Starting phenix.real_space_refine on Mon Jul 28 21:05:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ofg_20045/07_2025/6ofg_20045.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ofg_20045/07_2025/6ofg_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6ofg_20045/07_2025/6ofg_20045.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ofg_20045/07_2025/6ofg_20045.map" model { file = "/net/cci-nas-00/data/ceres_data/6ofg_20045/07_2025/6ofg_20045.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ofg_20045/07_2025/6ofg_20045.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10980 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" 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: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, R Time building chain proxies: 3.11, per 1000 atoms: 0.28 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: 2.76 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.03 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: 2.89 Time building geometry restraints manager: 3.24 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'R' } 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: 0.990 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 23.410 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.770 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.019 0.005 TRP N 5 PHE 0.012 0.002 PHE M 79 TYR 0.011 0.003 TYR Q 57 ARG 0.002 0.001 ARG F 58 Details of bonding type rmsd hydrogen bonds : bond 0.23865 ( 900) hydrogen bonds : angle 9.55916 ( 2700) covalent geometry : bond 0.00771 (11178) covalent geometry : angle 0.74966 (15210) *********************** 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 : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 33 LYS cc_start: 0.8552 (mttt) cc_final: 0.8324 (mttm) REVERT: N 28 THR cc_start: 0.8841 (m) cc_final: 0.8033 (m) REVERT: N 29 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7477 (mt-10) REVERT: N 32 ASP cc_start: 0.7471 (m-30) cc_final: 0.7138 (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: 0.7623 (tppt) REVERT: A 72 ASP cc_start: 0.8867 (m-30) cc_final: 0.8639 (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: 0.8613 (m-30) outliers start: 0 outliers final: 0 residues processed: 353 average time/residue: 1.0648 time to fit residues: 411.2528 Evaluate side-chains 242 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 38 optimal weight: 0.0050 chunk 60 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- 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 = 0.3407 r_free = 0.3407 target = 0.115228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.100725 restraints weight = 15328.153| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.62 r_work: 0.3020 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 11178 Z= 0.126 Angle : 0.484 3.541 15210 Z= 0.273 Chirality : 0.033 0.100 1728 Planarity : 0.005 0.027 1998 Dihedral : 4.246 21.101 1512 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.31 % Allowed : 14.96 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.18), residues: 1368 helix: -0.12 (0.11), residues: 1242 sheet: None (None), residues: 0 loop : -2.31 (0.48), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP N 5 PHE 0.005 0.001 PHE A 79 TYR 0.010 0.001 TYR E 57 ARG 0.001 0.000 ARG I 58 Details of bonding type rmsd hydrogen bonds : bond 0.04467 ( 900) hydrogen bonds : angle 3.30200 ( 2700) covalent geometry : bond 0.00255 (11178) covalent geometry : angle 0.48391 (15210) *********************** 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 295 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 268 time to evaluate : 1.820 Fit side-chains REVERT: P 59 ASN cc_start: 0.8639 (OUTLIER) cc_final: 0.8409 (t0) REVERT: Q 25 THR cc_start: 0.8650 (m) cc_final: 0.8335 (p) REVERT: Q 32 ASP cc_start: 0.8194 (m-30) cc_final: 0.7729 (m-30) REVERT: R 11 ASP cc_start: 0.8822 (m-30) cc_final: 0.8610 (m-30) REVERT: K 59 ASN cc_start: 0.8843 (OUTLIER) cc_final: 0.8553 (m-40) REVERT: K 69 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.7898 (tptm) REVERT: L 33 LYS cc_start: 0.8743 (mttt) cc_final: 0.8443 (mttm) REVERT: N 28 THR cc_start: 0.8945 (m) cc_final: 0.8121 (m) REVERT: N 29 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7773 (mt-10) REVERT: N 32 ASP cc_start: 0.8143 (m-30) cc_final: 0.7721 (m-30) REVERT: O 32 ASP cc_start: 0.8408 (m-30) cc_final: 0.8169 (m-30) REVERT: H 29 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7622 (pt0) REVERT: H 59 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.8498 (t0) REVERT: I 53 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8102 (mm-30) REVERT: I 59 ASN cc_start: 0.8622 (OUTLIER) cc_final: 0.8151 (t0) REVERT: J 59 ASN cc_start: 0.8701 (OUTLIER) cc_final: 0.8335 (t0) REVERT: A 37 LYS cc_start: 0.8443 (ttmt) cc_final: 0.7119 (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: 0.8664 (m-30) REVERT: D 49 SER cc_start: 0.8953 (p) cc_final: 0.8739 (m) REVERT: E 10 ASP cc_start: 0.8425 (m-30) cc_final: 0.8160 (m-30) REVERT: E 15 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8366 (mtpt) REVERT: E 22 ASN cc_start: 0.7775 (p0) cc_final: 0.7567 (p0) REVERT: E 72 ASP cc_start: 0.9110 (m-30) cc_final: 0.8862 (m-30) outliers start: 27 outliers final: 6 residues processed: 271 average time/residue: 1.5372 time to fit residues: 457.4366 Evaluate side-chains 244 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 231 time to evaluate : 4.226 ------------------------------------------------------------------------------- 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 E residue 15 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 5 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 D 77 GLN E 77 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.113814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.099180 restraints weight = 15575.339| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.60 r_work: 0.3043 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2731 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= 0.131 Angle : 0.454 3.446 15210 Z= 0.250 Chirality : 0.034 0.105 1728 Planarity : 0.004 0.024 1998 Dihedral : 3.882 18.736 1512 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.99 % Allowed : 14.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.21), residues: 1368 helix: 1.90 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.88 (0.49), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 5 PHE 0.005 0.001 PHE K 68 TYR 0.009 0.001 TYR E 57 ARG 0.001 0.000 ARG J 58 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 900) hydrogen bonds : angle 2.93975 ( 2700) covalent geometry : bond 0.00276 (11178) covalent geometry : angle 0.45391 (15210) *********************** 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 293 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 258 time to evaluate : 1.171 Fit side-chains REVERT: P 57 TYR cc_start: 0.9152 (OUTLIER) cc_final: 0.8564 (t80) REVERT: P 59 ASN cc_start: 0.8630 (OUTLIER) cc_final: 0.8420 (t0) REVERT: Q 25 THR cc_start: 0.8646 (m) cc_final: 0.8430 (p) REVERT: Q 32 ASP cc_start: 0.8294 (m-30) cc_final: 0.7839 (m-30) REVERT: R 11 ASP cc_start: 0.8761 (m-30) cc_final: 0.8553 (m-30) REVERT: K 59 ASN cc_start: 0.8771 (OUTLIER) cc_final: 0.8509 (m-40) REVERT: K 69 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8058 (tptm) REVERT: L 33 LYS cc_start: 0.8826 (mttt) cc_final: 0.8538 (mttm) REVERT: N 28 THR cc_start: 0.8955 (m) cc_final: 0.8295 (m) REVERT: N 29 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7852 (mt-10) REVERT: N 32 ASP cc_start: 0.8145 (m-30) cc_final: 0.7683 (m-30) REVERT: N 59 ASN cc_start: 0.8677 (t0) cc_final: 0.8394 (t0) REVERT: G 33 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8545 (mtmt) REVERT: G 72 ASP cc_start: 0.8928 (m-30) cc_final: 0.8722 (m-30) REVERT: I 59 ASN cc_start: 0.8562 (OUTLIER) cc_final: 0.8177 (t0) REVERT: J 59 ASN cc_start: 0.8672 (OUTLIER) cc_final: 0.8392 (t0) REVERT: J 69 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8548 (tttm) REVERT: A 37 LYS cc_start: 0.8527 (ttmt) cc_final: 0.7235 (tttp) REVERT: B 69 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8586 (tptm) REVERT: C 10 ASP cc_start: 0.9190 (m-30) cc_final: 0.8903 (m-30) REVERT: C 72 ASP cc_start: 0.8905 (m-30) cc_final: 0.8646 (m-30) REVERT: E 15 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.7875 (mppt) REVERT: E 59 ASN cc_start: 0.8593 (OUTLIER) cc_final: 0.8199 (t0) REVERT: E 72 ASP cc_start: 0.9037 (m-30) cc_final: 0.8789 (m-30) outliers start: 35 outliers final: 13 residues processed: 272 average time/residue: 0.9421 time to fit residues: 281.6618 Evaluate side-chains 265 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 241 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 57 TYR 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 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 N residue 62 SER 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 F residue 59 ASN 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 E residue 15 LYS Chi-restraints excluded: chain E residue 57 TYR 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 2 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 63 optimal weight: 0.0370 chunk 35 optimal weight: 5.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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 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 = 0.114534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.099960 restraints weight = 15386.857| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.59 r_work: 0.3020 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 11178 Z= 0.105 Angle : 0.418 3.314 15210 Z= 0.229 Chirality : 0.033 0.100 1728 Planarity : 0.003 0.021 1998 Dihedral : 3.677 16.835 1512 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.68 % Allowed : 13.08 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.35 (0.21), residues: 1368 helix: 2.70 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.57 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP O 5 PHE 0.004 0.001 PHE K 68 TYR 0.013 0.001 TYR H 57 ARG 0.001 0.000 ARG E 58 Details of bonding type rmsd hydrogen bonds : bond 0.03426 ( 900) hydrogen bonds : angle 2.75588 ( 2700) covalent geometry : bond 0.00218 (11178) covalent geometry : angle 0.41778 (15210) *********************** 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 304 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 261 time to evaluate : 1.239 Fit side-chains REVERT: P 57 TYR cc_start: 0.9162 (OUTLIER) cc_final: 0.8569 (t80) REVERT: P 59 ASN cc_start: 0.8599 (OUTLIER) cc_final: 0.8397 (t0) REVERT: Q 25 THR cc_start: 0.8577 (m) cc_final: 0.8364 (p) REVERT: Q 32 ASP cc_start: 0.8275 (m-30) cc_final: 0.7807 (m-30) REVERT: R 11 ASP cc_start: 0.8771 (m-30) cc_final: 0.8522 (m-30) REVERT: K 59 ASN cc_start: 0.8780 (OUTLIER) cc_final: 0.8355 (t0) REVERT: K 69 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.7945 (tptm) REVERT: L 33 LYS cc_start: 0.8760 (mttt) cc_final: 0.8449 (mttm) REVERT: M 69 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8024 (tptm) REVERT: N 28 THR cc_start: 0.8968 (m) cc_final: 0.8424 (m) REVERT: N 32 ASP cc_start: 0.8316 (m-30) cc_final: 0.7628 (m-30) REVERT: N 59 ASN cc_start: 0.8696 (t0) cc_final: 0.8426 (t0) REVERT: N 69 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.7370 (tptm) REVERT: O 32 ASP cc_start: 0.8048 (m-30) cc_final: 0.7787 (m-30) REVERT: F 69 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8255 (tttm) REVERT: H 53 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8427 (mm-30) REVERT: I 15 LYS cc_start: 0.8444 (mttt) cc_final: 0.8090 (tttt) REVERT: I 59 ASN cc_start: 0.8561 (OUTLIER) cc_final: 0.8146 (t0) REVERT: I 77 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8330 (tt0) REVERT: J 15 LYS cc_start: 0.8679 (ttmm) cc_final: 0.8113 (tttt) REVERT: J 59 ASN cc_start: 0.8673 (OUTLIER) cc_final: 0.8398 (t0) REVERT: J 69 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8288 (tptm) REVERT: A 37 LYS cc_start: 0.8492 (ttmt) cc_final: 0.7179 (tttp) REVERT: B 69 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8468 (tptm) REVERT: C 10 ASP cc_start: 0.9138 (m-30) cc_final: 0.8860 (m-30) REVERT: C 72 ASP cc_start: 0.8931 (m-30) cc_final: 0.8713 (m-30) REVERT: E 15 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.7765 (mppt) REVERT: E 59 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.8092 (t0) outliers start: 43 outliers final: 11 residues processed: 287 average time/residue: 0.9452 time to fit residues: 297.9975 Evaluate side-chains 269 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 244 time to evaluate : 1.239 ------------------------------------------------------------------------------- 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 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 57 TYR 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 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 15 LYS Chi-restraints excluded: chain E residue 57 TYR 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 63 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 73 optimal weight: 0.0070 chunk 67 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- 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 = 0.3384 r_free = 0.3384 target = 0.113470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.098860 restraints weight = 15400.826| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.59 r_work: 0.3008 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3100 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= 0.111 Angle : 0.420 3.387 15210 Z= 0.230 Chirality : 0.033 0.101 1728 Planarity : 0.003 0.021 1998 Dihedral : 3.544 15.747 1512 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.02 % Allowed : 12.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.92 (0.22), residues: 1368 helix: 3.10 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.54 (0.52), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP O 5 PHE 0.004 0.001 PHE K 68 TYR 0.010 0.001 TYR J 57 ARG 0.001 0.000 ARG J 58 Details of bonding type rmsd hydrogen bonds : bond 0.03412 ( 900) hydrogen bonds : angle 2.72524 ( 2700) covalent geometry : bond 0.00234 (11178) covalent geometry : angle 0.42032 (15210) *********************** 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 301 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 254 time to evaluate : 1.286 Fit side-chains REVERT: P 57 TYR cc_start: 0.9169 (OUTLIER) cc_final: 0.8488 (t80) REVERT: Q 32 ASP cc_start: 0.8326 (m-30) cc_final: 0.7839 (m-30) REVERT: R 11 ASP cc_start: 0.8779 (m-30) cc_final: 0.8545 (m-30) REVERT: K 59 ASN cc_start: 0.8775 (OUTLIER) cc_final: 0.8358 (t0) REVERT: K 69 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8019 (tptm) REVERT: L 33 LYS cc_start: 0.8764 (mttt) cc_final: 0.8460 (mttm) REVERT: M 69 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8065 (tptm) REVERT: N 28 THR cc_start: 0.8931 (m) cc_final: 0.8291 (m) REVERT: N 29 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7840 (mt-10) REVERT: N 32 ASP cc_start: 0.8316 (m-30) cc_final: 0.7861 (m-30) REVERT: N 59 ASN cc_start: 0.8686 (t0) cc_final: 0.8434 (t0) REVERT: N 69 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.7387 (tptm) REVERT: O 32 ASP cc_start: 0.8113 (m-30) cc_final: 0.7883 (m-30) REVERT: O 69 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8230 (tptm) REVERT: F 69 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8240 (tttm) REVERT: H 59 ASN cc_start: 0.8704 (m-40) cc_final: 0.8499 (t0) REVERT: H 69 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8159 (tttm) REVERT: I 59 ASN cc_start: 0.8579 (OUTLIER) cc_final: 0.8173 (t0) REVERT: I 72 ASP cc_start: 0.8289 (m-30) cc_final: 0.7984 (m-30) REVERT: J 15 LYS cc_start: 0.8707 (ttmm) cc_final: 0.8116 (tttt) REVERT: J 59 ASN cc_start: 0.8683 (OUTLIER) cc_final: 0.8396 (t0) REVERT: J 69 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8580 (tttm) REVERT: A 32 ASP cc_start: 0.8058 (m-30) cc_final: 0.7573 (m-30) REVERT: A 37 LYS cc_start: 0.8495 (ttmt) cc_final: 0.7207 (tttp) REVERT: B 69 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8473 (tptm) REVERT: C 10 ASP cc_start: 0.9139 (m-30) cc_final: 0.8830 (m-30) REVERT: C 72 ASP cc_start: 0.8965 (m-30) cc_final: 0.8725 (m-30) REVERT: E 15 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.7855 (mppt) REVERT: E 59 ASN cc_start: 0.8493 (OUTLIER) cc_final: 0.8115 (t0) outliers start: 47 outliers final: 16 residues processed: 283 average time/residue: 1.0838 time to fit residues: 335.8901 Evaluate side-chains 275 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 245 time to evaluate : 1.275 ------------------------------------------------------------------------------- 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 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 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 59 ASN Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain B residue 57 TYR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 24 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 38 optimal weight: 0.0270 chunk 102 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 D 77 GLN E 77 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.114596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.099932 restraints weight = 15529.813| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.60 r_work: 0.3020 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 11178 Z= 0.100 Angle : 0.408 3.308 15210 Z= 0.223 Chirality : 0.033 0.099 1728 Planarity : 0.003 0.020 1998 Dihedral : 3.440 14.542 1512 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.50 % Allowed : 13.76 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.33 (0.22), residues: 1368 helix: 3.37 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.52 (0.52), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP O 5 PHE 0.005 0.001 PHE K 68 TYR 0.012 0.001 TYR H 57 ARG 0.001 0.000 ARG G 58 Details of bonding type rmsd hydrogen bonds : bond 0.03207 ( 900) hydrogen bonds : angle 2.67656 ( 2700) covalent geometry : bond 0.00207 (11178) covalent geometry : angle 0.40831 (15210) *********************** 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 294 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 253 time to evaluate : 1.163 Fit side-chains revert: symmetry clash REVERT: P 53 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8151 (mm-30) REVERT: P 57 TYR cc_start: 0.9166 (OUTLIER) cc_final: 0.8573 (t80) REVERT: Q 32 ASP cc_start: 0.8323 (m-30) cc_final: 0.7807 (m-30) REVERT: R 11 ASP cc_start: 0.8806 (m-30) cc_final: 0.8543 (m-30) REVERT: K 59 ASN cc_start: 0.8757 (OUTLIER) cc_final: 0.8356 (t0) REVERT: K 69 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.7950 (tptm) REVERT: L 15 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8202 (tttt) REVERT: L 33 LYS cc_start: 0.8723 (mttt) cc_final: 0.8466 (mttm) REVERT: M 69 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.7944 (tptm) REVERT: N 28 THR cc_start: 0.8919 (m) cc_final: 0.8358 (m) REVERT: N 29 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7866 (mt-10) REVERT: N 32 ASP cc_start: 0.8350 (m-30) cc_final: 0.7864 (m-30) REVERT: N 59 ASN cc_start: 0.8682 (t0) cc_final: 0.8430 (t0) REVERT: N 69 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.7352 (tptm) REVERT: O 32 ASP cc_start: 0.8108 (m-30) cc_final: 0.7829 (m-30) REVERT: F 10 ASP cc_start: 0.9101 (m-30) cc_final: 0.8843 (m-30) REVERT: F 69 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8187 (tttm) REVERT: G 33 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8540 (mtmt) REVERT: H 69 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8123 (tttm) REVERT: I 59 ASN cc_start: 0.8594 (OUTLIER) cc_final: 0.8187 (t0) REVERT: I 72 ASP cc_start: 0.8275 (m-30) cc_final: 0.7973 (m-30) REVERT: J 15 LYS cc_start: 0.8680 (ttmm) cc_final: 0.8103 (tttt) REVERT: J 59 ASN cc_start: 0.8682 (OUTLIER) cc_final: 0.8367 (t0) REVERT: J 69 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8313 (tptm) REVERT: A 37 LYS cc_start: 0.8480 (ttmt) cc_final: 0.7165 (tttp) REVERT: B 69 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8472 (tptm) REVERT: C 10 ASP cc_start: 0.9058 (m-30) cc_final: 0.8775 (m-30) REVERT: C 72 ASP cc_start: 0.8961 (m-30) cc_final: 0.8727 (m-30) REVERT: E 15 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.7796 (mppt) REVERT: E 59 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.8109 (t0) outliers start: 41 outliers final: 12 residues processed: 282 average time/residue: 0.9822 time to fit residues: 303.9396 Evaluate side-chains 271 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 244 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 13 SER 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 57 TYR Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain I residue 59 ASN 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 15 LYS Chi-restraints excluded: chain E residue 57 TYR 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 1 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 94 optimal weight: 0.0270 chunk 87 optimal weight: 0.6980 chunk 123 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 38 optimal weight: 0.4980 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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 = 0.3394 r_free = 0.3394 target = 0.114484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.099699 restraints weight = 15671.142| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.61 r_work: 0.3027 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 11178 Z= 0.094 Angle : 0.404 3.286 15210 Z= 0.221 Chirality : 0.032 0.098 1728 Planarity : 0.003 0.022 1998 Dihedral : 3.331 13.469 1512 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.25 % Allowed : 13.85 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.58 (0.22), residues: 1368 helix: 3.56 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.62 (0.52), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 5 PHE 0.004 0.001 PHE O 68 TYR 0.010 0.001 TYR J 57 ARG 0.006 0.000 ARG H 80 Details of bonding type rmsd hydrogen bonds : bond 0.03115 ( 900) hydrogen bonds : angle 2.64243 ( 2700) covalent geometry : bond 0.00192 (11178) covalent geometry : angle 0.40420 (15210) *********************** 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 295 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 257 time to evaluate : 1.348 Fit side-chains REVERT: P 15 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8394 (mmtm) REVERT: P 53 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8190 (mm-30) REVERT: P 57 TYR cc_start: 0.9162 (OUTLIER) cc_final: 0.8585 (t80) REVERT: Q 32 ASP cc_start: 0.8337 (m-30) cc_final: 0.7838 (m-30) REVERT: R 11 ASP cc_start: 0.8814 (m-30) cc_final: 0.8539 (m-30) REVERT: K 59 ASN cc_start: 0.8764 (OUTLIER) cc_final: 0.8394 (t0) REVERT: K 69 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.7975 (tptm) REVERT: L 15 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8236 (mttt) REVERT: L 33 LYS cc_start: 0.8738 (mttt) cc_final: 0.8486 (mttm) REVERT: M 69 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.7968 (tptm) REVERT: N 28 THR cc_start: 0.8941 (m) cc_final: 0.8189 (m) REVERT: N 29 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7878 (mt-10) REVERT: N 32 ASP cc_start: 0.8417 (m-30) cc_final: 0.7853 (m-30) REVERT: N 59 ASN cc_start: 0.8687 (t0) cc_final: 0.8431 (t0) REVERT: N 69 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.7354 (tptm) REVERT: O 32 ASP cc_start: 0.8104 (m-30) cc_final: 0.7778 (m-30) REVERT: O 69 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8262 (tptm) REVERT: F 10 ASP cc_start: 0.9066 (m-30) cc_final: 0.8832 (m-30) REVERT: F 69 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8146 (tttm) REVERT: H 69 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8118 (tttm) REVERT: I 15 LYS cc_start: 0.8714 (tppt) cc_final: 0.8266 (mttt) REVERT: I 59 ASN cc_start: 0.8591 (OUTLIER) cc_final: 0.8216 (t0) REVERT: I 72 ASP cc_start: 0.8294 (m-30) cc_final: 0.7980 (m-30) REVERT: J 15 LYS cc_start: 0.8705 (ttmm) cc_final: 0.8108 (tttt) REVERT: J 59 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.8372 (t0) REVERT: J 69 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8319 (tptm) REVERT: A 32 ASP cc_start: 0.8013 (m-30) cc_final: 0.7552 (m-30) REVERT: A 37 LYS cc_start: 0.8499 (ttmt) cc_final: 0.7199 (tttp) REVERT: B 69 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8450 (tptm) REVERT: C 10 ASP cc_start: 0.9066 (m-30) cc_final: 0.8769 (m-30) REVERT: C 72 ASP cc_start: 0.8945 (m-30) cc_final: 0.8722 (m-30) REVERT: E 15 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.7822 (mppt) REVERT: E 59 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.8137 (t0) outliers start: 38 outliers final: 14 residues processed: 284 average time/residue: 1.0172 time to fit residues: 316.1261 Evaluate side-chains 272 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 242 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 13 SER 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 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 A residue 25 THR Chi-restraints excluded: chain B residue 57 TYR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 35 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 59 optimal weight: 0.0170 chunk 9 optimal weight: 4.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- 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 E 77 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.111117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.095692 restraints weight = 15692.373| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.70 r_work: 0.3001 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3372 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= 0.106 Angle : 0.419 3.745 15210 Z= 0.228 Chirality : 0.033 0.100 1728 Planarity : 0.003 0.026 1998 Dihedral : 3.312 12.899 1512 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.85 % Allowed : 13.59 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.67 (0.22), residues: 1368 helix: 3.62 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.64 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 5 PHE 0.004 0.001 PHE E 68 TYR 0.012 0.001 TYR H 57 ARG 0.007 0.000 ARG H 80 Details of bonding type rmsd hydrogen bonds : bond 0.03187 ( 900) hydrogen bonds : angle 2.66357 ( 2700) covalent geometry : bond 0.00224 (11178) covalent geometry : angle 0.41932 (15210) *********************** 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 297 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 252 time to evaluate : 1.171 Fit side-chains revert: symmetry clash REVERT: P 15 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8416 (mmtm) REVERT: P 57 TYR cc_start: 0.9178 (OUTLIER) cc_final: 0.8502 (t80) REVERT: Q 32 ASP cc_start: 0.8371 (m-30) cc_final: 0.7862 (m-30) REVERT: R 11 ASP cc_start: 0.8828 (m-30) cc_final: 0.8559 (m-30) REVERT: K 59 ASN cc_start: 0.8775 (OUTLIER) cc_final: 0.8391 (t0) REVERT: K 69 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.7996 (tptm) REVERT: L 15 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8208 (tttt) REVERT: L 33 LYS cc_start: 0.8759 (mttt) cc_final: 0.8505 (mttm) REVERT: M 69 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.7950 (tptm) REVERT: N 28 THR cc_start: 0.8961 (m) cc_final: 0.8207 (m) REVERT: N 29 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7931 (mt-10) REVERT: N 32 ASP cc_start: 0.8432 (m-30) cc_final: 0.7922 (m-30) REVERT: N 59 ASN cc_start: 0.8709 (t0) cc_final: 0.8453 (t0) REVERT: N 69 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.7382 (tptm) REVERT: O 32 ASP cc_start: 0.8093 (m-30) cc_final: 0.7723 (m-30) REVERT: O 69 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8277 (tptm) REVERT: F 10 ASP cc_start: 0.9083 (m-30) cc_final: 0.8851 (m-30) REVERT: F 69 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8222 (tttm) REVERT: H 69 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8136 (tttm) REVERT: I 15 LYS cc_start: 0.8732 (tppt) cc_final: 0.8074 (tttt) REVERT: I 59 ASN cc_start: 0.8598 (OUTLIER) cc_final: 0.8224 (t0) REVERT: I 72 ASP cc_start: 0.8324 (m-30) cc_final: 0.8014 (m-30) REVERT: J 10 ASP cc_start: 0.8888 (m-30) cc_final: 0.8667 (m-30) REVERT: J 15 LYS cc_start: 0.8717 (ttmm) cc_final: 0.8122 (tttt) REVERT: J 59 ASN cc_start: 0.8690 (OUTLIER) cc_final: 0.8402 (t0) REVERT: J 69 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8328 (tptm) REVERT: A 32 ASP cc_start: 0.8071 (m-30) cc_final: 0.7612 (m-30) REVERT: A 37 LYS cc_start: 0.8493 (ttmt) cc_final: 0.7191 (tttp) REVERT: B 69 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8497 (tptm) REVERT: C 10 ASP cc_start: 0.9078 (m-30) cc_final: 0.8770 (m-30) REVERT: C 15 LYS cc_start: 0.8905 (ttmm) cc_final: 0.8646 (mtmt) REVERT: C 72 ASP cc_start: 0.8971 (m-30) cc_final: 0.8755 (m-30) REVERT: E 15 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.7794 (mppt) REVERT: E 53 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8172 (tp30) REVERT: E 59 ASN cc_start: 0.8488 (OUTLIER) cc_final: 0.8146 (t0) outliers start: 45 outliers final: 18 residues processed: 282 average time/residue: 1.0338 time to fit residues: 321.1990 Evaluate side-chains 278 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 244 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 13 SER 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 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 13 SER 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 G residue 15 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 A residue 25 THR Chi-restraints excluded: chain B residue 57 TYR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 121 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 63 optimal weight: 0.0570 chunk 46 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- 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 D 77 GLN E 77 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.110890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.095298 restraints weight = 15890.728| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.72 r_work: 0.2993 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 11178 Z= 0.109 Angle : 0.429 4.630 15210 Z= 0.233 Chirality : 0.033 0.108 1728 Planarity : 0.003 0.028 1998 Dihedral : 3.316 12.648 1512 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.69 (0.22), residues: 1368 helix: 3.64 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.69 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP O 5 PHE 0.004 0.001 PHE E 68 TYR 0.010 0.001 TYR J 57 ARG 0.007 0.000 ARG H 80 Details of bonding type rmsd hydrogen bonds : bond 0.03221 ( 900) hydrogen bonds : angle 2.67527 ( 2700) covalent geometry : bond 0.00231 (11178) covalent geometry : angle 0.42925 (15210) *********************** 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 290 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 250 time to evaluate : 1.362 Fit side-chains REVERT: P 15 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8414 (mmtm) REVERT: P 57 TYR cc_start: 0.9187 (OUTLIER) cc_final: 0.8600 (t80) REVERT: Q 32 ASP cc_start: 0.8365 (m-30) cc_final: 0.7882 (m-30) REVERT: R 11 ASP cc_start: 0.8830 (m-30) cc_final: 0.8549 (m-30) REVERT: K 59 ASN cc_start: 0.8788 (OUTLIER) cc_final: 0.8402 (t0) REVERT: K 69 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.7984 (tptm) REVERT: L 15 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8194 (tttt) REVERT: L 33 LYS cc_start: 0.8754 (mttt) cc_final: 0.8501 (mttm) REVERT: M 69 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8025 (tptm) REVERT: N 28 THR cc_start: 0.8970 (m) cc_final: 0.8304 (m) REVERT: N 32 ASP cc_start: 0.8479 (m-30) cc_final: 0.8064 (m-30) REVERT: N 59 ASN cc_start: 0.8734 (t0) cc_final: 0.8478 (t0) REVERT: N 69 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.7345 (tptm) REVERT: O 32 ASP cc_start: 0.8109 (m-30) cc_final: 0.7735 (m-30) REVERT: O 69 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8256 (tptm) REVERT: F 10 ASP cc_start: 0.9091 (m-30) cc_final: 0.8854 (m-30) REVERT: F 69 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8270 (tttm) REVERT: G 33 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8561 (mtmt) REVERT: H 69 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8120 (tttm) REVERT: I 59 ASN cc_start: 0.8612 (OUTLIER) cc_final: 0.8241 (t0) REVERT: I 72 ASP cc_start: 0.8330 (m-30) cc_final: 0.8015 (m-30) REVERT: J 15 LYS cc_start: 0.8726 (ttmm) cc_final: 0.8137 (tttt) REVERT: J 59 ASN cc_start: 0.8707 (OUTLIER) cc_final: 0.8408 (t0) REVERT: J 69 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8340 (tptm) REVERT: A 32 ASP cc_start: 0.8092 (m-30) cc_final: 0.7598 (m-30) REVERT: A 37 LYS cc_start: 0.8482 (ttmt) cc_final: 0.7183 (tttp) REVERT: B 69 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8489 (tptm) REVERT: C 10 ASP cc_start: 0.9058 (m-30) cc_final: 0.8746 (m-30) REVERT: C 15 LYS cc_start: 0.8880 (ttmm) cc_final: 0.8619 (mtmt) REVERT: C 72 ASP cc_start: 0.8978 (m-30) cc_final: 0.8761 (m-30) REVERT: E 22 ASN cc_start: 0.8043 (p0) cc_final: 0.7624 (p0) REVERT: E 53 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8193 (tp30) REVERT: E 59 ASN cc_start: 0.8521 (OUTLIER) cc_final: 0.8143 (t0) outliers start: 40 outliers final: 15 residues processed: 277 average time/residue: 1.0146 time to fit residues: 307.3684 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 : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 13 SER 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 13 SER 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 G residue 33 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 16 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 125 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 A 77 GLN D 77 GLN E 77 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.113922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.099113 restraints weight = 15555.555| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.62 r_work: 0.3000 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11178 Z= 0.114 Angle : 0.437 4.132 15210 Z= 0.237 Chirality : 0.033 0.102 1728 Planarity : 0.003 0.028 1998 Dihedral : 3.323 12.942 1512 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.91 % Allowed : 15.30 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.70 (0.22), residues: 1368 helix: 3.65 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.71 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 5 PHE 0.005 0.001 PHE K 68 TYR 0.013 0.001 TYR J 57 ARG 0.007 0.000 ARG H 80 Details of bonding type rmsd hydrogen bonds : bond 0.03259 ( 900) hydrogen bonds : angle 2.68829 ( 2700) covalent geometry : bond 0.00246 (11178) covalent geometry : angle 0.43733 (15210) ********************** 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 286 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 252 time to evaluate : 1.152 Fit side-chains revert: symmetry clash REVERT: P 57 TYR cc_start: 0.9190 (OUTLIER) cc_final: 0.8425 (t80) REVERT: Q 15 LYS cc_start: 0.8440 (tmtt) cc_final: 0.8239 (mtpp) REVERT: Q 32 ASP cc_start: 0.8346 (m-30) cc_final: 0.7861 (m-30) REVERT: R 11 ASP cc_start: 0.8817 (m-30) cc_final: 0.8523 (m-30) REVERT: K 59 ASN cc_start: 0.8758 (OUTLIER) cc_final: 0.8351 (t0) REVERT: K 69 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8012 (tptm) REVERT: L 33 LYS cc_start: 0.8747 (mttt) cc_final: 0.8490 (mttm) REVERT: M 69 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8003 (tptm) REVERT: N 28 THR cc_start: 0.8971 (m) cc_final: 0.8298 (m) REVERT: N 29 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7872 (mt-10) REVERT: N 32 ASP cc_start: 0.8434 (m-30) cc_final: 0.7999 (m-30) REVERT: N 59 ASN cc_start: 0.8687 (t0) cc_final: 0.8431 (t0) REVERT: N 69 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.7404 (tptm) REVERT: O 32 ASP cc_start: 0.8110 (m-30) cc_final: 0.7751 (m-30) REVERT: O 69 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8251 (tptm) REVERT: F 69 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8251 (tttm) REVERT: G 33 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8573 (mtmt) REVERT: H 69 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8114 (tttm) REVERT: I 59 ASN cc_start: 0.8582 (OUTLIER) cc_final: 0.8212 (t0) REVERT: I 72 ASP cc_start: 0.8303 (m-30) cc_final: 0.7979 (m-30) REVERT: J 15 LYS cc_start: 0.8722 (ttmm) cc_final: 0.8117 (tttt) REVERT: J 59 ASN cc_start: 0.8687 (OUTLIER) cc_final: 0.8388 (t0) REVERT: J 69 LYS cc_start: 0.9177 (OUTLIER) cc_final: 0.8320 (tptm) REVERT: A 37 LYS cc_start: 0.8488 (ttmt) cc_final: 0.7178 (tttp) REVERT: B 69 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8470 (tptm) REVERT: C 10 ASP cc_start: 0.9059 (m-30) cc_final: 0.8737 (m-30) REVERT: C 15 LYS cc_start: 0.8856 (ttmm) cc_final: 0.8610 (mtmt) REVERT: C 72 ASP cc_start: 0.8955 (m-30) cc_final: 0.8724 (m-30) REVERT: E 10 ASP cc_start: 0.8545 (m-30) cc_final: 0.8344 (m-30) REVERT: E 59 ASN cc_start: 0.8508 (OUTLIER) cc_final: 0.8160 (t0) outliers start: 34 outliers final: 16 residues processed: 275 average time/residue: 0.9924 time to fit residues: 298.7496 Evaluate side-chains 274 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 244 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 13 SER 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 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 13 SER 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 G residue 33 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 116 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 77 optimal weight: 0.4980 chunk 103 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 D 77 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.111348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.095752 restraints weight = 15796.153| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.72 r_work: 0.3005 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11178 Z= 0.106 Angle : 0.434 4.447 15210 Z= 0.236 Chirality : 0.033 0.114 1728 Planarity : 0.003 0.028 1998 Dihedral : 3.292 12.732 1512 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.91 % Allowed : 15.30 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.77 (0.22), residues: 1368 helix: 3.69 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.70 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 5 PHE 0.004 0.001 PHE K 68 TYR 0.013 0.001 TYR H 57 ARG 0.007 0.000 ARG H 80 Details of bonding type rmsd hydrogen bonds : bond 0.03171 ( 900) hydrogen bonds : angle 2.65873 ( 2700) covalent geometry : bond 0.00226 (11178) covalent geometry : angle 0.43351 (15210) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8737.04 seconds wall clock time: 159 minutes 38.70 seconds (9578.70 seconds total)