Starting phenix.real_space_refine on Wed Mar 4 04:02:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ofg_20045/03_2026/6ofg_20045.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ofg_20045/03_2026/6ofg_20045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ofg_20045/03_2026/6ofg_20045.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ofg_20045/03_2026/6ofg_20045.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ofg_20045/03_2026/6ofg_20045.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ofg_20045/03_2026/6ofg_20045.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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: 3 Type Number sf(0) Gaussians C 6930 2.51 5 N 1818 2.21 5 O 2232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10980 Number of models: 1 Model: "" Number of chains: 1 Chain: "P" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Restraints were copied for chains: Q, R, K, L, M, N, O, F, G, H, I, J, A, B, C, D, E Time building chain proxies: 1.08, per 1000 atoms: 0.10 Number of scatterers: 10980 At special positions: 0 Unit cell: (90.915, 90.915, 147.345, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 2232 8.00 N 1818 7.00 C 6930 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 492.6 milliseconds 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2736 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 0 sheets defined 91.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'P' and resid 7 through 20 removed outlier: 3.580A pdb=" N PHE P 16 " --> pdb=" O VAL P 12 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP P 17 " --> pdb=" O SER P 13 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 37 removed outlier: 3.663A pdb=" N THR P 28 " --> pdb=" O GLN P 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA P 36 " --> pdb=" O ASP P 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS P 37 " --> pdb=" O LYS P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 77 removed outlier: 3.562A pdb=" N ALA P 74 " --> pdb=" O ASP P 70 " (cutoff:3.500A) Processing helix chain 'P' and resid 78 through 80 No H-bonds generated for 'chain 'P' and resid 78 through 80' Processing helix chain 'Q' and resid 7 through 20 removed outlier: 3.580A pdb=" N PHE Q 16 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP Q 17 " --> pdb=" O SER Q 13 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 37 removed outlier: 3.663A pdb=" N THR Q 28 " --> pdb=" O GLN Q 24 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA Q 36 " --> pdb=" O ASP Q 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS Q 37 " --> pdb=" O LYS Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 77 removed outlier: 3.563A pdb=" N ALA Q 74 " --> pdb=" O ASP Q 70 " (cutoff:3.500A) Processing helix chain 'Q' and resid 78 through 80 No H-bonds generated for 'chain 'Q' and resid 78 through 80' Processing helix chain 'R' and resid 7 through 20 removed outlier: 3.580A pdb=" N PHE R 16 " --> pdb=" O VAL R 12 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP R 17 " --> pdb=" O SER R 13 " (cutoff:3.500A) Processing helix chain 'R' and resid 22 through 37 removed outlier: 3.662A pdb=" N THR R 28 " --> pdb=" O GLN R 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA R 36 " --> pdb=" O ASP R 32 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS R 37 " --> pdb=" O LYS R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 77 removed outlier: 3.563A pdb=" N ALA R 74 " --> pdb=" O ASP R 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 80 No H-bonds generated for 'chain 'R' and resid 78 through 80' Processing helix chain 'K' and resid 7 through 20 removed outlier: 3.580A pdb=" N PHE K 16 " --> pdb=" O VAL K 12 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP K 17 " --> pdb=" O SER K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 37 removed outlier: 3.662A pdb=" N THR K 28 " --> pdb=" O GLN K 24 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA K 36 " --> pdb=" O ASP K 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS K 37 " --> pdb=" O LYS K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 77 removed outlier: 3.562A pdb=" N ALA K 74 " --> pdb=" O ASP K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 80 No H-bonds generated for 'chain 'K' and resid 78 through 80' Processing helix chain 'L' and resid 7 through 20 removed outlier: 3.580A pdb=" N PHE L 16 " --> pdb=" O VAL L 12 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP L 17 " --> pdb=" O SER L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 37 removed outlier: 3.662A pdb=" N THR L 28 " --> pdb=" O GLN L 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA L 36 " --> pdb=" O ASP L 32 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS L 37 " --> pdb=" O LYS L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 77 removed outlier: 3.563A pdb=" N ALA L 74 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 80 No H-bonds generated for 'chain 'L' and resid 78 through 80' Processing helix chain 'M' and resid 7 through 20 removed outlier: 3.579A pdb=" N PHE M 16 " --> pdb=" O VAL M 12 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP M 17 " --> pdb=" O SER M 13 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 37 removed outlier: 3.663A pdb=" N THR M 28 " --> pdb=" O GLN M 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA M 36 " --> pdb=" O ASP M 32 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS M 37 " --> pdb=" O LYS M 33 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 77 removed outlier: 3.563A pdb=" N ALA M 74 " --> pdb=" O ASP M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 78 through 80 No H-bonds generated for 'chain 'M' and resid 78 through 80' Processing helix chain 'N' and resid 7 through 20 removed outlier: 3.579A pdb=" N PHE N 16 " --> pdb=" O VAL N 12 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP N 17 " --> pdb=" O SER N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 37 removed outlier: 3.663A pdb=" N THR N 28 " --> pdb=" O GLN N 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA N 36 " --> pdb=" O ASP N 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS N 37 " --> pdb=" O LYS N 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 77 removed outlier: 3.562A pdb=" N ALA N 74 " --> pdb=" O ASP N 70 " (cutoff:3.500A) Processing helix chain 'N' and resid 78 through 80 No H-bonds generated for 'chain 'N' and resid 78 through 80' Processing helix chain 'O' and resid 7 through 20 removed outlier: 3.580A pdb=" N PHE O 16 " --> pdb=" O VAL O 12 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP O 17 " --> pdb=" O SER O 13 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 37 removed outlier: 3.662A pdb=" N THR O 28 " --> pdb=" O GLN O 24 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA O 36 " --> pdb=" O ASP O 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS O 37 " --> pdb=" O LYS O 33 " (cutoff:3.500A) Processing helix chain 'O' and resid 40 through 77 removed outlier: 3.563A pdb=" N ALA O 74 " --> pdb=" O ASP O 70 " (cutoff:3.500A) Processing helix chain 'O' and resid 78 through 80 No H-bonds generated for 'chain 'O' and resid 78 through 80' Processing helix chain 'F' and resid 7 through 20 removed outlier: 3.580A pdb=" N PHE F 16 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP F 17 " --> pdb=" O SER F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 37 removed outlier: 3.663A pdb=" N THR F 28 " --> pdb=" O GLN F 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA F 36 " --> pdb=" O ASP F 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS F 37 " --> pdb=" O LYS F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 77 removed outlier: 3.562A pdb=" N ALA F 74 " --> pdb=" O ASP F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 80 No H-bonds generated for 'chain 'F' and resid 78 through 80' Processing helix chain 'G' and resid 7 through 20 removed outlier: 3.579A pdb=" N PHE G 16 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP G 17 " --> pdb=" O SER G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 37 removed outlier: 3.662A pdb=" N THR G 28 " --> pdb=" O GLN G 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA G 36 " --> pdb=" O ASP G 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS G 37 " --> pdb=" O LYS G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 77 removed outlier: 3.563A pdb=" N ALA G 74 " --> pdb=" O ASP G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 80 No H-bonds generated for 'chain 'G' and resid 78 through 80' Processing helix chain 'H' and resid 7 through 20 removed outlier: 3.580A pdb=" N PHE H 16 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP H 17 " --> pdb=" O SER H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 37 removed outlier: 3.662A pdb=" N THR H 28 " --> pdb=" O GLN H 24 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA H 36 " --> pdb=" O ASP H 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS H 37 " --> pdb=" O LYS H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 77 removed outlier: 3.562A pdb=" N ALA H 74 " --> pdb=" O ASP H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 80 No H-bonds generated for 'chain 'H' and resid 78 through 80' Processing helix chain 'I' and resid 7 through 20 removed outlier: 3.579A pdb=" N PHE I 16 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP I 17 " --> pdb=" O SER I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 37 removed outlier: 3.662A pdb=" N THR I 28 " --> pdb=" O GLN I 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA I 36 " --> pdb=" O ASP I 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS I 37 " --> pdb=" O LYS I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 77 removed outlier: 3.563A pdb=" N ALA I 74 " --> pdb=" O ASP I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 80 No H-bonds generated for 'chain 'I' and resid 78 through 80' Processing helix chain 'J' and resid 7 through 20 removed outlier: 3.579A pdb=" N PHE J 16 " --> pdb=" O VAL J 12 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP J 17 " --> pdb=" O SER J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 37 removed outlier: 3.663A pdb=" N THR J 28 " --> pdb=" O GLN J 24 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA J 36 " --> pdb=" O ASP J 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS J 37 " --> pdb=" O LYS J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 77 removed outlier: 3.563A pdb=" N ALA J 74 " --> pdb=" O ASP J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 80 No H-bonds generated for 'chain 'J' and resid 78 through 80' Processing helix chain 'A' and resid 7 through 20 removed outlier: 3.580A pdb=" N PHE A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP A 17 " --> pdb=" O SER A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 37 removed outlier: 3.662A pdb=" N THR A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 36 " --> pdb=" O ASP A 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 77 removed outlier: 3.563A pdb=" N ALA A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 80 No H-bonds generated for 'chain 'A' and resid 78 through 80' Processing helix chain 'B' and resid 7 through 20 removed outlier: 3.580A pdb=" N PHE B 16 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP B 17 " --> pdb=" O SER B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 37 removed outlier: 3.663A pdb=" N THR B 28 " --> pdb=" O GLN B 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA B 36 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS B 37 " --> pdb=" O LYS B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 77 removed outlier: 3.562A pdb=" N ALA B 74 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'C' and resid 7 through 20 removed outlier: 3.580A pdb=" N PHE C 16 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP C 17 " --> pdb=" O SER C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 37 removed outlier: 3.662A pdb=" N THR C 28 " --> pdb=" O GLN C 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA C 36 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS C 37 " --> pdb=" O LYS C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 77 removed outlier: 3.562A pdb=" N ALA C 74 " --> pdb=" O ASP C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 80 No H-bonds generated for 'chain 'C' and resid 78 through 80' Processing helix chain 'D' and resid 7 through 20 removed outlier: 3.580A pdb=" N PHE D 16 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP D 17 " --> pdb=" O SER D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 37 removed outlier: 3.662A pdb=" N THR D 28 " --> pdb=" O GLN D 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA D 36 " --> pdb=" O ASP D 32 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS D 37 " --> pdb=" O LYS D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 77 removed outlier: 3.563A pdb=" N ALA D 74 " --> pdb=" O ASP D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 80 No H-bonds generated for 'chain 'D' and resid 78 through 80' Processing helix chain 'E' and resid 7 through 20 removed outlier: 3.579A pdb=" N PHE E 16 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP E 17 " --> pdb=" O SER E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 37 removed outlier: 3.663A pdb=" N THR E 28 " --> pdb=" O GLN E 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS E 37 " --> pdb=" O LYS E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 77 removed outlier: 3.563A pdb=" N ALA E 74 " --> pdb=" O ASP E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 80 No H-bonds generated for 'chain 'E' and resid 78 through 80' 900 hydrogen bonds defined for protein. 2700 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.74 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 1962 1.29 - 1.35: 1674 1.35 - 1.41: 1087 1.41 - 1.48: 1689 1.48 - 1.54: 4766 Bond restraints: 11178 Sorted by residual: bond pdb=" CB GLU O 53 " pdb=" CG GLU O 53 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.58e+00 bond pdb=" CB GLU D 53 " pdb=" CG GLU D 53 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.58e+00 bond pdb=" CB GLU L 53 " pdb=" CG GLU L 53 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.58e+00 bond pdb=" CB GLU K 53 " pdb=" CG GLU K 53 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.57e+00 bond pdb=" CB GLU Q 53 " pdb=" CG GLU Q 53 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.57e+00 ... (remaining 11173 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.91: 13081 0.91 - 1.82: 1534 1.82 - 2.73: 415 2.73 - 3.64: 140 3.64 - 4.55: 40 Bond angle restraints: 15210 Sorted by residual: angle pdb=" C VAL M 20 " pdb=" N ASP M 21 " pdb=" CA ASP M 21 " ideal model delta sigma weight residual 121.81 117.26 4.55 1.83e+00 2.99e-01 6.17e+00 angle pdb=" C VAL H 20 " pdb=" N ASP H 21 " pdb=" CA ASP H 21 " ideal model delta sigma weight residual 121.81 117.29 4.52 1.83e+00 2.99e-01 6.09e+00 angle pdb=" C VAL O 20 " pdb=" N ASP O 21 " pdb=" CA ASP O 21 " ideal model delta sigma weight residual 121.81 117.30 4.51 1.83e+00 2.99e-01 6.07e+00 angle pdb=" C VAL G 20 " pdb=" N ASP G 21 " pdb=" CA ASP G 21 " ideal model delta sigma weight residual 121.81 117.32 4.49 1.83e+00 2.99e-01 6.03e+00 angle pdb=" C VAL R 20 " pdb=" N ASP R 21 " pdb=" CA ASP R 21 " ideal model delta sigma weight residual 121.81 117.32 4.49 1.83e+00 2.99e-01 6.03e+00 ... (remaining 15205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.84: 6534 14.84 - 29.68: 180 29.68 - 44.52: 54 44.52 - 59.37: 0 59.37 - 74.21: 18 Dihedral angle restraints: 6786 sinusoidal: 2592 harmonic: 4194 Sorted by residual: dihedral pdb=" CA GLY N 19 " pdb=" C GLY N 19 " pdb=" N VAL N 20 " pdb=" CA VAL N 20 " ideal model delta harmonic sigma weight residual 180.00 159.80 20.20 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA GLY H 19 " pdb=" C GLY H 19 " pdb=" N VAL H 20 " pdb=" CA VAL H 20 " ideal model delta harmonic sigma weight residual 180.00 159.80 20.20 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA GLY D 19 " pdb=" C GLY D 19 " pdb=" N VAL D 20 " pdb=" CA VAL D 20 " ideal model delta harmonic sigma weight residual 180.00 159.80 20.20 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 6783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.020: 425 0.020 - 0.040: 694 0.040 - 0.059: 305 0.059 - 0.079: 184 0.079 - 0.099: 120 Chirality restraints: 1728 Sorted by residual: chirality pdb=" CA PRO D 38 " pdb=" N PRO D 38 " pdb=" C PRO D 38 " pdb=" CB PRO D 38 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.44e-01 chirality pdb=" CA PRO L 38 " pdb=" N PRO L 38 " pdb=" C PRO L 38 " pdb=" CB PRO L 38 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.44e-01 chirality pdb=" CA PRO B 41 " pdb=" N PRO B 41 " pdb=" C PRO B 41 " pdb=" CB PRO B 41 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.38e-01 ... (remaining 1725 not shown) Planarity restraints: 1998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 20 " -0.007 2.00e-02 2.50e+03 1.36e-02 1.85e+00 pdb=" C VAL A 20 " 0.024 2.00e-02 2.50e+03 pdb=" O VAL A 20 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP A 21 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL N 20 " -0.007 2.00e-02 2.50e+03 1.36e-02 1.85e+00 pdb=" C VAL N 20 " 0.024 2.00e-02 2.50e+03 pdb=" O VAL N 20 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP N 21 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL G 20 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.82e+00 pdb=" C VAL G 20 " 0.023 2.00e-02 2.50e+03 pdb=" O VAL G 20 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP G 21 " -0.008 2.00e-02 2.50e+03 ... (remaining 1995 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3286 2.79 - 3.32: 10703 3.32 - 3.85: 18136 3.85 - 4.37: 23422 4.37 - 4.90: 38800 Nonbonded interactions: 94347 Sorted by model distance: nonbonded pdb=" OD1 ASP K 17 " pdb=" OH TYR K 57 " model vdw 2.263 3.040 nonbonded pdb=" OD1 ASP Q 17 " pdb=" OH TYR Q 57 " model vdw 2.263 3.040 nonbonded pdb=" OD1 ASP G 17 " pdb=" OH TYR G 57 " model vdw 2.263 3.040 nonbonded pdb=" OD1 ASP C 17 " pdb=" OH TYR C 57 " model vdw 2.263 3.040 nonbonded pdb=" OD1 ASP D 17 " pdb=" OH TYR D 57 " model vdw 2.263 3.040 ... (remaining 94342 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: 0.03 Found NCS groups: ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.530 Find NCS groups from input model: 0.090 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: 0.000 Load rotamer database and sin/cos tables:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 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 0.040 11178 Z= 0.334 Angle : 0.750 4.546 15210 Z= 0.406 Chirality : 0.043 0.099 1728 Planarity : 0.005 0.030 1998 Dihedral : 10.039 74.208 4050 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % 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: -6.09 (0.10), residues: 1368 helix: -3.76 (0.06), residues: 1170 sheet: None (None), residues: 0 loop : -3.57 (0.31), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG F 58 TYR 0.011 0.003 TYR Q 57 PHE 0.012 0.002 PHE M 79 TRP 0.019 0.005 TRP N 5 Details of bonding type rmsd covalent geometry : bond 0.00771 (11178) covalent geometry : angle 0.74966 (15210) hydrogen bonds : bond 0.23865 ( 900) hydrogen bonds : angle 9.55916 ( 2700) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 33 LYS cc_start: 0.8552 (mttt) cc_final: 0.8323 (mttm) REVERT: N 28 THR cc_start: 0.8841 (m) cc_final: 0.8044 (m) REVERT: N 29 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7488 (mt-10) REVERT: N 32 ASP cc_start: 0.7471 (m-30) cc_final: 0.7096 (m-30) REVERT: O 10 ASP cc_start: 0.8938 (m-30) cc_final: 0.8720 (m-30) REVERT: A 37 LYS cc_start: 0.8407 (ttmt) cc_final: 0.7090 (tttp) REVERT: A 66 LYS cc_start: 0.8971 (tptp) cc_final: 0.7622 (tppt) REVERT: A 72 ASP cc_start: 0.8867 (m-30) cc_final: 0.8640 (m-30) REVERT: B 66 LYS cc_start: 0.9050 (tptp) cc_final: 0.7748 (tppt) REVERT: D 72 ASP cc_start: 0.8868 (m-30) cc_final: 0.8614 (m-30) outliers start: 0 outliers final: 0 residues processed: 353 average time/residue: 0.5050 time to fit residues: 193.8284 Evaluate side-chains 241 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 123 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 77 GLN L 55 ASN L 77 GLN M 55 ASN N 55 ASN O 55 ASN G 77 GLN I 77 GLN E 63 ASN E 77 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.114283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.099738 restraints weight = 15592.123| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.60 r_work: 0.3004 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 11178 Z= 0.139 Angle : 0.499 3.655 15210 Z= 0.280 Chirality : 0.034 0.101 1728 Planarity : 0.005 0.028 1998 Dihedral : 4.273 21.657 1512 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.48 % Allowed : 14.70 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.18), residues: 1368 helix: -0.14 (0.11), residues: 1242 sheet: None (None), residues: 0 loop : -2.30 (0.48), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 58 TYR 0.011 0.001 TYR E 57 PHE 0.006 0.001 PHE A 79 TRP 0.011 0.002 TRP N 5 Details of bonding type rmsd covalent geometry : bond 0.00291 (11178) covalent geometry : angle 0.49889 (15210) hydrogen bonds : bond 0.04499 ( 900) hydrogen bonds : angle 3.34143 ( 2700) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 268 time to evaluate : 0.412 Fit side-chains REVERT: P 59 ASN cc_start: 0.8641 (OUTLIER) cc_final: 0.8424 (t0) REVERT: Q 25 THR cc_start: 0.8656 (m) cc_final: 0.8364 (p) REVERT: Q 32 ASP cc_start: 0.8269 (m-30) cc_final: 0.7794 (m-30) REVERT: K 59 ASN cc_start: 0.8822 (OUTLIER) cc_final: 0.8535 (m-40) REVERT: K 69 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8105 (tptm) REVERT: L 33 LYS cc_start: 0.8763 (mttt) cc_final: 0.8471 (mttm) REVERT: N 28 THR cc_start: 0.8947 (m) cc_final: 0.8141 (m) REVERT: N 32 ASP cc_start: 0.8183 (m-30) cc_final: 0.7658 (m-30) REVERT: O 32 ASP cc_start: 0.8403 (m-30) cc_final: 0.8168 (m-30) REVERT: F 11 ASP cc_start: 0.8561 (m-30) cc_final: 0.8303 (m-30) REVERT: H 29 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7650 (pt0) REVERT: H 59 ASN cc_start: 0.8753 (OUTLIER) cc_final: 0.8546 (t0) REVERT: I 59 ASN cc_start: 0.8618 (OUTLIER) cc_final: 0.8155 (t0) REVERT: J 59 ASN cc_start: 0.8731 (OUTLIER) cc_final: 0.8378 (t0) REVERT: J 69 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8521 (tttm) REVERT: A 37 LYS cc_start: 0.8470 (ttmt) cc_final: 0.7156 (tttp) REVERT: B 72 ASP cc_start: 0.8903 (m-30) cc_final: 0.8690 (m-30) REVERT: C 72 ASP cc_start: 0.8941 (m-30) cc_final: 0.8648 (m-30) REVERT: D 26 GLN cc_start: 0.8918 (mt0) cc_final: 0.8584 (mt0) REVERT: D 32 ASP cc_start: 0.8366 (m-30) cc_final: 0.8068 (m-30) REVERT: D 49 SER cc_start: 0.8970 (p) cc_final: 0.8753 (m) REVERT: E 6 SER cc_start: 0.8428 (m) cc_final: 0.8208 (p) REVERT: E 10 ASP cc_start: 0.8557 (m-30) cc_final: 0.8295 (m-30) REVERT: E 15 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8378 (mtpt) REVERT: E 22 ASN cc_start: 0.7827 (p0) cc_final: 0.7560 (p0) REVERT: E 72 ASP cc_start: 0.9102 (m-30) cc_final: 0.8879 (m-30) outliers start: 29 outliers final: 6 residues processed: 272 average time/residue: 0.4394 time to fit residues: 131.0525 Evaluate side-chains 249 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 235 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 59 ASN Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain K residue 59 ASN Chi-restraints excluded: chain K residue 69 LYS Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain O residue 59 ASN Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain J residue 32 ASP Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain E residue 15 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 36 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 108 optimal weight: 0.0050 chunk 106 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 77 GLN L 77 GLN G 77 GLN I 55 ASN J 55 ASN D 77 GLN E 77 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.114788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.100198 restraints weight = 15568.317| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.59 r_work: 0.3009 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 11178 Z= 0.119 Angle : 0.441 3.378 15210 Z= 0.243 Chirality : 0.034 0.103 1728 Planarity : 0.004 0.023 1998 Dihedral : 3.871 18.908 1512 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.42 % Allowed : 14.36 % Favored : 82.22 % 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: 2.16 (0.21), residues: 1368 helix: 1.91 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.86 (0.49), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 58 TYR 0.008 0.001 TYR E 57 PHE 0.005 0.001 PHE K 68 TRP 0.007 0.001 TRP N 5 Details of bonding type rmsd covalent geometry : bond 0.00246 (11178) covalent geometry : angle 0.44074 (15210) hydrogen bonds : bond 0.03784 ( 900) hydrogen bonds : angle 2.90993 ( 2700) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 265 time to evaluate : 0.432 Fit side-chains REVERT: P 32 ASP cc_start: 0.8462 (m-30) cc_final: 0.8205 (m-30) REVERT: P 57 TYR cc_start: 0.9164 (OUTLIER) cc_final: 0.8651 (t80) REVERT: P 59 ASN cc_start: 0.8590 (OUTLIER) cc_final: 0.8389 (t0) REVERT: Q 25 THR cc_start: 0.8599 (m) cc_final: 0.8364 (p) REVERT: Q 32 ASP cc_start: 0.8285 (m-30) cc_final: 0.7824 (m-30) REVERT: K 15 LYS cc_start: 0.8758 (mmmm) cc_final: 0.8152 (tttt) REVERT: K 59 ASN cc_start: 0.8768 (OUTLIER) cc_final: 0.8491 (m-40) REVERT: K 69 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8017 (tptm) REVERT: L 15 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8506 (mmtm) REVERT: L 33 LYS cc_start: 0.8762 (mttt) cc_final: 0.8453 (mttm) REVERT: M 69 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8057 (tptm) REVERT: N 28 THR cc_start: 0.8956 (m) cc_final: 0.8283 (m) REVERT: N 29 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7830 (mt-10) REVERT: N 32 ASP cc_start: 0.8191 (m-30) cc_final: 0.7682 (m-30) REVERT: O 32 ASP cc_start: 0.8264 (m-30) cc_final: 0.7902 (m-30) REVERT: F 69 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8266 (tttm) REVERT: G 33 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8512 (mtmt) REVERT: G 72 ASP cc_start: 0.8834 (m-30) cc_final: 0.8616 (m-30) REVERT: H 32 ASP cc_start: 0.8241 (m-30) cc_final: 0.8037 (m-30) REVERT: I 53 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8071 (mm-30) REVERT: I 59 ASN cc_start: 0.8583 (OUTLIER) cc_final: 0.8161 (t0) REVERT: J 15 LYS cc_start: 0.8697 (ttmm) cc_final: 0.8100 (tttt) REVERT: J 59 ASN cc_start: 0.8696 (OUTLIER) cc_final: 0.8387 (t0) REVERT: J 69 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8485 (tttm) REVERT: A 15 LYS cc_start: 0.8657 (ttmt) cc_final: 0.8444 (tppt) REVERT: A 37 LYS cc_start: 0.8474 (ttmt) cc_final: 0.7131 (tttp) REVERT: B 69 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8540 (tptm) REVERT: B 72 ASP cc_start: 0.8920 (m-30) cc_final: 0.8713 (m-30) REVERT: C 10 ASP cc_start: 0.9119 (m-30) cc_final: 0.8873 (m-30) REVERT: C 72 ASP cc_start: 0.8927 (m-30) cc_final: 0.8679 (m-30) REVERT: D 26 GLN cc_start: 0.8842 (mt0) cc_final: 0.8527 (mt0) REVERT: E 15 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.7846 (mppt) REVERT: E 22 ASN cc_start: 0.8131 (p0) cc_final: 0.7863 (p0) REVERT: E 59 ASN cc_start: 0.8520 (OUTLIER) cc_final: 0.8110 (t0) REVERT: E 72 ASP cc_start: 0.9073 (m-30) cc_final: 0.8843 (m-30) outliers start: 40 outliers final: 12 residues processed: 285 average time/residue: 0.4410 time to fit residues: 137.8267 Evaluate side-chains 273 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 247 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 57 TYR Chi-restraints excluded: chain P residue 59 ASN Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain K residue 59 ASN Chi-restraints excluded: chain K residue 69 LYS Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 69 LYS Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain O residue 59 ASN Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain J residue 32 ASP Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain E residue 15 LYS Chi-restraints excluded: chain E residue 59 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 14 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 77 GLN L 77 GLN G 77 GLN I 77 GLN J 77 GLN D 77 GLN E 77 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.107999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.092494 restraints weight = 15944.217| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.72 r_work: 0.2950 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 11178 Z= 0.166 Angle : 0.476 3.887 15210 Z= 0.259 Chirality : 0.036 0.108 1728 Planarity : 0.003 0.021 1998 Dihedral : 3.871 17.870 1512 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.19 % Allowed : 12.65 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.04 (0.21), residues: 1368 helix: 2.49 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.59 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 58 TYR 0.013 0.001 TYR H 57 PHE 0.007 0.001 PHE K 68 TRP 0.007 0.001 TRP F 5 Details of bonding type rmsd covalent geometry : bond 0.00365 (11178) covalent geometry : angle 0.47639 (15210) hydrogen bonds : bond 0.03968 ( 900) hydrogen bonds : angle 2.92088 ( 2700) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 256 time to evaluate : 0.402 Fit side-chains REVERT: P 57 TYR cc_start: 0.9208 (OUTLIER) cc_final: 0.8360 (t80) REVERT: Q 25 THR cc_start: 0.8601 (m) cc_final: 0.8359 (p) REVERT: Q 32 ASP cc_start: 0.8350 (m-30) cc_final: 0.7900 (m-30) REVERT: K 59 ASN cc_start: 0.8808 (OUTLIER) cc_final: 0.8535 (m-40) REVERT: K 69 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8100 (tptm) REVERT: L 24 GLN cc_start: 0.8200 (mp10) cc_final: 0.7268 (tp-100) REVERT: L 33 LYS cc_start: 0.8780 (mttt) cc_final: 0.8479 (mttm) REVERT: M 69 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8033 (tptm) REVERT: N 28 THR cc_start: 0.8956 (m) cc_final: 0.8474 (m) REVERT: N 32 ASP cc_start: 0.8329 (m-30) cc_final: 0.7598 (m-30) REVERT: N 59 ASN cc_start: 0.8755 (t0) cc_final: 0.8501 (t0) REVERT: N 69 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.7388 (tptm) REVERT: O 32 ASP cc_start: 0.8216 (m-30) cc_final: 0.7951 (m-30) REVERT: O 69 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8197 (tptm) REVERT: F 69 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8315 (tttm) REVERT: G 72 ASP cc_start: 0.8955 (m-30) cc_final: 0.8731 (m-30) REVERT: H 53 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8471 (mm-30) REVERT: I 15 LYS cc_start: 0.8439 (tttt) cc_final: 0.8129 (tttt) REVERT: I 59 ASN cc_start: 0.8609 (OUTLIER) cc_final: 0.8153 (t0) REVERT: I 77 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8497 (tt0) REVERT: J 59 ASN cc_start: 0.8718 (OUTLIER) cc_final: 0.8426 (t0) REVERT: J 69 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8653 (tttm) REVERT: A 37 LYS cc_start: 0.8506 (ttmt) cc_final: 0.7204 (tttp) REVERT: B 15 LYS cc_start: 0.8627 (tttt) cc_final: 0.8415 (tttt) REVERT: B 69 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8619 (tptm) REVERT: C 10 ASP cc_start: 0.9188 (m-30) cc_final: 0.8900 (m-30) REVERT: C 72 ASP cc_start: 0.8987 (m-30) cc_final: 0.8714 (m-30) REVERT: D 32 ASP cc_start: 0.8561 (m-30) cc_final: 0.8121 (m-30) REVERT: E 15 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.7826 (mppt) REVERT: E 59 ASN cc_start: 0.8563 (OUTLIER) cc_final: 0.8162 (t0) outliers start: 49 outliers final: 13 residues processed: 283 average time/residue: 0.4723 time to fit residues: 145.7805 Evaluate side-chains 270 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 243 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 57 TYR Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain K residue 59 ASN Chi-restraints excluded: chain K residue 69 LYS Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 69 LYS Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 69 LYS Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain O residue 59 ASN Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 77 GLN Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain E residue 15 LYS Chi-restraints excluded: chain E residue 59 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 117 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 77 GLN L 77 GLN G 77 GLN I 77 GLN J 77 GLN C 77 GLN D 77 GLN E 77 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.106670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.091049 restraints weight = 15939.618| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.73 r_work: 0.2925 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 11178 Z= 0.202 Angle : 0.504 4.226 15210 Z= 0.271 Chirality : 0.037 0.112 1728 Planarity : 0.003 0.021 1998 Dihedral : 3.883 17.302 1512 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.44 % Allowed : 12.39 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.36 (0.21), residues: 1368 helix: 2.71 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.56 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 58 TYR 0.016 0.001 TYR C 57 PHE 0.008 0.001 PHE K 68 TRP 0.006 0.001 TRP O 5 Details of bonding type rmsd covalent geometry : bond 0.00453 (11178) covalent geometry : angle 0.50365 (15210) hydrogen bonds : bond 0.04153 ( 900) hydrogen bonds : angle 2.98277 ( 2700) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 247 time to evaluate : 0.466 Fit side-chains REVERT: P 57 TYR cc_start: 0.9209 (OUTLIER) cc_final: 0.8273 (t80) REVERT: Q 25 THR cc_start: 0.8652 (m) cc_final: 0.8399 (p) REVERT: Q 32 ASP cc_start: 0.8415 (m-30) cc_final: 0.7939 (m-30) REVERT: K 59 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8448 (m-40) REVERT: K 69 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8132 (tptm) REVERT: L 24 GLN cc_start: 0.8167 (mp10) cc_final: 0.7298 (tp-100) REVERT: L 33 LYS cc_start: 0.8814 (mttt) cc_final: 0.8517 (mttm) REVERT: M 69 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8045 (tptm) REVERT: N 28 THR cc_start: 0.8958 (m) cc_final: 0.8372 (m) REVERT: N 29 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7980 (mt-10) REVERT: N 32 ASP cc_start: 0.8371 (m-30) cc_final: 0.7844 (m-30) REVERT: N 59 ASN cc_start: 0.8752 (t0) cc_final: 0.8512 (t0) REVERT: N 69 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.7422 (tptm) REVERT: O 32 ASP cc_start: 0.8222 (m-30) cc_final: 0.7702 (m-30) REVERT: O 69 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8224 (tptm) REVERT: F 69 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8303 (tttm) REVERT: G 32 ASP cc_start: 0.8237 (m-30) cc_final: 0.7911 (t70) REVERT: H 69 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8223 (tttm) REVERT: I 59 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.8188 (t0) REVERT: J 15 LYS cc_start: 0.8765 (ttmm) cc_final: 0.8085 (tttt) REVERT: J 59 ASN cc_start: 0.8708 (OUTLIER) cc_final: 0.8437 (t0) REVERT: J 69 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8662 (tttm) REVERT: A 32 ASP cc_start: 0.8110 (m-30) cc_final: 0.7580 (m-30) REVERT: A 37 LYS cc_start: 0.8637 (ttmt) cc_final: 0.7327 (tttp) REVERT: B 69 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8645 (tptm) REVERT: C 10 ASP cc_start: 0.9067 (m-30) cc_final: 0.8756 (m-30) REVERT: C 72 ASP cc_start: 0.9005 (m-30) cc_final: 0.8712 (m-30) REVERT: D 32 ASP cc_start: 0.8538 (m-30) cc_final: 0.8090 (m-30) REVERT: E 59 ASN cc_start: 0.8594 (OUTLIER) cc_final: 0.8211 (t0) outliers start: 52 outliers final: 18 residues processed: 277 average time/residue: 0.4808 time to fit residues: 145.2355 Evaluate side-chains 266 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 235 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 15 LYS Chi-restraints excluded: chain P residue 57 TYR Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain K residue 59 ASN Chi-restraints excluded: chain K residue 69 LYS Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 33 LYS Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 69 LYS Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 69 LYS Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain O residue 59 ASN Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain J residue 32 ASP Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain E residue 59 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 58 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 3 optimal weight: 0.0040 chunk 37 optimal weight: 1.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 77 GLN L 77 GLN G 77 GLN J 77 GLN A 77 GLN D 77 GLN E 77 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.110439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.094859 restraints weight = 15821.843| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.72 r_work: 0.2985 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 11178 Z= 0.100 Angle : 0.419 3.478 15210 Z= 0.228 Chirality : 0.033 0.098 1728 Planarity : 0.003 0.022 1998 Dihedral : 3.578 15.277 1512 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.93 % Allowed : 12.74 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 4.09 (0.22), residues: 1368 helix: 3.20 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.47 (0.52), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 80 TYR 0.013 0.001 TYR H 57 PHE 0.004 0.001 PHE O 68 TRP 0.007 0.001 TRP O 5 Details of bonding type rmsd covalent geometry : bond 0.00207 (11178) covalent geometry : angle 0.41900 (15210) hydrogen bonds : bond 0.03302 ( 900) hydrogen bonds : angle 2.73861 ( 2700) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 262 time to evaluate : 0.457 Fit side-chains REVERT: P 57 TYR cc_start: 0.9184 (OUTLIER) cc_final: 0.8455 (t80) REVERT: Q 25 THR cc_start: 0.8595 (m) cc_final: 0.8385 (p) REVERT: Q 32 ASP cc_start: 0.8332 (m-30) cc_final: 0.7835 (m-30) REVERT: K 59 ASN cc_start: 0.8754 (OUTLIER) cc_final: 0.8406 (t0) REVERT: K 69 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8025 (tptm) REVERT: L 33 LYS cc_start: 0.8795 (mttt) cc_final: 0.8512 (mttm) REVERT: M 69 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8004 (tptm) REVERT: N 28 THR cc_start: 0.8965 (m) cc_final: 0.8352 (m) REVERT: N 29 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7975 (mt-10) REVERT: N 32 ASP cc_start: 0.8336 (m-30) cc_final: 0.7868 (m-30) REVERT: N 59 ASN cc_start: 0.8687 (t0) cc_final: 0.8450 (t0) REVERT: N 69 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.7452 (tptm) REVERT: O 32 ASP cc_start: 0.8166 (m-30) cc_final: 0.7665 (m-30) REVERT: O 69 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8214 (tptm) REVERT: F 69 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.8272 (tttm) REVERT: H 69 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8181 (tttm) REVERT: I 59 ASN cc_start: 0.8560 (OUTLIER) cc_final: 0.8187 (t0) REVERT: I 72 ASP cc_start: 0.8324 (m-30) cc_final: 0.8007 (m-30) REVERT: J 15 LYS cc_start: 0.8704 (ttmm) cc_final: 0.8065 (tttt) REVERT: J 59 ASN cc_start: 0.8720 (OUTLIER) cc_final: 0.8440 (t0) REVERT: J 69 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8587 (tttm) REVERT: A 37 LYS cc_start: 0.8569 (ttmt) cc_final: 0.7243 (tttp) REVERT: B 15 LYS cc_start: 0.8551 (tttt) cc_final: 0.8342 (tttt) REVERT: B 69 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8481 (tptm) REVERT: C 10 ASP cc_start: 0.9042 (m-30) cc_final: 0.8721 (m-30) REVERT: C 72 ASP cc_start: 0.8951 (m-30) cc_final: 0.8718 (m-30) REVERT: E 59 ASN cc_start: 0.8510 (OUTLIER) cc_final: 0.8161 (t0) outliers start: 46 outliers final: 14 residues processed: 290 average time/residue: 0.4388 time to fit residues: 139.2887 Evaluate side-chains 274 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 247 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 15 LYS Chi-restraints excluded: chain P residue 57 TYR Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain K residue 59 ASN Chi-restraints excluded: chain K residue 69 LYS Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 69 LYS Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 69 LYS Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 21 ASP Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain J residue 32 ASP Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain E residue 59 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 80 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 109 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 77 GLN L 77 GLN G 77 GLN J 77 GLN D 77 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.109370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.093850 restraints weight = 15723.115| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.71 r_work: 0.2971 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 11178 Z= 0.123 Angle : 0.439 3.691 15210 Z= 0.239 Chirality : 0.034 0.102 1728 Planarity : 0.003 0.025 1998 Dihedral : 3.527 14.347 1512 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.76 % Allowed : 13.16 % Favored : 83.08 % 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: 4.23 (0.22), residues: 1368 helix: 3.31 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.55 (0.52), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 80 TYR 0.012 0.001 TYR Q 57 PHE 0.005 0.001 PHE K 68 TRP 0.006 0.001 TRP O 5 Details of bonding type rmsd covalent geometry : bond 0.00265 (11178) covalent geometry : angle 0.43920 (15210) hydrogen bonds : bond 0.03520 ( 900) hydrogen bonds : angle 2.77203 ( 2700) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 258 time to evaluate : 0.410 Fit side-chains REVERT: P 57 TYR cc_start: 0.9206 (OUTLIER) cc_final: 0.8371 (t80) REVERT: Q 25 THR cc_start: 0.8603 (m) cc_final: 0.8389 (p) REVERT: Q 32 ASP cc_start: 0.8333 (m-30) cc_final: 0.7884 (m-30) REVERT: K 59 ASN cc_start: 0.8754 (OUTLIER) cc_final: 0.8470 (m-40) REVERT: K 69 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8073 (tptm) REVERT: L 33 LYS cc_start: 0.8787 (mttt) cc_final: 0.8516 (mttm) REVERT: M 69 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.7986 (tptm) REVERT: N 28 THR cc_start: 0.8931 (m) cc_final: 0.8313 (m) REVERT: N 29 GLU cc_start: 0.8271 (mt-10) cc_final: 0.8037 (mt-10) REVERT: N 32 ASP cc_start: 0.8338 (m-30) cc_final: 0.7880 (m-30) REVERT: N 59 ASN cc_start: 0.8705 (t0) cc_final: 0.8460 (t0) REVERT: N 69 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.7914 (tptm) REVERT: O 32 ASP cc_start: 0.8149 (m-30) cc_final: 0.7648 (m-30) REVERT: O 69 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8277 (tptm) REVERT: F 69 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8227 (tttm) REVERT: H 69 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8180 (tttm) REVERT: I 15 LYS cc_start: 0.8435 (mttt) cc_final: 0.8205 (tttt) REVERT: I 59 ASN cc_start: 0.8576 (OUTLIER) cc_final: 0.8198 (t0) REVERT: I 72 ASP cc_start: 0.8334 (m-30) cc_final: 0.8030 (m-30) REVERT: J 15 LYS cc_start: 0.8756 (ttmm) cc_final: 0.8136 (tttt) REVERT: J 59 ASN cc_start: 0.8681 (OUTLIER) cc_final: 0.8409 (t0) REVERT: J 69 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8599 (tttm) REVERT: A 32 ASP cc_start: 0.8080 (m-30) cc_final: 0.7600 (m-30) REVERT: A 37 LYS cc_start: 0.8615 (ttmt) cc_final: 0.7278 (tttp) REVERT: B 15 LYS cc_start: 0.8608 (tttt) cc_final: 0.8373 (tttt) REVERT: B 69 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8522 (tptm) REVERT: C 10 ASP cc_start: 0.9100 (m-30) cc_final: 0.8754 (m-30) REVERT: C 72 ASP cc_start: 0.8996 (m-30) cc_final: 0.8769 (m-30) REVERT: D 32 ASP cc_start: 0.8580 (m-30) cc_final: 0.8098 (m-30) REVERT: E 59 ASN cc_start: 0.8517 (OUTLIER) cc_final: 0.8158 (t0) outliers start: 44 outliers final: 17 residues processed: 284 average time/residue: 0.4868 time to fit residues: 150.9433 Evaluate side-chains 277 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 247 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 15 LYS Chi-restraints excluded: chain P residue 57 TYR Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain Q residue 59 ASN Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain K residue 59 ASN Chi-restraints excluded: chain K residue 69 LYS Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 33 LYS Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 69 LYS Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 69 LYS Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 21 ASP Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain J residue 32 ASP Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain E residue 59 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 36 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 chunk 31 optimal weight: 0.4980 chunk 15 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 77 GLN L 77 GLN G 77 GLN J 77 GLN A 77 GLN D 77 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.109739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.094163 restraints weight = 15706.913| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.74 r_work: 0.2974 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 11178 Z= 0.115 Angle : 0.435 3.667 15210 Z= 0.236 Chirality : 0.033 0.101 1728 Planarity : 0.003 0.028 1998 Dihedral : 3.433 13.166 1512 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.08 % Allowed : 13.93 % Favored : 82.99 % 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: 4.41 (0.22), residues: 1368 helix: 3.43 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.56 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 80 TYR 0.013 0.001 TYR H 57 PHE 0.005 0.001 PHE K 68 TRP 0.005 0.001 TRP O 5 Details of bonding type rmsd covalent geometry : bond 0.00247 (11178) covalent geometry : angle 0.43527 (15210) hydrogen bonds : bond 0.03370 ( 900) hydrogen bonds : angle 2.74389 ( 2700) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 254 time to evaluate : 0.338 Fit side-chains REVERT: P 57 TYR cc_start: 0.9203 (OUTLIER) cc_final: 0.8462 (t80) REVERT: Q 25 THR cc_start: 0.8594 (m) cc_final: 0.8386 (p) REVERT: Q 32 ASP cc_start: 0.8353 (m-30) cc_final: 0.7857 (m-30) REVERT: K 59 ASN cc_start: 0.8756 (OUTLIER) cc_final: 0.8360 (t0) REVERT: K 69 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8046 (tptm) REVERT: L 33 LYS cc_start: 0.8790 (mttt) cc_final: 0.8514 (mttm) REVERT: M 69 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.7968 (tptm) REVERT: N 28 THR cc_start: 0.8964 (m) cc_final: 0.8313 (m) REVERT: N 29 GLU cc_start: 0.8267 (mt-10) cc_final: 0.8044 (mt-10) REVERT: N 32 ASP cc_start: 0.8389 (m-30) cc_final: 0.7878 (m-30) REVERT: N 59 ASN cc_start: 0.8706 (t0) cc_final: 0.8464 (t0) REVERT: N 69 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.7443 (tptm) REVERT: O 32 ASP cc_start: 0.8205 (m-30) cc_final: 0.7660 (m-30) REVERT: F 10 ASP cc_start: 0.9087 (m-30) cc_final: 0.8829 (m-30) REVERT: F 69 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.8264 (tttm) REVERT: H 69 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8167 (tttm) REVERT: I 59 ASN cc_start: 0.8570 (OUTLIER) cc_final: 0.8193 (t0) REVERT: I 72 ASP cc_start: 0.8334 (m-30) cc_final: 0.8024 (m-30) REVERT: J 15 LYS cc_start: 0.8745 (ttmm) cc_final: 0.8115 (tttt) REVERT: J 59 ASN cc_start: 0.8712 (OUTLIER) cc_final: 0.8427 (t0) REVERT: J 69 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8584 (tttm) REVERT: A 32 ASP cc_start: 0.8096 (m-30) cc_final: 0.7551 (m-30) REVERT: A 37 LYS cc_start: 0.8613 (ttmt) cc_final: 0.7273 (tttp) REVERT: B 15 LYS cc_start: 0.8576 (tttt) cc_final: 0.8321 (tttt) REVERT: B 69 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8517 (tptm) REVERT: C 10 ASP cc_start: 0.9098 (m-30) cc_final: 0.8744 (m-30) REVERT: C 72 ASP cc_start: 0.8991 (m-30) cc_final: 0.8763 (m-30) REVERT: E 22 ASN cc_start: 0.8068 (p0) cc_final: 0.7697 (p0) REVERT: E 53 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8130 (tp30) REVERT: E 59 ASN cc_start: 0.8530 (OUTLIER) cc_final: 0.8176 (t0) outliers start: 36 outliers final: 16 residues processed: 277 average time/residue: 0.4650 time to fit residues: 140.5444 Evaluate side-chains 274 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 246 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 15 LYS Chi-restraints excluded: chain P residue 57 TYR Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain Q residue 59 ASN Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain K residue 59 ASN Chi-restraints excluded: chain K residue 69 LYS Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 33 LYS Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 69 LYS Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 69 LYS Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain J residue 32 ASP Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain E residue 59 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 55 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 77 GLN L 77 GLN G 77 GLN J 77 GLN D 77 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.106176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.090495 restraints weight = 15810.803| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.72 r_work: 0.2916 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 11178 Z= 0.215 Angle : 0.521 4.742 15210 Z= 0.278 Chirality : 0.037 0.113 1728 Planarity : 0.003 0.024 1998 Dihedral : 3.688 14.718 1512 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.42 % Allowed : 14.19 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.02 (0.21), residues: 1368 helix: 3.18 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.65 (0.50), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 80 TYR 0.017 0.001 TYR C 57 PHE 0.010 0.001 PHE K 68 TRP 0.005 0.001 TRP O 5 Details of bonding type rmsd covalent geometry : bond 0.00485 (11178) covalent geometry : angle 0.52142 (15210) hydrogen bonds : bond 0.04144 ( 900) hydrogen bonds : angle 2.95292 ( 2700) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 252 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: P 57 TYR cc_start: 0.9227 (OUTLIER) cc_final: 0.8313 (t80) REVERT: Q 25 THR cc_start: 0.8692 (m) cc_final: 0.8428 (p) REVERT: Q 32 ASP cc_start: 0.8425 (m-30) cc_final: 0.7932 (m-30) REVERT: K 59 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8472 (m-40) REVERT: K 69 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8136 (tptm) REVERT: L 24 GLN cc_start: 0.8023 (mp10) cc_final: 0.7272 (tp-100) REVERT: L 33 LYS cc_start: 0.8893 (mttt) cc_final: 0.8644 (mttp) REVERT: M 69 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8086 (tptm) REVERT: N 32 ASP cc_start: 0.8359 (m-30) cc_final: 0.7865 (m-30) REVERT: N 59 ASN cc_start: 0.8705 (t0) cc_final: 0.8496 (t0) REVERT: N 69 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.7441 (tptm) REVERT: O 32 ASP cc_start: 0.8174 (m-30) cc_final: 0.7617 (m-30) REVERT: O 33 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8656 (mtpt) REVERT: F 69 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8405 (tttm) REVERT: G 32 ASP cc_start: 0.8311 (m-30) cc_final: 0.8019 (t70) REVERT: H 69 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8203 (tttm) REVERT: I 59 ASN cc_start: 0.8591 (OUTLIER) cc_final: 0.8148 (t0) REVERT: J 15 LYS cc_start: 0.8775 (ttmm) cc_final: 0.8139 (tttt) REVERT: J 59 ASN cc_start: 0.8716 (OUTLIER) cc_final: 0.8452 (t0) REVERT: J 69 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8676 (tttm) REVERT: A 37 LYS cc_start: 0.8688 (ttmt) cc_final: 0.7366 (tttp) REVERT: B 69 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8674 (tptm) REVERT: C 10 ASP cc_start: 0.9021 (m-30) cc_final: 0.8653 (m-30) REVERT: C 72 ASP cc_start: 0.9026 (m-30) cc_final: 0.8743 (m-30) REVERT: D 32 ASP cc_start: 0.8609 (m-30) cc_final: 0.8115 (m-30) REVERT: D 69 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8292 (tptm) REVERT: E 22 ASN cc_start: 0.8118 (p0) cc_final: 0.7713 (p0) REVERT: E 59 ASN cc_start: 0.8606 (OUTLIER) cc_final: 0.8226 (t0) outliers start: 40 outliers final: 17 residues processed: 279 average time/residue: 0.4884 time to fit residues: 148.6446 Evaluate side-chains 273 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 242 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 15 LYS Chi-restraints excluded: chain P residue 57 TYR Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain Q residue 59 ASN Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain K residue 59 ASN Chi-restraints excluded: chain K residue 69 LYS Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 33 LYS Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 69 LYS Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 69 LYS Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 33 LYS Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain J residue 32 ASP Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain E residue 59 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 9 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 77 GLN L 77 GLN G 77 GLN J 77 GLN A 77 GLN D 77 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.108637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.092991 restraints weight = 15658.808| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.72 r_work: 0.2955 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 11178 Z= 0.129 Angle : 0.461 3.903 15210 Z= 0.249 Chirality : 0.034 0.102 1728 Planarity : 0.003 0.030 1998 Dihedral : 3.511 13.397 1512 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.65 % Allowed : 15.73 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.35 (0.22), residues: 1368 helix: 3.39 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.57 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 80 TYR 0.014 0.001 TYR K 57 PHE 0.005 0.001 PHE P 68 TRP 0.008 0.001 TRP O 5 Details of bonding type rmsd covalent geometry : bond 0.00281 (11178) covalent geometry : angle 0.46053 (15210) hydrogen bonds : bond 0.03499 ( 900) hydrogen bonds : angle 2.79092 ( 2700) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 246 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: P 57 TYR cc_start: 0.9203 (OUTLIER) cc_final: 0.8462 (t80) REVERT: Q 25 THR cc_start: 0.8607 (m) cc_final: 0.8370 (p) REVERT: Q 32 ASP cc_start: 0.8349 (m-30) cc_final: 0.7886 (m-30) REVERT: K 59 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8395 (t0) REVERT: K 69 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8077 (tptm) REVERT: L 33 LYS cc_start: 0.8812 (mttt) cc_final: 0.8538 (mttm) REVERT: M 69 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8017 (tptm) REVERT: N 29 GLU cc_start: 0.8219 (mt-10) cc_final: 0.8005 (mt-10) REVERT: N 32 ASP cc_start: 0.8314 (m-30) cc_final: 0.7864 (m-30) REVERT: N 59 ASN cc_start: 0.8728 (t0) cc_final: 0.8481 (t0) REVERT: N 69 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.7459 (tptm) REVERT: O 32 ASP cc_start: 0.8088 (m-30) cc_final: 0.7653 (m-30) REVERT: O 69 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8234 (tptm) REVERT: F 69 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8332 (tttm) REVERT: H 69 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8186 (tttm) REVERT: I 59 ASN cc_start: 0.8570 (OUTLIER) cc_final: 0.8173 (t0) REVERT: I 72 ASP cc_start: 0.8351 (m-30) cc_final: 0.8041 (m-30) REVERT: J 15 LYS cc_start: 0.8770 (ttmm) cc_final: 0.8129 (tttt) REVERT: J 59 ASN cc_start: 0.8653 (OUTLIER) cc_final: 0.8408 (t0) REVERT: J 69 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8614 (tttm) REVERT: A 37 LYS cc_start: 0.8641 (ttmt) cc_final: 0.7319 (tttp) REVERT: B 69 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8491 (tptm) REVERT: C 10 ASP cc_start: 0.9029 (m-30) cc_final: 0.8683 (m-30) REVERT: C 15 LYS cc_start: 0.8927 (ttmm) cc_final: 0.8633 (mtmt) REVERT: C 72 ASP cc_start: 0.8990 (m-30) cc_final: 0.8734 (m-30) REVERT: D 32 ASP cc_start: 0.8574 (m-30) cc_final: 0.8072 (m-30) REVERT: E 22 ASN cc_start: 0.8108 (p0) cc_final: 0.7779 (p0) REVERT: E 53 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8188 (tp30) REVERT: E 59 ASN cc_start: 0.8534 (OUTLIER) cc_final: 0.8175 (t0) outliers start: 31 outliers final: 14 residues processed: 265 average time/residue: 0.4873 time to fit residues: 140.6263 Evaluate side-chains 269 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 242 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 15 LYS Chi-restraints excluded: chain P residue 57 TYR Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain K residue 59 ASN Chi-restraints excluded: chain K residue 69 LYS Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 33 LYS Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 69 LYS Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 69 LYS Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain J residue 32 ASP Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain E residue 59 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 75 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 63 optimal weight: 0.3980 chunk 34 optimal weight: 0.9990 chunk 91 optimal weight: 0.2980 chunk 87 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 77 GLN L 77 GLN G 77 GLN J 77 GLN A 77 GLN D 77 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.109972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.094404 restraints weight = 15743.426| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.71 r_work: 0.2981 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11178 Z= 0.107 Angle : 0.442 4.539 15210 Z= 0.240 Chirality : 0.033 0.099 1728 Planarity : 0.003 0.031 1998 Dihedral : 3.374 12.536 1512 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.48 % Allowed : 16.07 % Favored : 81.45 % 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: 4.55 (0.22), residues: 1368 helix: 3.54 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.64 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 80 TYR 0.014 0.001 TYR K 57 PHE 0.005 0.001 PHE O 68 TRP 0.009 0.001 TRP O 5 Details of bonding type rmsd covalent geometry : bond 0.00229 (11178) covalent geometry : angle 0.44178 (15210) hydrogen bonds : bond 0.03231 ( 900) hydrogen bonds : angle 2.71485 ( 2700) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3843.93 seconds wall clock time: 66 minutes 23.04 seconds (3983.04 seconds total)