm160) REVERT: K 423 ARG cc_start: 0.7785 (ttm170) cc_final: 0.7011 (ttp80) REVERT: K 435 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7752 (mt-10) REVERT: N 384 GLU cc_start: 0.8135 (tp30) cc_final: 0.7850 (mm-30) REVERT: N 391 GLN cc_start: 0.8216 (mt0) cc_final: 0.7828 (mt0) REVERT: N 410 ARG cc_start: 0.8046 (mtp-110) cc_final: 0.6891 (mmm160) REVERT: N 435 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7862 (mt-10) REVERT: Q 410 ARG cc_start: 0.7910 (mtp-110) cc_final: 0.6936 (mmm160) REVERT: Q 426 ARG cc_start: 0.7892 (mtt90) cc_final: 0.7560 (mtm110) REVERT: Q 427 ASP cc_start: 0.8342 (m-30) cc_final: 0.8134 (m-30) REVERT: Q 435 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7747 (mt-10) REVERT: T 410 ARG cc_start: 0.8010 (mtp-110) cc_final: 0.7136 (mmm160) REVERT: T 435 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7776 (mt-10) outliers start: 54 outliers final: 14 residues processed: 459 average time/residue: 0.9327 time to fit residues: 454.0706 Evaluate side-chains 436 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 416 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain E residue 418 LEU Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain I residue 396 LEU Chi-restraints excluded: chain L residue 364 GLU Chi-restraints excluded: chain O residue 396 LEU Chi-restraints excluded: chain R residue 364 GLU Chi-restraints excluded: chain J residue 413 ARG Chi-restraints excluded: chain M residue 364 GLU Chi-restraints excluded: chain M residue 396 LEU Chi-restraints excluded: chain P residue 364 GLU Chi-restraints excluded: chain P residue 396 LEU Chi-restraints excluded: chain S residue 364 GLU Chi-restraints excluded: chain H residue 418 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 22 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 121 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 391 GLN F 391 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.126346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.103749 restraints weight = 14701.922| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.25 r_work: 0.2888 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14580 Z= 0.104 Angle : 0.414 5.253 19700 Z= 0.215 Chirality : 0.035 0.114 2200 Planarity : 0.004 0.034 2580 Dihedral : 3.731 14.312 2020 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.18 % Allowed : 7.99 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.72 (0.21), residues: 1700 helix: 1.94 (0.14), residues: 1480 sheet: None (None), residues: 0 loop : 1.16 (0.35), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 410 TYR 0.010 0.003 TYR M 401 PHE 0.006 0.001 PHE P 374 TRP 0.007 0.001 TRP F 371 HIS 0.001 0.000 HIS E 383 Details of bonding type rmsd covalent geometry : bond 0.00239 (14580) covalent geometry : angle 0.41360 (19700) hydrogen bonds : bond 0.03775 ( 980) hydrogen bonds : angle 3.03533 ( 2820) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 418 time to evaluate : 0.592 Fit side-chains revert: symmetry clash REVERT: A 364 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7785 (mt-10) REVERT: A 394 ARG cc_start: 0.7435 (mmm160) cc_final: 0.7155 (mmp-170) REVERT: A 418 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7333 (tt) REVERT: B 394 ARG cc_start: 0.7242 (mmm160) cc_final: 0.6713 (mmm160) REVERT: B 418 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7500 (tt) REVERT: B 423 ARG cc_start: 0.8231 (ttm110) cc_final: 0.7759 (ttm170) REVERT: B 436 ASP cc_start: 0.8054 (m-30) cc_final: 0.7787 (m-30) REVERT: C 410 ARG cc_start: 0.7887 (mtp-110) cc_final: 0.7143 (mtt-85) REVERT: F 410 ARG cc_start: 0.8103 (mtp-110) cc_final: 0.7735 (mtp180) REVERT: I 394 ARG cc_start: 0.7777 (mmm160) cc_final: 0.7463 (mmm160) REVERT: I 410 ARG cc_start: 0.8078 (mtp-110) cc_final: 0.7828 (mtp180) REVERT: I 423 ARG cc_start: 0.8025 (ttm110) cc_final: 0.7780 (ttm110) REVERT: I 435 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7877 (mt-10) REVERT: L 384 GLU cc_start: 0.8087 (tp30) cc_final: 0.7847 (tp30) REVERT: L 410 ARG cc_start: 0.7975 (mtp-110) cc_final: 0.7624 (mtp180) REVERT: O 435 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7596 (mt-10) REVERT: R 423 ARG cc_start: 0.7990 (ttm110) cc_final: 0.7771 (ttp-110) REVERT: G 384 GLU cc_start: 0.8113 (tp30) cc_final: 0.7742 (tp30) REVERT: G 410 ARG cc_start: 0.7921 (mtp-110) cc_final: 0.7599 (mtp180) REVERT: G 435 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7835 (mt-10) REVERT: J 384 GLU cc_start: 0.8129 (tp30) cc_final: 0.7845 (tp30) REVERT: J 410 ARG cc_start: 0.8022 (mtp-110) cc_final: 0.7767 (mtp180) REVERT: J 435 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7833 (mt-10) REVERT: M 364 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7247 (mp0) REVERT: S 364 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7474 (mp0) REVERT: S 384 GLU cc_start: 0.7966 (tp30) cc_final: 0.7706 (tp30) REVERT: S 391 GLN cc_start: 0.8208 (mt0) cc_final: 0.7961 (mt0) REVERT: S 398 GLU cc_start: 0.8665 (tp30) cc_final: 0.8286 (mm-30) REVERT: S 418 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7505 (tt) REVERT: H 389 GLU cc_start: 0.8223 (tt0) cc_final: 0.7985 (tt0) REVERT: H 410 ARG cc_start: 0.7714 (mtp-110) cc_final: 0.6719 (mmm160) REVERT: H 435 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7801 (mt-10) REVERT: K 391 GLN cc_start: 0.8312 (mt0) cc_final: 0.8001 (mt0) REVERT: K 410 ARG cc_start: 0.7974 (mtp-110) cc_final: 0.6725 (mmm160) REVERT: K 423 ARG cc_start: 0.7748 (ttm170) cc_final: 0.6917 (ttp80) REVERT: K 435 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7944 (mt-10) REVERT: N 384 GLU cc_start: 0.8127 (tp30) cc_final: 0.7840 (mm-30) REVERT: N 410 ARG cc_start: 0.7972 (mtp-110) cc_final: 0.6876 (mmm160) REVERT: N 435 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7895 (mt-10) REVERT: Q 410 ARG cc_start: 0.7931 (mtp-110) cc_final: 0.6936 (mmm160) REVERT: Q 426 ARG cc_start: 0.7966 (mtt90) cc_final: 0.7619 (mtm-85) REVERT: Q 427 ASP cc_start: 0.8255 (m-30) cc_final: 0.8042 (m-30) REVERT: Q 435 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7855 (mt-10) REVERT: T 410 ARG cc_start: 0.8044 (mtp-110) cc_final: 0.7140 (mmm160) REVERT: T 435 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7844 (mt-10) outliers start: 49 outliers final: 16 residues processed: 437 average time/residue: 0.9396 time to fit residues: 435.3293 Evaluate side-chains 430 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 408 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain E residue 418 LEU Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain I residue 396 LEU Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain O residue 396 LEU Chi-restraints excluded: chain R residue 364 GLU Chi-restraints excluded: chain R residue 418 LEU Chi-restraints excluded: chain J residue 420 LEU Chi-restraints excluded: chain M residue 364 GLU Chi-restraints excluded: chain M residue 396 LEU Chi-restraints excluded: chain P residue 364 GLU Chi-restraints excluded: chain P residue 396 LEU Chi-restraints excluded: chain S residue 364 GLU Chi-restraints excluded: chain S residue 418 LEU Chi-restraints excluded: chain T residue 420 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 76 optimal weight: 5.9990 chunk 118 optimal weight: 0.0980 chunk 64 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 158 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 156 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 391 GLN N 391 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.122082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.098689 restraints weight = 13990.549| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.24 r_work: 0.2811 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14580 Z= 0.136 Angle : 0.451 5.149 19700 Z= 0.233 Chirality : 0.037 0.123 2200 Planarity : 0.005 0.037 2580 Dihedral : 3.822 13.300 2020 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.12 % Allowed : 9.81 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.05 (0.21), residues: 1700 helix: 2.12 (0.14), residues: 1480 sheet: None (None), residues: 0 loop : 1.54 (0.36), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG O 410 TYR 0.011 0.003 TYR G 360 PHE 0.006 0.001 PHE P 374 TRP 0.010 0.002 TRP H 371 HIS 0.002 0.000 HIS E 383 Details of bonding type rmsd covalent geometry : bond 0.00324 (14580) covalent geometry : angle 0.45070 (19700) hydrogen bonds : bond 0.04407 ( 980) hydrogen bonds : angle 3.06821 ( 2820) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 411 time to evaluate : 0.602 Fit side-chains REVERT: B 394 ARG cc_start: 0.7268 (mmm160) cc_final: 0.6750 (mmm160) REVERT: B 423 ARG cc_start: 0.8205 (ttm110) cc_final: 0.7763 (ttm170) REVERT: B 436 ASP cc_start: 0.8024 (m-30) cc_final: 0.7723 (m-30) REVERT: C 410 ARG cc_start: 0.7947 (mtp-110) cc_final: 0.7173 (mtt-85) REVERT: F 410 ARG cc_start: 0.8195 (mtp-110) cc_final: 0.7791 (mtp180) REVERT: F 423 ARG cc_start: 0.7907 (ttm110) cc_final: 0.7629 (ttp-110) REVERT: I 394 ARG cc_start: 0.7761 (mmm160) cc_final: 0.7445 (mmm160) REVERT: I 410 ARG cc_start: 0.8141 (mtp-110) cc_final: 0.7858 (mtp180) REVERT: I 423 ARG cc_start: 0.8032 (ttm110) cc_final: 0.7399 (mtm110) REVERT: I 435 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7840 (mt-10) REVERT: L 384 GLU cc_start: 0.8076 (tp30) cc_final: 0.7857 (tp30) REVERT: L 410 ARG cc_start: 0.8057 (mtp-110) cc_final: 0.7713 (mtp180) REVERT: L 423 ARG cc_start: 0.8004 (ttp80) cc_final: 0.7514 (ttp-110) REVERT: O 435 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7509 (mt-10) REVERT: R 423 ARG cc_start: 0.7969 (ttm110) cc_final: 0.7755 (ttp-110) REVERT: G 384 GLU cc_start: 0.8123 (tp30) cc_final: 0.7758 (tp30) REVERT: G 410 ARG cc_start: 0.7962 (mtp-110) cc_final: 0.7708 (mtp180) REVERT: J 384 GLU cc_start: 0.8144 (tp30) cc_final: 0.7874 (tp30) REVERT: J 410 ARG cc_start: 0.8122 (mtp-110) cc_final: 0.7825 (mtp180) REVERT: J 435 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7865 (mt-10) REVERT: M 415 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7851 (mt-10) REVERT: S 364 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7481 (mp0) REVERT: S 384 GLU cc_start: 0.7976 (tp30) cc_final: 0.7722 (tp30) REVERT: S 391 GLN cc_start: 0.8260 (mt0) cc_final: 0.7980 (mt0) REVERT: S 418 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7504 (tt) REVERT: H 410 ARG cc_start: 0.7910 (mtp-110) cc_final: 0.6855 (mmm160) REVERT: H 435 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7909 (mt-10) REVERT: K 391 GLN cc_start: 0.8322 (mt0) cc_final: 0.7986 (mt0) REVERT: K 410 ARG cc_start: 0.7997 (mtp-110) cc_final: 0.6757 (mmm160) REVERT: K 423 ARG cc_start: 0.7755 (ttm170) cc_final: 0.6931 (ttp80) REVERT: K 435 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7895 (mt-10) REVERT: N 384 GLU cc_start: 0.8143 (tp30) cc_final: 0.7879 (mm-30) REVERT: N 410 ARG cc_start: 0.8020 (mtp-110) cc_final: 0.6945 (mmm160) REVERT: N 418 LEU cc_start: 0.8015 (tp) cc_final: 0.7692 (tp) REVERT: N 435 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7869 (mt-10) REVERT: Q 410 ARG cc_start: 0.7909 (mtp-110) cc_final: 0.6858 (mmm160) REVERT: Q 426 ARG cc_start: 0.7971 (mtt90) cc_final: 0.7609 (mtm-85) REVERT: Q 427 ASP cc_start: 0.8232 (m-30) cc_final: 0.8029 (m-30) REVERT: Q 435 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7744 (mt-10) REVERT: T 364 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7651 (mt-10) REVERT: T 410 ARG cc_start: 0.8108 (mtp-110) cc_final: 0.7136 (mmm160) REVERT: T 435 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7895 (mt-10) outliers start: 48 outliers final: 17 residues processed: 425 average time/residue: 0.9259 time to fit residues: 417.4181 Evaluate side-chains 429 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 409 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain E residue 418 LEU Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain I residue 396 LEU Chi-restraints excluded: chain L residue 396 LEU Chi-restraints excluded: chain O residue 396 LEU Chi-restraints excluded: chain R residue 364 GLU Chi-restraints excluded: chain J residue 420 LEU Chi-restraints excluded: chain M residue 396 LEU Chi-restraints excluded: chain P residue 364 GLU Chi-restraints excluded: chain P residue 396 LEU Chi-restraints excluded: chain S residue 364 GLU Chi-restraints excluded: chain S residue 418 LEU Chi-restraints excluded: chain T residue 364 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 91 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 127 optimal weight: 7.9990 chunk 92 optimal weight: 0.5980 chunk 120 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 391 GLN N 391 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.121458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.098811 restraints weight = 14627.924| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.24 r_work: 0.2773 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14580 Z= 0.191 Angle : 0.519 5.652 19700 Z= 0.267 Chirality : 0.041 0.137 2200 Planarity : 0.006 0.047 2580 Dihedral : 4.082 13.073 2020 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.12 % Allowed : 12.08 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.93 (0.20), residues: 1700 helix: 2.02 (0.14), residues: 1480 sheet: None (None), residues: 0 loop : 1.67 (0.37), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 410 TYR 0.013 0.004 TYR H 360 PHE 0.006 0.001 PHE P 374 TRP 0.013 0.002 TRP F 371 HIS 0.002 0.001 HIS E 383 Details of bonding type rmsd covalent geometry : bond 0.00471 (14580) covalent geometry : angle 0.51888 (19700) hydrogen bonds : bond 0.05240 ( 980) hydrogen bonds : angle 3.21782 ( 2820) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 410 time to evaluate : 0.629 Fit side-chains REVERT: B 394 ARG cc_start: 0.7413 (mmm160) cc_final: 0.6899 (mmm160) REVERT: B 423 ARG cc_start: 0.8157 (ttm110) cc_final: 0.7635 (ttm170) REVERT: B 436 ASP cc_start: 0.7983 (m-30) cc_final: 0.7675 (m-30) REVERT: C 410 ARG cc_start: 0.7958 (mtp-110) cc_final: 0.7174 (mtt-85) REVERT: F 410 ARG cc_start: 0.8178 (mtp-110) cc_final: 0.7806 (mtp180) REVERT: I 389 GLU cc_start: 0.8247 (tt0) cc_final: 0.7895 (mm-30) REVERT: I 394 ARG cc_start: 0.7832 (mmm160) cc_final: 0.7521 (mmm160) REVERT: I 410 ARG cc_start: 0.8181 (mtp-110) cc_final: 0.7908 (mtp180) REVERT: I 435 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7824 (mt-10) REVERT: L 410 ARG cc_start: 0.8135 (mtp-110) cc_final: 0.7723 (mtp180) REVERT: L 423 ARG cc_start: 0.8055 (ttp80) cc_final: 0.7556 (ttp-110) REVERT: O 417 THR cc_start: 0.8974 (p) cc_final: 0.8715 (p) REVERT: O 435 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7579 (mt-10) REVERT: G 384 GLU cc_start: 0.8152 (tp30) cc_final: 0.7806 (tp30) REVERT: G 410 ARG cc_start: 0.8058 (mtp-110) cc_final: 0.7804 (mtp180) REVERT: J 384 GLU cc_start: 0.8163 (tp30) cc_final: 0.7908 (tp30) REVERT: J 410 ARG cc_start: 0.8221 (mtp-110) cc_final: 0.7862 (mtp180) REVERT: J 413 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7094 (ttp-170) REVERT: M 413 ARG cc_start: 0.7841 (ttp-170) cc_final: 0.7460 (ttm-80) REVERT: S 364 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7423 (mp0) REVERT: S 384 GLU cc_start: 0.7999 (tp30) cc_final: 0.7762 (tp30) REVERT: S 391 GLN cc_start: 0.8275 (mt0) cc_final: 0.7988 (mt0) REVERT: S 418 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7580 (tt) REVERT: H 410 ARG cc_start: 0.7969 (mtp-110) cc_final: 0.6899 (mmm160) REVERT: H 435 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7869 (mt-10) REVERT: K 391 GLN cc_start: 0.8345 (mt0) cc_final: 0.8056 (mt0) REVERT: K 410 ARG cc_start: 0.8041 (mtp-110) cc_final: 0.6772 (mmm160) REVERT: K 413 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7408 (ttp-170) REVERT: K 423 ARG cc_start: 0.7743 (ttm170) cc_final: 0.6936 (ttp80) REVERT: K 435 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7879 (mt-10) REVERT: N 384 GLU cc_start: 0.8174 (tp30) cc_final: 0.7922 (mm-30) REVERT: N 410 ARG cc_start: 0.8066 (mtp-110) cc_final: 0.6992 (mmm160) REVERT: N 418 LEU cc_start: 0.8079 (tp) cc_final: 0.7759 (tp) REVERT: N 435 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7839 (mt-10) REVERT: Q 396 LEU cc_start: 0.8741 (tp) cc_final: 0.8534 (tt) REVERT: Q 410 ARG cc_start: 0.7942 (mtp-110) cc_final: 0.6903 (mmm160) REVERT: Q 413 ARG cc_start: 0.7698 (ttm170) cc_final: 0.7377 (ttp-170) REVERT: Q 426 ARG cc_start: 0.7968 (mtt90) cc_final: 0.7740 (mtm-85) REVERT: Q 427 ASP cc_start: 0.8250 (m-30) cc_final: 0.8027 (m-30) REVERT: Q 435 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7704 (mt-10) REVERT: T 364 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7614 (mt-10) REVERT: T 410 ARG cc_start: 0.8087 (mtp-110) cc_final: 0.7067 (mmm160) REVERT: T 435 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7884 (mt-10) outliers start: 48 outliers final: 20 residues processed: 426 average time/residue: 0.9382 time to fit residues: 423.9871 Evaluate side-chains 432 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 407 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain E residue 418 LEU Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain I residue 396 LEU Chi-restraints excluded: chain L residue 396 LEU Chi-restraints excluded: chain R residue 364 GLU Chi-restraints excluded: chain G residue 396 LEU Chi-restraints excluded: chain J residue 413 ARG Chi-restraints excluded: chain J residue 420 LEU Chi-restraints excluded: chain M residue 396 LEU Chi-restraints excluded: chain P residue 364 GLU Chi-restraints excluded: chain P residue 396 LEU Chi-restraints excluded: chain S residue 364 GLU Chi-restraints excluded: chain S residue 418 LEU Chi-restraints excluded: chain H residue 381 SER Chi-restraints excluded: chain H residue 417 THR Chi-restraints excluded: chain K residue 413 ARG Chi-restraints excluded: chain T residue 364 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 45 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 391 GLN N 391 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.123211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.099741 restraints weight = 14035.687| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.25 r_work: 0.2866 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14580 Z= 0.101 Angle : 0.410 6.730 19700 Z= 0.212 Chirality : 0.035 0.134 2200 Planarity : 0.005 0.049 2580 Dihedral : 3.644 13.134 2020 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.60 % Allowed : 13.51 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.50 (0.21), residues: 1700 helix: 2.40 (0.14), residues: 1480 sheet: None (None), residues: 0 loop : 1.86 (0.38), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG O 410 TYR 0.009 0.002 TYR E 401 PHE 0.005 0.001 PHE P 374 TRP 0.007 0.001 TRP F 371 HIS 0.001 0.000 HIS D 383 Details of bonding type rmsd covalent geometry : bond 0.00228 (14580) covalent geometry : angle 0.41015 (19700) hydrogen bonds : bond 0.03679 ( 980) hydrogen bonds : angle 2.89498 ( 2820) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 408 time to evaluate : 0.613 Fit side-chains REVERT: B 394 ARG cc_start: 0.7256 (mmm160) cc_final: 0.6746 (mmm160) REVERT: B 418 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7533 (tt) REVERT: B 423 ARG cc_start: 0.8207 (ttm110) cc_final: 0.7779 (ttm170) REVERT: B 431 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8435 (mp) REVERT: B 436 ASP cc_start: 0.7930 (m-30) cc_final: 0.7648 (m-30) REVERT: C 410 ARG cc_start: 0.7910 (mtp-110) cc_final: 0.7185 (mtt-85) REVERT: F 410 ARG cc_start: 0.8028 (mtp-110) cc_final: 0.7666 (mtp180) REVERT: F 418 LEU cc_start: 0.8095 (tp) cc_final: 0.7786 (tt) REVERT: F 423 ARG cc_start: 0.7921 (ttm110) cc_final: 0.7664 (ttp-110) REVERT: I 389 GLU cc_start: 0.8242 (tt0) cc_final: 0.7897 (mm-30) REVERT: I 394 ARG cc_start: 0.7662 (mmm160) cc_final: 0.7374 (mmm160) REVERT: I 410 ARG cc_start: 0.8137 (mtp-110) cc_final: 0.7880 (mtp180) REVERT: I 423 ARG cc_start: 0.7955 (ttm110) cc_final: 0.7384 (mtm110) REVERT: I 435 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7819 (mt-10) REVERT: L 396 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8267 (mt) REVERT: L 410 ARG cc_start: 0.8056 (mtp-110) cc_final: 0.7711 (mtp180) REVERT: L 423 ARG cc_start: 0.8069 (ttp80) cc_final: 0.7560 (ttp-110) REVERT: O 435 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7458 (mt-10) REVERT: R 423 ARG cc_start: 0.7968 (ttm110) cc_final: 0.7762 (ttp-110) REVERT: G 384 GLU cc_start: 0.8121 (tp30) cc_final: 0.7754 (tp30) REVERT: G 410 ARG cc_start: 0.7975 (mtp-110) cc_final: 0.7707 (mtp180) REVERT: J 384 GLU cc_start: 0.8190 (tp30) cc_final: 0.7940 (tp30) REVERT: J 410 ARG cc_start: 0.8160 (mtp-110) cc_final: 0.7819 (mtp180) REVERT: M 414 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7389 (ptt180) REVERT: P 418 LEU cc_start: 0.7718 (mp) cc_final: 0.7463 (tt) REVERT: S 364 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7412 (mp0) REVERT: S 384 GLU cc_start: 0.7968 (tp30) cc_final: 0.7718 (tp30) REVERT: S 391 GLN cc_start: 0.8182 (mt0) cc_final: 0.7962 (mt0) REVERT: S 398 GLU cc_start: 0.8697 (tp30) cc_final: 0.8329 (mm-30) REVERT: S 418 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7482 (tt) REVERT: H 410 ARG cc_start: 0.7902 (mtp-110) cc_final: 0.6869 (mmm160) REVERT: H 435 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7895 (mt-10) REVERT: H 436 ASP cc_start: 0.8185 (m-30) cc_final: 0.7843 (m-30) REVERT: K 391 GLN cc_start: 0.8270 (mt0) cc_final: 0.7952 (mt0) REVERT: K 410 ARG cc_start: 0.7960 (mtp-110) cc_final: 0.6777 (mmm160) REVERT: K 423 ARG cc_start: 0.7797 (ttm170) cc_final: 0.6985 (ttp80) REVERT: K 435 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7950 (mt-10) REVERT: N 384 GLU cc_start: 0.8126 (tp30) cc_final: 0.7852 (mm-30) REVERT: N 410 ARG cc_start: 0.8032 (mtp-110) cc_final: 0.6981 (mmm160) REVERT: N 418 LEU cc_start: 0.8016 (tp) cc_final: 0.7690 (tp) REVERT: N 435 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7861 (mt-10) REVERT: Q 410 ARG cc_start: 0.7903 (mtp-110) cc_final: 0.6892 (mmm160) REVERT: Q 413 ARG cc_start: 0.7638 (ttm170) cc_final: 0.7322 (ttp-170) REVERT: Q 426 ARG cc_start: 0.7971 (mtt90) cc_final: 0.7629 (mtm-85) REVERT: T 410 ARG cc_start: 0.8073 (mtp-110) cc_final: 0.7125 (mmm160) REVERT: T 435 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7868 (mt-10) outliers start: 40 outliers final: 13 residues processed: 423 average time/residue: 0.9503 time to fit residues: 425.9696 Evaluate side-chains 425 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 407 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain E residue 418 LEU Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain I residue 396 LEU Chi-restraints excluded: chain L residue 396 LEU Chi-restraints excluded: chain O residue 396 LEU Chi-restraints excluded: chain J residue 420 LEU Chi-restraints excluded: chain M residue 396 LEU Chi-restraints excluded: chain M residue 414 ARG Chi-restraints excluded: chain P residue 364 GLU Chi-restraints excluded: chain P residue 396 LEU Chi-restraints excluded: chain S residue 418 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 73 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 126 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 391 GLN G 391 GLN N 391 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.124536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.102410 restraints weight = 14437.442| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.22 r_work: 0.2845 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14580 Z= 0.136 Angle : 0.450 6.980 19700 Z= 0.231 Chirality : 0.037 0.122 2200 Planarity : 0.005 0.054 2580 Dihedral : 3.743 11.592 2020 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.40 % Allowed : 13.96 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.51 (0.20), residues: 1700 helix: 2.41 (0.14), residues: 1480 sheet: None (None), residues: 0 loop : 1.93 (0.39), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG O 410 TYR 0.011 0.003 TYR H 360 PHE 0.005 0.001 PHE P 374 TRP 0.010 0.002 TRP F 371 HIS 0.001 0.001 HIS H 383 Details of bonding type rmsd covalent geometry : bond 0.00326 (14580) covalent geometry : angle 0.44952 (19700) hydrogen bonds : bond 0.04322 ( 980) hydrogen bonds : angle 2.98087 ( 2820) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 409 time to evaluate : 0.555 Fit side-chains REVERT: B 394 ARG cc_start: 0.7326 (mmm160) cc_final: 0.6795 (mmm160) REVERT: B 418 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7560 (tt) REVERT: B 423 ARG cc_start: 0.8203 (ttm110) cc_final: 0.7766 (ttm170) REVERT: B 436 ASP cc_start: 0.7936 (m-30) cc_final: 0.7630 (m-30) REVERT: C 410 ARG cc_start: 0.7913 (mtp-110) cc_final: 0.7178 (mtt-85) REVERT: F 410 ARG cc_start: 0.8077 (mtp-110) cc_final: 0.7702 (mtp180) REVERT: F 423 ARG cc_start: 0.7920 (ttm110) cc_final: 0.7672 (ttp-110) REVERT: I 389 GLU cc_start: 0.8227 (tt0) cc_final: 0.7841 (mm-30) REVERT: I 394 ARG cc_start: 0.7742 (mmm160) cc_final: 0.7467 (mmm160) REVERT: I 410 ARG cc_start: 0.8147 (mtp-110) cc_final: 0.7877 (mtp180) REVERT: I 423 ARG cc_start: 0.7934 (ttm110) cc_final: 0.7331 (mtm110) REVERT: I 435 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7803 (mt-10) REVERT: L 410 ARG cc_start: 0.8072 (mtp-110) cc_final: 0.7730 (mtp180) REVERT: L 423 ARG cc_start: 0.8065 (ttp80) cc_final: 0.7554 (ttp-110) REVERT: O 435 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7473 (mt-10) REVERT: G 384 GLU cc_start: 0.8140 (tp30) cc_final: 0.7773 (tp30) REVERT: G 410 ARG cc_start: 0.8009 (mtp-110) cc_final: 0.7738 (mtp180) REVERT: J 384 GLU cc_start: 0.8192 (tp30) cc_final: 0.7926 (tp30) REVERT: J 410 ARG cc_start: 0.8151 (mtp-110) cc_final: 0.7783 (mtp180) REVERT: M 364 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7333 (mp0) REVERT: M 414 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.7396 (ptt180) REVERT: P 418 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7482 (tt) REVERT: S 364 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7443 (mp0) REVERT: S 384 GLU cc_start: 0.7929 (tp30) cc_final: 0.7686 (tp30) REVERT: S 391 GLN cc_start: 0.8246 (mt0) cc_final: 0.7969 (mt0) REVERT: S 418 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7590 (tt) REVERT: H 410 ARG cc_start: 0.7918 (mtp-110) cc_final: 0.6888 (mmm160) REVERT: H 435 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7914 (mt-10) REVERT: K 391 GLN cc_start: 0.8298 (mt0) cc_final: 0.7991 (mt0) REVERT: K 410 ARG cc_start: 0.7948 (mtp-110) cc_final: 0.6693 (mmm160) REVERT: K 423 ARG cc_start: 0.7794 (ttm170) cc_final: 0.6965 (ttp80) REVERT: K 435 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7917 (mt-10) REVERT: N 384 GLU cc_start: 0.8113 (tp30) cc_final: 0.7836 (mm-30) REVERT: N 410 ARG cc_start: 0.8046 (mtp-110) cc_final: 0.7021 (mmm160) REVERT: N 418 LEU cc_start: 0.8035 (tp) cc_final: 0.7710 (tp) REVERT: N 435 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7879 (mt-10) REVERT: Q 410 ARG cc_start: 0.7899 (mtp-110) cc_final: 0.6897 (mmm160) REVERT: Q 413 ARG cc_start: 0.7654 (ttm170) cc_final: 0.7329 (ttp-170) REVERT: Q 426 ARG cc_start: 0.7961 (mtt90) cc_final: 0.7739 (mtm-85) REVERT: T 364 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7579 (mt-10) REVERT: T 410 ARG cc_start: 0.8098 (mtp-110) cc_final: 0.7124 (mmm160) REVERT: T 435 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7804 (mt-10) outliers start: 37 outliers final: 19 residues processed: 418 average time/residue: 0.9326 time to fit residues: 413.1431 Evaluate side-chains 432 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 406 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain E residue 418 LEU Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain I residue 396 LEU Chi-restraints excluded: chain L residue 396 LEU Chi-restraints excluded: chain O residue 396 LEU Chi-restraints excluded: chain R residue 364 GLU Chi-restraints excluded: chain R residue 389 GLU Chi-restraints excluded: chain J residue 420 LEU Chi-restraints excluded: chain M residue 364 GLU Chi-restraints excluded: chain M residue 396 LEU Chi-restraints excluded: chain M residue 414 ARG Chi-restraints excluded: chain P residue 364 GLU Chi-restraints excluded: chain P residue 396 LEU Chi-restraints excluded: chain P residue 418 LEU Chi-restraints excluded: chain S residue 364 GLU Chi-restraints excluded: chain S residue 418 LEU Chi-restraints excluded: chain T residue 364 GLU Chi-restraints excluded: chain T residue 420 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 138 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 391 GLN G 391 GLN N 391 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.126232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.104350 restraints weight = 14353.216| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.20 r_work: 0.2862 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14580 Z= 0.118 Angle : 0.431 7.410 19700 Z= 0.222 Chirality : 0.036 0.116 2200 Planarity : 0.005 0.057 2580 Dihedral : 3.660 11.507 2020 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.08 % Allowed : 14.35 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.65 (0.20), residues: 1700 helix: 2.50 (0.14), residues: 1480 sheet: None (None), residues: 0 loop : 2.00 (0.39), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG O 410 TYR 0.010 0.003 TYR G 360 PHE 0.005 0.001 PHE P 374 TRP 0.009 0.001 TRP H 371 HIS 0.001 0.000 HIS H 383 Details of bonding type rmsd covalent geometry : bond 0.00279 (14580) covalent geometry : angle 0.43072 (19700) hydrogen bonds : bond 0.03981 ( 980) hydrogen bonds : angle 2.91086 ( 2820) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 406 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: B 394 ARG cc_start: 0.7279 (mmm160) cc_final: 0.6762 (mmm160) REVERT: B 418 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7557 (tt) REVERT: B 423 ARG cc_start: 0.8204 (ttm110) cc_final: 0.7776 (ttm170) REVERT: B 431 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8429 (mp) REVERT: C 410 ARG cc_start: 0.7897 (mtp-110) cc_final: 0.7180 (mtt-85) REVERT: F 410 ARG cc_start: 0.8019 (mtp-110) cc_final: 0.7647 (mtp180) REVERT: F 418 LEU cc_start: 0.8092 (tp) cc_final: 0.7802 (tt) REVERT: F 423 ARG cc_start: 0.7919 (ttm110) cc_final: 0.7675 (ttp-110) REVERT: I 389 GLU cc_start: 0.8231 (tt0) cc_final: 0.7842 (mm-30) REVERT: I 394 ARG cc_start: 0.7688 (mmm160) cc_final: 0.7398 (mmm160) REVERT: I 410 ARG cc_start: 0.8132 (mtp-110) cc_final: 0.7863 (mtp180) REVERT: I 423 ARG cc_start: 0.7939 (ttm110) cc_final: 0.7349 (mtm110) REVERT: I 435 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7798 (mt-10) REVERT: L 396 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8304 (mt) REVERT: L 410 ARG cc_start: 0.8082 (mtp-110) cc_final: 0.7744 (mtp180) REVERT: L 423 ARG cc_start: 0.8068 (ttp80) cc_final: 0.7553 (ttp-110) REVERT: O 435 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7456 (mt-10) REVERT: G 384 GLU cc_start: 0.8109 (tp30) cc_final: 0.7740 (tp30) REVERT: G 410 ARG cc_start: 0.7988 (mtp-110) cc_final: 0.7711 (mtp180) REVERT: J 384 GLU cc_start: 0.8174 (tp30) cc_final: 0.7925 (tp30) REVERT: J 410 ARG cc_start: 0.8107 (mtp-110) cc_final: 0.7762 (mtp180) REVERT: J 413 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7046 (ttp-170) REVERT: M 364 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7324 (mp0) REVERT: P 418 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7503 (tt) REVERT: S 364 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: S 384 GLU cc_start: 0.7926 (tp30) cc_final: 0.7674 (tp30) REVERT: S 391 GLN cc_start: 0.8200 (mt0) cc_final: 0.7918 (mt0) REVERT: S 418 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7548 (tt) REVERT: H 410 ARG cc_start: 0.7894 (mtp-110) cc_final: 0.6879 (mmm160) REVERT: H 435 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7906 (mt-10) REVERT: H 436 ASP cc_start: 0.8228 (m-30) cc_final: 0.7853 (m-30) REVERT: K 391 GLN cc_start: 0.8272 (mt0) cc_final: 0.7950 (mt0) REVERT: K 410 ARG cc_start: 0.7927 (mtp-110) cc_final: 0.6680 (mmm160) REVERT: K 423 ARG cc_start: 0.7800 (ttm170) cc_final: 0.6964 (ttp80) REVERT: K 435 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7921 (mt-10) REVERT: N 384 GLU cc_start: 0.8124 (tp30) cc_final: 0.7856 (mm-30) REVERT: N 410 ARG cc_start: 0.8022 (mtp-110) cc_final: 0.7020 (mmm160) REVERT: N 418 LEU cc_start: 0.8019 (tp) cc_final: 0.7695 (tp) REVERT: N 435 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7893 (mt-10) REVERT: Q 410 ARG cc_start: 0.7938 (mtp-110) cc_final: 0.6937 (mmm160) REVERT: Q 413 ARG cc_start: 0.7648 (ttm170) cc_final: 0.7323 (ttp-170) REVERT: Q 426 ARG cc_start: 0.7972 (mtt90) cc_final: 0.7766 (mtm-85) REVERT: T 364 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7563 (mt-10) REVERT: T 410 ARG cc_start: 0.8078 (mtp-110) cc_final: 0.7127 (mmm160) REVERT: T 435 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7836 (mt-10) outliers start: 32 outliers final: 16 residues processed: 417 average time/residue: 0.9414 time to fit residues: 415.9013 Evaluate side-chains 430 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 405 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain E residue 418 LEU Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain I residue 396 LEU Chi-restraints excluded: chain L residue 396 LEU Chi-restraints excluded: chain O residue 396 LEU Chi-restraints excluded: chain J residue 413 ARG Chi-restraints excluded: chain J residue 420 LEU Chi-restraints excluded: chain M residue 364 GLU Chi-restraints excluded: chain M residue 396 LEU Chi-restraints excluded: chain P residue 364 GLU Chi-restraints excluded: chain P residue 396 LEU Chi-restraints excluded: chain P residue 418 LEU Chi-restraints excluded: chain S residue 364 GLU Chi-restraints excluded: chain S residue 418 LEU Chi-restraints excluded: chain K residue 414 ARG Chi-restraints excluded: chain T residue 364 GLU Chi-restraints excluded: chain T residue 420 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 23 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 chunk 1 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 391 GLN F 391 GLN G 391 GLN N 391 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.124487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.101307 restraints weight = 14030.615| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.24 r_work: 0.2890 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14580 Z= 0.096 Angle : 0.399 7.773 19700 Z= 0.205 Chirality : 0.034 0.115 2200 Planarity : 0.004 0.059 2580 Dihedral : 3.480 10.406 2020 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.69 % Allowed : 14.87 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.94 (0.21), residues: 1700 helix: 2.69 (0.14), residues: 1480 sheet: None (None), residues: 0 loop : 2.13 (0.40), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG O 410 TYR 0.009 0.002 TYR E 401 PHE 0.005 0.001 PHE P 374 TRP 0.007 0.001 TRP F 371 HIS 0.001 0.000 HIS E 383 Details of bonding type rmsd covalent geometry : bond 0.00218 (14580) covalent geometry : angle 0.39873 (19700) hydrogen bonds : bond 0.03476 ( 980) hydrogen bonds : angle 2.79290 ( 2820) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 414 time to evaluate : 0.604 Fit side-chains REVERT: B 394 ARG cc_start: 0.7242 (mmm160) cc_final: 0.6731 (mmm160) REVERT: B 418 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7555 (tt) REVERT: B 423 ARG cc_start: 0.8224 (ttm110) cc_final: 0.7809 (ttm170) REVERT: B 431 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8443 (mp) REVERT: C 410 ARG cc_start: 0.7887 (mtp-110) cc_final: 0.7196 (mtt-85) REVERT: F 410 ARG cc_start: 0.7957 (mtp-110) cc_final: 0.7623 (mtp180) REVERT: F 418 LEU cc_start: 0.8092 (tp) cc_final: 0.7794 (tt) REVERT: F 423 ARG cc_start: 0.7964 (ttm110) cc_final: 0.7720 (ttp-110) REVERT: I 389 GLU cc_start: 0.8246 (tt0) cc_final: 0.7858 (mm-30) REVERT: I 394 ARG cc_start: 0.7705 (mmm160) cc_final: 0.7419 (mmm160) REVERT: I 410 ARG cc_start: 0.8145 (mtp-110) cc_final: 0.7889 (mtp180) REVERT: I 423 ARG cc_start: 0.8002 (ttm110) cc_final: 0.7434 (mtm110) REVERT: I 435 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7828 (mt-10) REVERT: L 396 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8261 (mt) REVERT: L 410 ARG cc_start: 0.8065 (mtp-110) cc_final: 0.7724 (mtp180) REVERT: L 423 ARG cc_start: 0.8104 (ttp80) cc_final: 0.7590 (ttp-110) REVERT: O 364 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7730 (mp0) REVERT: O 418 LEU cc_start: 0.8048 (mp) cc_final: 0.7661 (tt) REVERT: O 435 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7506 (mt-10) REVERT: G 384 GLU cc_start: 0.8129 (tp30) cc_final: 0.7757 (tp30) REVERT: G 410 ARG cc_start: 0.7991 (mtp-110) cc_final: 0.7716 (mtp180) REVERT: J 384 GLU cc_start: 0.8199 (tp30) cc_final: 0.7942 (tp30) REVERT: J 410 ARG cc_start: 0.8134 (mtp-110) cc_final: 0.7790 (mtp180) REVERT: J 413 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7023 (ttp-170) REVERT: M 364 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7328 (mp0) REVERT: P 418 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7493 (tt) REVERT: S 364 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7458 (mp0) REVERT: S 384 GLU cc_start: 0.7946 (tp30) cc_final: 0.7690 (tp30) REVERT: S 391 GLN cc_start: 0.8183 (mt0) cc_final: 0.7939 (mt0) REVERT: S 398 GLU cc_start: 0.8677 (tp30) cc_final: 0.8321 (mm-30) REVERT: S 410 ARG cc_start: 0.8061 (mtp-110) cc_final: 0.7754 (mtp180) REVERT: S 418 LEU cc_start: 0.7805 (mp) cc_final: 0.7576 (tt) REVERT: H 410 ARG cc_start: 0.7918 (mtp-110) cc_final: 0.6903 (mmm160) REVERT: H 435 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7922 (mt-10) REVERT: K 391 GLN cc_start: 0.8248 (mt0) cc_final: 0.7958 (mt0) REVERT: K 410 ARG cc_start: 0.7919 (mtp-110) cc_final: 0.6737 (mmm160) REVERT: K 423 ARG cc_start: 0.7856 (ttm170) cc_final: 0.6999 (ttp80) REVERT: K 435 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7979 (mt-10) REVERT: N 384 GLU cc_start: 0.8160 (tp30) cc_final: 0.7882 (mm-30) REVERT: N 410 ARG cc_start: 0.8036 (mtp-110) cc_final: 0.7030 (mmm160) REVERT: N 418 LEU cc_start: 0.8026 (tp) cc_final: 0.7698 (tp) REVERT: Q 410 ARG cc_start: 0.7961 (mtp-110) cc_final: 0.6896 (mmm160) REVERT: Q 413 ARG cc_start: 0.7644 (ttm170) cc_final: 0.7323 (ttp-170) REVERT: Q 426 ARG cc_start: 0.8021 (mtt90) cc_final: 0.7666 (mtm-85) REVERT: T 410 ARG cc_start: 0.8051 (mtp-110) cc_final: 0.7147 (mmm160) REVERT: T 435 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7896 (mt-10) outliers start: 26 outliers final: 13 residues processed: 424 average time/residue: 0.9255 time to fit residues: 416.0631 Evaluate side-chains 428 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 408 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain E residue 418 LEU Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain I residue 396 LEU Chi-restraints excluded: chain L residue 396 LEU Chi-restraints excluded: chain J residue 413 ARG Chi-restraints excluded: chain J residue 420 LEU Chi-restraints excluded: chain M residue 364 GLU Chi-restraints excluded: chain M residue 396 LEU Chi-restraints excluded: chain P residue 364 GLU Chi-restraints excluded: chain P residue 396 LEU Chi-restraints excluded: chain P residue 418 LEU Chi-restraints excluded: chain S residue 364 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 97 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 148 optimal weight: 0.7980 chunk 139 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 5 optimal weight: 0.0770 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 391 GLN N 391 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.125858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.103930 restraints weight = 14521.559| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.20 r_work: 0.2896 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14580 Z= 0.094 Angle : 0.397 7.727 19700 Z= 0.203 Chirality : 0.034 0.114 2200 Planarity : 0.004 0.062 2580 Dihedral : 3.420 10.094 2020 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.88 % Allowed : 14.87 % Favored : 83.25 % 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: 4.10 (0.21), residues: 1700 helix: 2.78 (0.14), residues: 1480 sheet: None (None), residues: 0 loop : 2.26 (0.41), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG O 410 TYR 0.009 0.002 TYR G 360 PHE 0.004 0.001 PHE P 374 TRP 0.007 0.001 TRP F 371 HIS 0.001 0.000 HIS H 383 Details of bonding type rmsd covalent geometry : bond 0.00213 (14580) covalent geometry : angle 0.39706 (19700) hydrogen bonds : bond 0.03400 ( 980) hydrogen bonds : angle 2.76479 ( 2820) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 407 time to evaluate : 0.583 Fit side-chains REVERT: B 394 ARG cc_start: 0.7163 (mmm160) cc_final: 0.6593 (mmm160) REVERT: B 418 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7529 (tt) REVERT: B 423 ARG cc_start: 0.8190 (ttm110) cc_final: 0.7773 (ttm170) REVERT: B 431 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8427 (mp) REVERT: C 410 ARG cc_start: 0.7869 (mtp-110) cc_final: 0.7177 (mtt-85) REVERT: F 410 ARG cc_start: 0.7963 (mtp-110) cc_final: 0.7552 (mtp180) REVERT: F 418 LEU cc_start: 0.8067 (tp) cc_final: 0.7771 (tt) REVERT: F 423 ARG cc_start: 0.7913 (ttm110) cc_final: 0.7679 (ttp-110) REVERT: I 389 GLU cc_start: 0.8221 (tt0) cc_final: 0.7826 (mm-30) REVERT: I 410 ARG cc_start: 0.8108 (mtp-110) cc_final: 0.7846 (mtp180) REVERT: I 423 ARG cc_start: 0.7975 (ttm110) cc_final: 0.7422 (mtm110) REVERT: I 435 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7800 (mt-10) REVERT: L 396 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8275 (mt) REVERT: L 410 ARG cc_start: 0.8056 (mtp-110) cc_final: 0.7708 (mtp180) REVERT: L 423 ARG cc_start: 0.8084 (ttp80) cc_final: 0.7564 (ttp-110) REVERT: O 364 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7740 (mp0) REVERT: O 418 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7634 (tt) REVERT: O 435 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7669 (mt-10) REVERT: G 410 ARG cc_start: 0.7947 (mtp-110) cc_final: 0.7666 (mtp180) REVERT: J 384 GLU cc_start: 0.8196 (tp30) cc_final: 0.7933 (tp30) REVERT: J 410 ARG cc_start: 0.8102 (mtp-110) cc_final: 0.7754 (mtp180) REVERT: J 413 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.6992 (ttp-170) REVERT: M 364 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7366 (mp0) REVERT: P 418 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7406 (tt) REVERT: S 364 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7478 (mp0) REVERT: S 384 GLU cc_start: 0.7928 (tp30) cc_final: 0.7669 (tp30) REVERT: S 391 GLN cc_start: 0.8167 (mt0) cc_final: 0.7933 (mt0) REVERT: S 398 GLU cc_start: 0.8659 (tp30) cc_final: 0.8312 (mm-30) REVERT: S 410 ARG cc_start: 0.8060 (mtp-110) cc_final: 0.7846 (mtp180) REVERT: S 418 LEU cc_start: 0.7802 (mp) cc_final: 0.7555 (tt) REVERT: S 423 ARG cc_start: 0.7934 (ttp-110) cc_final: 0.7625 (ttp80) REVERT: H 410 ARG cc_start: 0.7905 (mtp-110) cc_final: 0.6883 (mmm160) REVERT: H 435 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7894 (mt-10) REVERT: K 391 GLN cc_start: 0.8226 (mt0) cc_final: 0.7943 (mt0) REVERT: K 410 ARG cc_start: 0.7889 (mtp-110) cc_final: 0.6679 (mmm160) REVERT: K 423 ARG cc_start: 0.7815 (ttm170) cc_final: 0.6958 (ttp80) REVERT: K 435 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7953 (mt-10) REVERT: N 384 GLU cc_start: 0.8139 (tp30) cc_final: 0.7861 (mm-30) REVERT: N 410 ARG cc_start: 0.7995 (mtp-110) cc_final: 0.6999 (mmm160) REVERT: Q 410 ARG cc_start: 0.7945 (mtp-110) cc_final: 0.6871 (mmm160) REVERT: Q 413 ARG cc_start: 0.7619 (ttm170) cc_final: 0.7294 (ttp-170) REVERT: Q 426 ARG cc_start: 0.8001 (mtt90) cc_final: 0.7650 (mtm-85) REVERT: T 410 ARG cc_start: 0.8021 (mtp-110) cc_final: 0.7115 (mmm160) REVERT: T 435 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7872 (mt-10) outliers start: 29 outliers final: 11 residues processed: 414 average time/residue: 0.9546 time to fit residues: 418.5922 Evaluate side-chains 426 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 407 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain E residue 418 LEU Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain I residue 396 LEU Chi-restraints excluded: chain L residue 396 LEU Chi-restraints excluded: chain O residue 418 LEU Chi-restraints excluded: chain J residue 413 ARG Chi-restraints excluded: chain J residue 420 LEU Chi-restraints excluded: chain M residue 364 GLU Chi-restraints excluded: chain M residue 396 LEU Chi-restraints excluded: chain P residue 364 GLU Chi-restraints excluded: chain P residue 396 LEU Chi-restraints excluded: chain P residue 418 LEU Chi-restraints excluded: chain S residue 364 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 47 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 0.0870 chunk 101 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 107 optimal weight: 0.2980 chunk 92 optimal weight: 0.8980 chunk 135 optimal weight: 6.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 391 GLN G 391 GLN N 391 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.125338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.102876 restraints weight = 14575.753| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.24 r_work: 0.2830 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14580 Z= 0.102 Angle : 0.411 7.707 19700 Z= 0.209 Chirality : 0.035 0.136 2200 Planarity : 0.005 0.064 2580 Dihedral : 3.464 10.209 2020 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.49 % Allowed : 15.84 % Favored : 82.66 % 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: 4.08 (0.21), residues: 1700 helix: 2.77 (0.14), residues: 1480 sheet: None (None), residues: 0 loop : 2.28 (0.41), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG O 410 TYR 0.009 0.002 TYR G 360 PHE 0.004 0.001 PHE P 374 TRP 0.007 0.001 TRP F 371 HIS 0.001 0.000 HIS H 383 Details of bonding type rmsd covalent geometry : bond 0.00236 (14580) covalent geometry : angle 0.41058 (19700) hydrogen bonds : bond 0.03595 ( 980) hydrogen bonds : angle 2.79991 ( 2820) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7251.53 seconds wall clock time: 123 minutes 22.25 seconds (7402.25 seconds total)