Starting phenix.real_space_refine on Wed Sep 25 16:37:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6off_20044/09_2024/6off_20044_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6off_20044/09_2024/6off_20044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6off_20044/09_2024/6off_20044.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6off_20044/09_2024/6off_20044.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6off_20044/09_2024/6off_20044_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6off_20044/09_2024/6off_20044_neut.cif" } resolution = 3.2 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 6966 2.51 5 N 1818 2.21 5 O 2232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11016 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 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: 3.06, per 1000 atoms: 0.28 Number of scatterers: 11016 At special positions: 0 Unit cell: (90.915, 90.915, 145.255, 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 6966 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: 2.61 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: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 7 through 20 removed outlier: 3.883A pdb=" N PHE A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 37 removed outlier: 3.820A pdb=" N THR A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A 36 " --> pdb=" O ASP A 32 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 77 removed outlier: 3.700A pdb=" N LEU A 56 " --> pdb=" O SER A 52 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL A 65 " --> pdb=" O GLN A 61 " (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: 3.883A pdb=" N PHE B 16 " --> pdb=" O VAL B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 37 removed outlier: 3.819A pdb=" N THR B 28 " --> pdb=" O GLN B 24 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 36 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B 37 " --> pdb=" O LYS B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 77 removed outlier: 3.700A pdb=" N LEU B 56 " --> pdb=" O SER B 52 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL B 65 " --> pdb=" O GLN B 61 " (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: 3.884A pdb=" N PHE C 16 " --> pdb=" O VAL C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 37 removed outlier: 3.821A pdb=" N THR C 28 " --> pdb=" O GLN C 24 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA C 36 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS C 37 " --> pdb=" O LYS C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 77 removed outlier: 3.700A pdb=" N LEU C 56 " --> pdb=" O SER C 52 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL C 65 " --> pdb=" O GLN C 61 " (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: 3.884A pdb=" N PHE D 16 " --> pdb=" O VAL D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 37 removed outlier: 3.820A pdb=" N THR D 28 " --> pdb=" O GLN D 24 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA D 36 " --> pdb=" O ASP D 32 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS D 37 " --> pdb=" O LYS D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 77 removed outlier: 3.700A pdb=" N LEU D 56 " --> pdb=" O SER D 52 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL D 65 " --> pdb=" O GLN D 61 " (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: 3.883A pdb=" N PHE E 16 " --> pdb=" O VAL E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 37 removed outlier: 3.820A pdb=" N THR E 28 " --> pdb=" O GLN E 24 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS E 37 " --> pdb=" O LYS E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 77 removed outlier: 3.700A pdb=" N LEU E 56 " --> pdb=" O SER E 52 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL E 65 " --> pdb=" O GLN E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 80 No H-bonds generated for 'chain 'E' and resid 78 through 80' Processing helix chain 'F' and resid 7 through 20 removed outlier: 3.883A pdb=" N PHE F 16 " --> pdb=" O VAL F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 37 removed outlier: 3.820A pdb=" N THR F 28 " --> pdb=" O GLN F 24 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA F 36 " --> pdb=" O ASP F 32 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS F 37 " --> pdb=" O LYS F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 77 removed outlier: 3.700A pdb=" N LEU F 56 " --> pdb=" O SER F 52 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL F 65 " --> pdb=" O GLN F 61 " (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: 3.883A pdb=" N PHE G 16 " --> pdb=" O VAL G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 37 removed outlier: 3.819A pdb=" N THR G 28 " --> pdb=" O GLN G 24 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA G 36 " --> pdb=" O ASP G 32 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS G 37 " --> pdb=" O LYS G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 77 removed outlier: 3.700A pdb=" N LEU G 56 " --> pdb=" O SER G 52 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL G 65 " --> pdb=" O GLN G 61 " (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: 3.883A pdb=" N PHE H 16 " --> pdb=" O VAL H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 37 removed outlier: 3.819A pdb=" N THR H 28 " --> pdb=" O GLN H 24 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA H 36 " --> pdb=" O ASP H 32 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS H 37 " --> pdb=" O LYS H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 77 removed outlier: 3.699A pdb=" N LEU H 56 " --> pdb=" O SER H 52 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL H 65 " --> pdb=" O GLN H 61 " (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: 3.884A pdb=" N PHE I 16 " --> pdb=" O VAL I 12 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 37 removed outlier: 3.820A pdb=" N THR I 28 " --> pdb=" O GLN I 24 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA I 36 " --> pdb=" O ASP I 32 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS I 37 " --> pdb=" O LYS I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 77 removed outlier: 3.700A pdb=" N LEU I 56 " --> pdb=" O SER I 52 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL I 65 " --> pdb=" O GLN I 61 " (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: 3.884A pdb=" N PHE J 16 " --> pdb=" O VAL J 12 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 37 removed outlier: 3.819A pdb=" N THR J 28 " --> pdb=" O GLN J 24 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA J 36 " --> pdb=" O ASP J 32 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS J 37 " --> pdb=" O LYS J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 77 removed outlier: 3.701A pdb=" N LEU J 56 " --> pdb=" O SER J 52 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL J 65 " --> pdb=" O GLN J 61 " (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 'K' and resid 7 through 20 removed outlier: 3.884A pdb=" N PHE K 16 " --> pdb=" O VAL K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 37 removed outlier: 3.821A pdb=" N THR K 28 " --> pdb=" O GLN K 24 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA K 36 " --> pdb=" O ASP K 32 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS K 37 " --> pdb=" O LYS K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 77 removed outlier: 3.700A pdb=" N LEU K 56 " --> pdb=" O SER K 52 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL K 65 " --> pdb=" O GLN K 61 " (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: 3.883A pdb=" N PHE L 16 " --> pdb=" O VAL L 12 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 37 removed outlier: 3.820A pdb=" N THR L 28 " --> pdb=" O GLN L 24 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA L 36 " --> pdb=" O ASP L 32 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS L 37 " --> pdb=" O LYS L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 77 removed outlier: 3.700A pdb=" N LEU L 56 " --> pdb=" O SER L 52 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL L 65 " --> pdb=" O GLN L 61 " (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: 3.883A pdb=" N PHE M 16 " --> pdb=" O VAL M 12 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 37 removed outlier: 3.821A pdb=" N THR M 28 " --> pdb=" O GLN M 24 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA M 36 " --> pdb=" O ASP M 32 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS M 37 " --> pdb=" O LYS M 33 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 77 removed outlier: 3.700A pdb=" N LEU M 56 " --> pdb=" O SER M 52 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL M 65 " --> pdb=" O GLN M 61 " (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: 3.883A pdb=" N PHE N 16 " --> pdb=" O VAL N 12 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 37 removed outlier: 3.820A pdb=" N THR N 28 " --> pdb=" O GLN N 24 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA N 36 " --> pdb=" O ASP N 32 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS N 37 " --> pdb=" O LYS N 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 77 removed outlier: 3.699A pdb=" N LEU N 56 " --> pdb=" O SER N 52 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL N 65 " --> pdb=" O GLN N 61 " (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: 3.883A pdb=" N PHE O 16 " --> pdb=" O VAL O 12 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 37 removed outlier: 3.820A pdb=" N THR O 28 " --> pdb=" O GLN O 24 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA O 36 " --> pdb=" O ASP O 32 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS O 37 " --> pdb=" O LYS O 33 " (cutoff:3.500A) Processing helix chain 'O' and resid 40 through 77 removed outlier: 3.700A pdb=" N LEU O 56 " --> pdb=" O SER O 52 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL O 65 " --> pdb=" O GLN O 61 " (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 'P' and resid 7 through 20 removed outlier: 3.883A pdb=" N PHE P 16 " --> pdb=" O VAL P 12 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 37 removed outlier: 3.820A pdb=" N THR P 28 " --> pdb=" O GLN P 24 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA P 36 " --> pdb=" O ASP P 32 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS P 37 " --> pdb=" O LYS P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 77 removed outlier: 3.700A pdb=" N LEU P 56 " --> pdb=" O SER P 52 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL P 65 " --> pdb=" O GLN P 61 " (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: 3.883A pdb=" N PHE Q 16 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 37 removed outlier: 3.820A pdb=" N THR Q 28 " --> pdb=" O GLN Q 24 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA Q 36 " --> pdb=" O ASP Q 32 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS Q 37 " --> pdb=" O LYS Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 77 removed outlier: 3.699A pdb=" N LEU Q 56 " --> pdb=" O SER Q 52 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL Q 65 " --> pdb=" O GLN Q 61 " (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: 3.883A pdb=" N PHE R 16 " --> pdb=" O VAL R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 22 through 37 removed outlier: 3.821A pdb=" N THR R 28 " --> pdb=" O GLN R 24 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA R 36 " --> pdb=" O ASP R 32 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS R 37 " --> pdb=" O LYS R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 77 removed outlier: 3.700A pdb=" N LEU R 56 " --> pdb=" O SER R 52 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL R 65 " --> pdb=" O GLN R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 80 No H-bonds generated for 'chain 'R' 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: 3.14 Time building geometry restraints manager: 3.09 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: 1088 1.41 - 1.48: 1669 1.48 - 1.54: 4821 Bond restraints: 11214 Sorted by residual: bond pdb=" CG LEU Q 9 " pdb=" CD2 LEU Q 9 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.61e+00 bond pdb=" CG LEU L 9 " pdb=" CD2 LEU L 9 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.61e+00 bond pdb=" CG LEU R 9 " pdb=" CD2 LEU R 9 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.60e+00 bond pdb=" CG LEU B 9 " pdb=" CD2 LEU B 9 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.59e+00 bond pdb=" CG LEU H 9 " pdb=" CD2 LEU H 9 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.59e+00 ... (remaining 11209 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.06: 12885 1.06 - 2.11: 1956 2.11 - 3.17: 332 3.17 - 4.23: 55 4.23 - 5.28: 36 Bond angle restraints: 15264 Sorted by residual: angle pdb=" CA GLN N 61 " pdb=" CB GLN N 61 " pdb=" CG GLN N 61 " ideal model delta sigma weight residual 114.10 119.38 -5.28 2.00e+00 2.50e-01 6.97e+00 angle pdb=" CA GLN M 61 " pdb=" CB GLN M 61 " pdb=" CG GLN M 61 " ideal model delta sigma weight residual 114.10 119.37 -5.27 2.00e+00 2.50e-01 6.95e+00 angle pdb=" CA GLN B 61 " pdb=" CB GLN B 61 " pdb=" CG GLN B 61 " ideal model delta sigma weight residual 114.10 119.37 -5.27 2.00e+00 2.50e-01 6.95e+00 angle pdb=" CA GLN G 61 " pdb=" CB GLN G 61 " pdb=" CG GLN G 61 " ideal model delta sigma weight residual 114.10 119.37 -5.27 2.00e+00 2.50e-01 6.94e+00 angle pdb=" CA GLN O 61 " pdb=" CB GLN O 61 " pdb=" CG GLN O 61 " ideal model delta sigma weight residual 114.10 119.36 -5.26 2.00e+00 2.50e-01 6.91e+00 ... (remaining 15259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.01: 6462 15.01 - 30.03: 252 30.03 - 45.04: 54 45.04 - 60.05: 18 60.05 - 75.06: 18 Dihedral angle restraints: 6804 sinusoidal: 2610 harmonic: 4194 Sorted by residual: dihedral pdb=" CA GLY A 19 " pdb=" C GLY A 19 " pdb=" N VAL A 20 " pdb=" CA VAL A 20 " ideal model delta harmonic sigma weight residual 180.00 164.34 15.66 0 5.00e+00 4.00e-02 9.81e+00 dihedral pdb=" CA GLY P 19 " pdb=" C GLY P 19 " pdb=" N VAL P 20 " pdb=" CA VAL P 20 " ideal model delta harmonic sigma weight residual 180.00 164.36 15.64 0 5.00e+00 4.00e-02 9.79e+00 dihedral pdb=" CA GLY B 19 " pdb=" C GLY B 19 " pdb=" N VAL B 20 " pdb=" CA VAL B 20 " ideal model delta harmonic sigma weight residual 180.00 164.36 15.64 0 5.00e+00 4.00e-02 9.78e+00 ... (remaining 6801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.020: 471 0.020 - 0.041: 597 0.041 - 0.061: 317 0.061 - 0.081: 305 0.081 - 0.101: 56 Chirality restraints: 1746 Sorted by residual: chirality pdb=" CA PRO N 41 " pdb=" N PRO N 41 " pdb=" C PRO N 41 " pdb=" CB PRO N 41 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.56e-01 chirality pdb=" CA PRO H 41 " pdb=" N PRO H 41 " pdb=" C PRO H 41 " pdb=" CB PRO H 41 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.42e-01 chirality pdb=" CA PRO J 41 " pdb=" N PRO J 41 " pdb=" C PRO J 41 " pdb=" CB PRO J 41 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.42e-01 ... (remaining 1743 not shown) Planarity restraints: 1998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL K 20 " 0.008 2.00e-02 2.50e+03 1.56e-02 2.44e+00 pdb=" C VAL K 20 " -0.027 2.00e-02 2.50e+03 pdb=" O VAL K 20 " 0.010 2.00e-02 2.50e+03 pdb=" N ASP K 21 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 20 " 0.008 2.00e-02 2.50e+03 1.56e-02 2.43e+00 pdb=" C VAL A 20 " -0.027 2.00e-02 2.50e+03 pdb=" O VAL A 20 " 0.010 2.00e-02 2.50e+03 pdb=" N ASP A 21 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL Q 20 " 0.008 2.00e-02 2.50e+03 1.56e-02 2.43e+00 pdb=" C VAL Q 20 " -0.027 2.00e-02 2.50e+03 pdb=" O VAL Q 20 " 0.010 2.00e-02 2.50e+03 pdb=" N ASP Q 21 " 0.009 2.00e-02 2.50e+03 ... (remaining 1995 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 248 2.70 - 3.25: 11456 3.25 - 3.80: 17333 3.80 - 4.35: 23717 4.35 - 4.90: 40635 Nonbonded interactions: 93389 Sorted by model distance: nonbonded pdb=" OD1 ASP I 10 " pdb=" OG SER O 49 " model vdw 2.147 3.040 nonbonded pdb=" OD1 ASP J 10 " pdb=" OG SER P 49 " model vdw 2.192 3.040 nonbonded pdb=" OD1 ASP D 10 " pdb=" OG SER J 49 " model vdw 2.217 3.040 nonbonded pdb=" N ASP A 10 " pdb=" OE2 GLU G 53 " model vdw 2.252 3.120 nonbonded pdb=" OD1 ASP E 17 " pdb=" OH TYR E 57 " model vdw 2.310 3.040 ... (remaining 93384 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' 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: 0.980 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 21.920 Find NCS groups from input model: 0.370 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: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.720 ------------------------------------------------------------------------------- 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 : 0.009 0.042 11214 Z= 0.565 Angle : 0.831 5.282 15264 Z= 0.500 Chirality : 0.045 0.101 1746 Planarity : 0.005 0.031 1998 Dihedral : 10.880 75.065 4068 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.21 (0.13), residues: 1368 helix: -3.28 (0.09), residues: 1152 sheet: None (None), residues: 0 loop : -2.57 (0.28), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP H 5 PHE 0.012 0.003 PHE O 79 TYR 0.011 0.002 TYR O 57 ARG 0.004 0.001 ARG I 58 *********************** 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 389 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 389 time to evaluate : 1.259 Fit side-chains REVERT: A 66 LYS cc_start: 0.8617 (tptp) cc_final: 0.7191 (mttm) REVERT: B 37 LYS cc_start: 0.7539 (ttmt) cc_final: 0.6639 (tptt) REVERT: C 4 PRO cc_start: 0.7523 (Cg_endo) cc_final: 0.7248 (Cg_exo) REVERT: C 10 ASP cc_start: 0.8562 (m-30) cc_final: 0.7963 (m-30) REVERT: C 37 LYS cc_start: 0.9078 (ttmt) cc_final: 0.7713 (tptt) REVERT: C 72 ASP cc_start: 0.9174 (m-30) cc_final: 0.8948 (m-30) REVERT: D 10 ASP cc_start: 0.7896 (m-30) cc_final: 0.7502 (m-30) REVERT: E 10 ASP cc_start: 0.8060 (m-30) cc_final: 0.7723 (m-30) REVERT: E 37 LYS cc_start: 0.9093 (ttmt) cc_final: 0.7985 (tptt) REVERT: E 52 SER cc_start: 0.8568 (m) cc_final: 0.8250 (p) REVERT: E 70 ASP cc_start: 0.8333 (m-30) cc_final: 0.7939 (m-30) REVERT: F 10 ASP cc_start: 0.8421 (m-30) cc_final: 0.8061 (m-30) REVERT: F 37 LYS cc_start: 0.9074 (ttmt) cc_final: 0.7655 (tptt) REVERT: G 33 LYS cc_start: 0.8397 (mttt) cc_final: 0.7936 (mtpp) REVERT: G 37 LYS cc_start: 0.8503 (ttmt) cc_final: 0.6720 (tptp) REVERT: H 37 LYS cc_start: 0.8965 (ttmt) cc_final: 0.7269 (tptt) REVERT: H 72 ASP cc_start: 0.9104 (m-30) cc_final: 0.8750 (m-30) REVERT: I 53 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7514 (mt-10) REVERT: K 10 ASP cc_start: 0.7953 (m-30) cc_final: 0.7545 (m-30) REVERT: L 53 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7571 (mt-10) REVERT: M 8 TYR cc_start: 0.8717 (t80) cc_final: 0.8480 (t80) REVERT: M 29 GLU cc_start: 0.7362 (mt-10) cc_final: 0.7068 (mt-10) REVERT: M 69 LYS cc_start: 0.8962 (tmtt) cc_final: 0.7838 (ttmt) REVERT: N 25 THR cc_start: 0.8717 (m) cc_final: 0.8353 (p) REVERT: N 69 LYS cc_start: 0.8770 (tmtt) cc_final: 0.8159 (ttmt) REVERT: O 28 THR cc_start: 0.8751 (m) cc_final: 0.8371 (p) REVERT: O 33 LYS cc_start: 0.7967 (mttt) cc_final: 0.7095 (mttm) REVERT: R 33 LYS cc_start: 0.8610 (mttt) cc_final: 0.7864 (mttm) REVERT: R 69 LYS cc_start: 0.9078 (tmtt) cc_final: 0.7908 (ttmt) REVERT: R 72 ASP cc_start: 0.8863 (m-30) cc_final: 0.8630 (m-30) outliers start: 0 outliers final: 0 residues processed: 389 average time/residue: 0.2173 time to fit residues: 119.1688 Evaluate side-chains 275 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 1.113 ------------------------------------------------------------------------------- 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: 2.9990 chunk 95 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN B 61 GLN F 78 ASN G 61 GLN H 61 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 11214 Z= 0.167 Angle : 0.471 3.738 15264 Z= 0.263 Chirality : 0.033 0.114 1746 Planarity : 0.005 0.028 1998 Dihedral : 4.059 17.480 1512 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.18 % Allowed : 9.09 % Favored : 89.73 % 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: -0.60 (0.20), residues: 1368 helix: -0.08 (0.13), residues: 1206 sheet: None (None), residues: 0 loop : -1.76 (0.50), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 5 PHE 0.007 0.001 PHE B 79 TYR 0.015 0.001 TYR B 47 ARG 0.001 0.000 ARG B 80 *********************** 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 355 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 341 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8342 (m-30) cc_final: 0.8025 (m-30) REVERT: A 39 SER cc_start: 0.8580 (m) cc_final: 0.8332 (p) REVERT: A 69 LYS cc_start: 0.8695 (tmtt) cc_final: 0.8483 (tttm) REVERT: B 37 LYS cc_start: 0.8088 (ttmt) cc_final: 0.6937 (tptt) REVERT: B 66 LYS cc_start: 0.8123 (tptp) cc_final: 0.6725 (ttmm) REVERT: C 4 PRO cc_start: 0.7804 (Cg_endo) cc_final: 0.7565 (Cg_exo) REVERT: C 10 ASP cc_start: 0.8283 (m-30) cc_final: 0.7923 (m-30) REVERT: C 37 LYS cc_start: 0.9036 (ttmt) cc_final: 0.7635 (tptt) REVERT: C 69 LYS cc_start: 0.8831 (tmtt) cc_final: 0.8435 (tttm) REVERT: D 10 ASP cc_start: 0.8026 (m-30) cc_final: 0.7321 (m-30) REVERT: D 72 ASP cc_start: 0.9053 (m-30) cc_final: 0.8743 (m-30) REVERT: E 10 ASP cc_start: 0.8116 (m-30) cc_final: 0.7717 (m-30) REVERT: E 37 LYS cc_start: 0.9066 (ttmt) cc_final: 0.7925 (tptt) REVERT: E 52 SER cc_start: 0.8542 (m) cc_final: 0.8116 (p) REVERT: E 57 TYR cc_start: 0.9179 (t80) cc_final: 0.8883 (t80) REVERT: F 10 ASP cc_start: 0.8271 (m-30) cc_final: 0.7872 (m-30) REVERT: F 37 LYS cc_start: 0.8991 (ttmt) cc_final: 0.7604 (tptt) REVERT: G 33 LYS cc_start: 0.8596 (mttt) cc_final: 0.8278 (mtpp) REVERT: G 37 LYS cc_start: 0.8637 (ttmt) cc_final: 0.6957 (tptp) REVERT: H 37 LYS cc_start: 0.8907 (ttmt) cc_final: 0.7425 (tptt) REVERT: H 72 ASP cc_start: 0.8960 (m-30) cc_final: 0.8444 (m-30) REVERT: I 8 TYR cc_start: 0.8711 (t80) cc_final: 0.8333 (t80) REVERT: I 53 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7638 (mt-10) REVERT: J 10 ASP cc_start: 0.8212 (m-30) cc_final: 0.7873 (m-30) REVERT: J 24 GLN cc_start: 0.7805 (mp10) cc_final: 0.7604 (mp10) REVERT: J 37 LYS cc_start: 0.8957 (ttmm) cc_final: 0.8728 (ttmt) REVERT: K 31 LEU cc_start: 0.9143 (tp) cc_final: 0.8923 (tp) REVERT: L 10 ASP cc_start: 0.8278 (m-30) cc_final: 0.8025 (m-30) REVERT: M 8 TYR cc_start: 0.8752 (t80) cc_final: 0.8441 (t80) REVERT: M 69 LYS cc_start: 0.9034 (tmtt) cc_final: 0.7830 (ttmt) REVERT: N 15 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.7518 (ttpt) REVERT: N 25 THR cc_start: 0.8696 (m) cc_final: 0.8421 (p) REVERT: N 29 GLU cc_start: 0.7121 (tp30) cc_final: 0.6877 (tp30) REVERT: N 69 LYS cc_start: 0.8930 (tmtt) cc_final: 0.7920 (ttmt) REVERT: N 70 ASP cc_start: 0.8270 (m-30) cc_final: 0.7772 (m-30) REVERT: N 72 ASP cc_start: 0.8314 (m-30) cc_final: 0.8002 (m-30) REVERT: O 15 LYS cc_start: 0.8606 (ttmm) cc_final: 0.7370 (tttt) REVERT: O 29 GLU cc_start: 0.7647 (tm-30) cc_final: 0.7297 (tp30) REVERT: O 33 LYS cc_start: 0.8394 (mttt) cc_final: 0.8121 (mttm) REVERT: Q 32 ASP cc_start: 0.7818 (m-30) cc_final: 0.7597 (m-30) REVERT: Q 53 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7157 (mt-10) REVERT: R 69 LYS cc_start: 0.9007 (tmtt) cc_final: 0.7876 (ttmt) outliers start: 14 outliers final: 3 residues processed: 345 average time/residue: 0.2078 time to fit residues: 102.5918 Evaluate side-chains 295 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 291 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain J residue 33 LYS Chi-restraints excluded: chain N residue 15 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 55 ASN I 78 ASN J 78 ASN N 63 ASN O 61 GLN O 63 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11214 Z= 0.207 Angle : 0.456 4.885 15264 Z= 0.248 Chirality : 0.034 0.113 1746 Planarity : 0.004 0.028 1998 Dihedral : 3.759 16.487 1512 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.59 % Allowed : 12.46 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.21), residues: 1368 helix: 1.47 (0.14), residues: 1206 sheet: None (None), residues: 0 loop : -1.71 (0.52), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 5 PHE 0.008 0.001 PHE O 68 TYR 0.013 0.001 TYR B 47 ARG 0.002 0.000 ARG P 80 *********************** 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 345 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 338 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8765 (tmtt) cc_final: 0.8541 (tttm) REVERT: B 37 LYS cc_start: 0.8575 (ttmt) cc_final: 0.7310 (tptt) REVERT: B 56 LEU cc_start: 0.9258 (mt) cc_final: 0.8911 (mt) REVERT: B 66 LYS cc_start: 0.8581 (tptp) cc_final: 0.7416 (ttmt) REVERT: C 37 LYS cc_start: 0.8951 (ttmt) cc_final: 0.7542 (tptt) REVERT: C 69 LYS cc_start: 0.8809 (tmtt) cc_final: 0.8462 (tttm) REVERT: C 72 ASP cc_start: 0.9075 (m-30) cc_final: 0.8782 (m-30) REVERT: D 10 ASP cc_start: 0.8348 (m-30) cc_final: 0.7734 (m-30) REVERT: D 66 LYS cc_start: 0.8429 (tptp) cc_final: 0.7800 (ttmt) REVERT: D 69 LYS cc_start: 0.8773 (tmtt) cc_final: 0.8411 (tptp) REVERT: D 72 ASP cc_start: 0.9014 (m-30) cc_final: 0.8791 (m-30) REVERT: E 10 ASP cc_start: 0.8356 (m-30) cc_final: 0.7896 (m-30) REVERT: E 37 LYS cc_start: 0.9115 (ttmt) cc_final: 0.7935 (tptt) REVERT: F 10 ASP cc_start: 0.8302 (m-30) cc_final: 0.7847 (m-30) REVERT: F 37 LYS cc_start: 0.9007 (ttmt) cc_final: 0.7526 (tptt) REVERT: G 10 ASP cc_start: 0.8594 (m-30) cc_final: 0.8156 (m-30) REVERT: G 33 LYS cc_start: 0.8715 (mttt) cc_final: 0.8443 (mtpp) REVERT: G 52 SER cc_start: 0.8857 (m) cc_final: 0.8288 (p) REVERT: H 37 LYS cc_start: 0.9029 (ttmt) cc_final: 0.7495 (tptt) REVERT: H 72 ASP cc_start: 0.9098 (m-30) cc_final: 0.8658 (m-30) REVERT: I 8 TYR cc_start: 0.8685 (t80) cc_final: 0.8207 (t80) REVERT: I 77 GLN cc_start: 0.8506 (tp40) cc_final: 0.8173 (tp40) REVERT: J 37 LYS cc_start: 0.8925 (ttmm) cc_final: 0.8700 (ttmt) REVERT: J 72 ASP cc_start: 0.8412 (m-30) cc_final: 0.7879 (m-30) REVERT: L 39 SER cc_start: 0.8726 (m) cc_final: 0.7565 (m) REVERT: M 69 LYS cc_start: 0.9086 (tmtt) cc_final: 0.7829 (ttmt) REVERT: N 15 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.7534 (ttpt) REVERT: N 69 LYS cc_start: 0.8980 (tmtt) cc_final: 0.7921 (ttmt) REVERT: N 70 ASP cc_start: 0.8300 (m-30) cc_final: 0.7839 (m-30) REVERT: O 69 LYS cc_start: 0.8922 (tmtt) cc_final: 0.8117 (ttmt) REVERT: O 72 ASP cc_start: 0.8371 (m-30) cc_final: 0.8145 (m-30) REVERT: P 32 ASP cc_start: 0.7867 (m-30) cc_final: 0.7610 (m-30) REVERT: P 69 LYS cc_start: 0.8816 (tmtt) cc_final: 0.7982 (ttmt) REVERT: Q 25 THR cc_start: 0.9033 (m) cc_final: 0.8700 (p) REVERT: Q 69 LYS cc_start: 0.8862 (tmtt) cc_final: 0.7663 (tttt) REVERT: R 15 LYS cc_start: 0.8471 (mttp) cc_final: 0.7437 (ttpt) REVERT: R 69 LYS cc_start: 0.9033 (tmtt) cc_final: 0.7852 (ttmt) REVERT: R 77 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8007 (tm-30) outliers start: 7 outliers final: 3 residues processed: 342 average time/residue: 0.2247 time to fit residues: 107.4966 Evaluate side-chains 306 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 302 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain N residue 15 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 59 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 GLN D 55 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 11214 Z= 0.166 Angle : 0.418 4.116 15264 Z= 0.225 Chirality : 0.034 0.106 1746 Planarity : 0.003 0.023 1998 Dihedral : 3.624 16.259 1512 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.67 % Allowed : 13.80 % Favored : 85.52 % 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: 2.60 (0.21), residues: 1368 helix: 2.16 (0.14), residues: 1206 sheet: None (None), residues: 0 loop : -1.77 (0.51), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 5 PHE 0.006 0.001 PHE N 68 TYR 0.009 0.001 TYR B 47 ARG 0.001 0.000 ARG I 80 *********************** 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 329 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 321 time to evaluate : 1.234 Fit side-chains revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8787 (tmtt) cc_final: 0.8550 (tttm) REVERT: B 37 LYS cc_start: 0.8723 (ttmt) cc_final: 0.7478 (tptt) REVERT: B 40 ASP cc_start: 0.8055 (t0) cc_final: 0.7746 (t0) REVERT: B 53 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7315 (mm-30) REVERT: B 56 LEU cc_start: 0.9191 (mt) cc_final: 0.8835 (mt) REVERT: B 61 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8571 (tt0) REVERT: B 66 LYS cc_start: 0.8593 (tptp) cc_final: 0.7454 (ttmt) REVERT: B 69 LYS cc_start: 0.8639 (tttm) cc_final: 0.8354 (tttm) REVERT: C 10 ASP cc_start: 0.8579 (m-30) cc_final: 0.8375 (m-30) REVERT: C 37 LYS cc_start: 0.8936 (ttmt) cc_final: 0.7520 (tptt) REVERT: C 69 LYS cc_start: 0.8838 (tmtt) cc_final: 0.8481 (tttm) REVERT: C 72 ASP cc_start: 0.9068 (m-30) cc_final: 0.8649 (m-30) REVERT: D 10 ASP cc_start: 0.8343 (m-30) cc_final: 0.7725 (m-30) REVERT: D 66 LYS cc_start: 0.8573 (tptp) cc_final: 0.7791 (ttmt) REVERT: D 69 LYS cc_start: 0.8752 (tmtt) cc_final: 0.8443 (tttm) REVERT: E 37 LYS cc_start: 0.9095 (ttmt) cc_final: 0.7934 (tptt) REVERT: E 66 LYS cc_start: 0.8284 (tptp) cc_final: 0.7609 (tppt) REVERT: F 10 ASP cc_start: 0.8335 (m-30) cc_final: 0.7947 (m-30) REVERT: F 37 LYS cc_start: 0.8961 (ttmt) cc_final: 0.7526 (tptt) REVERT: G 10 ASP cc_start: 0.8472 (m-30) cc_final: 0.8263 (m-30) REVERT: G 33 LYS cc_start: 0.8639 (mttt) cc_final: 0.8426 (mtpp) REVERT: G 39 SER cc_start: 0.9083 (m) cc_final: 0.8843 (m) REVERT: G 52 SER cc_start: 0.8905 (m) cc_final: 0.8309 (p) REVERT: G 53 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7436 (mm-30) REVERT: H 37 LYS cc_start: 0.9047 (ttmt) cc_final: 0.7531 (tptt) REVERT: H 72 ASP cc_start: 0.9087 (m-30) cc_final: 0.8684 (m-30) REVERT: I 8 TYR cc_start: 0.8634 (t80) cc_final: 0.8264 (t80) REVERT: I 69 LYS cc_start: 0.8666 (tmtt) cc_final: 0.8241 (tttp) REVERT: I 77 GLN cc_start: 0.8650 (tp40) cc_final: 0.8441 (tp40) REVERT: J 72 ASP cc_start: 0.8398 (m-30) cc_final: 0.7828 (m-30) REVERT: L 39 SER cc_start: 0.8643 (m) cc_final: 0.7906 (m) REVERT: M 69 LYS cc_start: 0.9063 (tmtt) cc_final: 0.7790 (ttmt) REVERT: N 15 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.7526 (ttpt) REVERT: N 24 GLN cc_start: 0.7433 (mp10) cc_final: 0.7218 (mp10) REVERT: N 69 LYS cc_start: 0.8948 (tmtt) cc_final: 0.7873 (ttmt) REVERT: N 70 ASP cc_start: 0.8273 (m-30) cc_final: 0.7899 (m-30) REVERT: O 69 LYS cc_start: 0.9023 (tmtt) cc_final: 0.8074 (ttmt) REVERT: O 72 ASP cc_start: 0.8591 (m-30) cc_final: 0.8333 (m-30) REVERT: P 69 LYS cc_start: 0.8818 (tmtt) cc_final: 0.7821 (ttmt) REVERT: Q 15 LYS cc_start: 0.8745 (mttp) cc_final: 0.7675 (ttpt) REVERT: Q 25 THR cc_start: 0.9037 (m) cc_final: 0.8730 (p) REVERT: Q 69 LYS cc_start: 0.8924 (tmtt) cc_final: 0.7514 (tttt) REVERT: R 15 LYS cc_start: 0.8455 (mttp) cc_final: 0.7454 (ttpt) REVERT: R 69 LYS cc_start: 0.9043 (tmtt) cc_final: 0.7859 (ttmt) REVERT: R 77 GLN cc_start: 0.8552 (tm-30) cc_final: 0.7992 (tm-30) outliers start: 8 outliers final: 4 residues processed: 324 average time/residue: 0.2221 time to fit residues: 100.7729 Evaluate side-chains 298 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 292 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain N residue 15 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.4980 chunk 69 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 GLN C 63 ASN D 55 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 11214 Z= 0.168 Angle : 0.422 5.313 15264 Z= 0.225 Chirality : 0.034 0.105 1746 Planarity : 0.003 0.028 1998 Dihedral : 3.556 16.545 1512 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.18 % Allowed : 14.65 % Favored : 84.18 % 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: 3.13 (0.21), residues: 1368 helix: 2.54 (0.13), residues: 1206 sheet: None (None), residues: 0 loop : -1.90 (0.49), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 5 PHE 0.006 0.001 PHE N 68 TYR 0.009 0.001 TYR B 47 ARG 0.001 0.000 ARG A 80 *********************** 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 327 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 313 time to evaluate : 1.131 Fit side-chains revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8812 (tmtt) cc_final: 0.8603 (tttm) REVERT: B 37 LYS cc_start: 0.8774 (ttmt) cc_final: 0.7483 (tptt) REVERT: B 40 ASP cc_start: 0.8104 (t0) cc_final: 0.7776 (t0) REVERT: B 56 LEU cc_start: 0.9177 (mt) cc_final: 0.8819 (mt) REVERT: B 61 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8684 (tt0) REVERT: B 66 LYS cc_start: 0.8610 (tptp) cc_final: 0.7482 (ttmt) REVERT: B 69 LYS cc_start: 0.8646 (tttm) cc_final: 0.8372 (tttm) REVERT: C 10 ASP cc_start: 0.8513 (m-30) cc_final: 0.8248 (m-30) REVERT: C 37 LYS cc_start: 0.8941 (ttmt) cc_final: 0.7526 (tptt) REVERT: C 69 LYS cc_start: 0.8859 (tmtt) cc_final: 0.8544 (tttm) REVERT: C 72 ASP cc_start: 0.9056 (m-30) cc_final: 0.8648 (m-30) REVERT: D 10 ASP cc_start: 0.8356 (m-30) cc_final: 0.7748 (m-30) REVERT: D 66 LYS cc_start: 0.8578 (tptp) cc_final: 0.7160 (mttm) REVERT: D 69 LYS cc_start: 0.8754 (tmtt) cc_final: 0.8466 (tttm) REVERT: E 37 LYS cc_start: 0.9098 (ttmt) cc_final: 0.7927 (tptt) REVERT: E 66 LYS cc_start: 0.8303 (tptp) cc_final: 0.7604 (tppt) REVERT: F 10 ASP cc_start: 0.8312 (m-30) cc_final: 0.7956 (m-30) REVERT: F 37 LYS cc_start: 0.8948 (ttmt) cc_final: 0.7494 (tptt) REVERT: G 10 ASP cc_start: 0.8489 (m-30) cc_final: 0.8251 (m-30) REVERT: G 33 LYS cc_start: 0.8627 (mttt) cc_final: 0.8424 (mtpp) REVERT: G 52 SER cc_start: 0.8905 (m) cc_final: 0.8346 (p) REVERT: H 72 ASP cc_start: 0.9093 (m-30) cc_final: 0.8653 (m-30) REVERT: I 8 TYR cc_start: 0.8634 (t80) cc_final: 0.8229 (t80) REVERT: I 69 LYS cc_start: 0.8674 (tmtt) cc_final: 0.8229 (tttp) REVERT: J 72 ASP cc_start: 0.8406 (m-30) cc_final: 0.7814 (m-30) REVERT: L 39 SER cc_start: 0.8671 (m) cc_final: 0.7964 (m) REVERT: M 69 LYS cc_start: 0.9052 (tmtt) cc_final: 0.7794 (ttmt) REVERT: N 15 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.7523 (ttpt) REVERT: N 69 LYS cc_start: 0.8943 (tmtt) cc_final: 0.7856 (ttmt) REVERT: O 33 LYS cc_start: 0.8824 (mtmm) cc_final: 0.8621 (mtmt) REVERT: O 69 LYS cc_start: 0.9010 (tmtt) cc_final: 0.8026 (ttmt) REVERT: O 72 ASP cc_start: 0.8597 (m-30) cc_final: 0.8394 (m-30) REVERT: P 69 LYS cc_start: 0.8894 (tmtt) cc_final: 0.7856 (ttmt) REVERT: Q 25 THR cc_start: 0.9017 (m) cc_final: 0.8725 (p) REVERT: Q 69 LYS cc_start: 0.8930 (tmtt) cc_final: 0.7502 (tttt) REVERT: R 15 LYS cc_start: 0.8469 (mttp) cc_final: 0.7449 (ttpt) REVERT: R 69 LYS cc_start: 0.9037 (tmtt) cc_final: 0.7834 (ttmt) REVERT: R 77 GLN cc_start: 0.8533 (tm-30) cc_final: 0.7978 (tm-30) outliers start: 14 outliers final: 9 residues processed: 320 average time/residue: 0.2163 time to fit residues: 98.1605 Evaluate side-chains 313 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 302 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain M residue 53 GLU Chi-restraints excluded: chain N residue 15 LYS Chi-restraints excluded: chain P residue 59 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.6980 chunk 109 optimal weight: 0.5980 chunk 24 optimal weight: 0.0060 chunk 71 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 101 optimal weight: 0.2980 chunk 56 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 55 ASN P 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 11214 Z= 0.116 Angle : 0.392 3.860 15264 Z= 0.208 Chirality : 0.033 0.101 1746 Planarity : 0.003 0.024 1998 Dihedral : 3.456 15.659 1512 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.01 % Allowed : 15.32 % Favored : 83.67 % 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: 3.63 (0.21), residues: 1368 helix: 2.91 (0.13), residues: 1206 sheet: None (None), residues: 0 loop : -2.02 (0.48), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP K 5 PHE 0.005 0.001 PHE J 16 TYR 0.016 0.001 TYR K 47 ARG 0.001 0.000 ARG O 80 *********************** 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 323 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 311 time to evaluate : 1.197 Fit side-chains revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8797 (tmtt) cc_final: 0.8406 (tttm) REVERT: B 37 LYS cc_start: 0.8766 (ttmt) cc_final: 0.7451 (tptt) REVERT: B 40 ASP cc_start: 0.8076 (t0) cc_final: 0.7728 (t0) REVERT: B 56 LEU cc_start: 0.9161 (mt) cc_final: 0.8773 (mt) REVERT: B 66 LYS cc_start: 0.8558 (tptp) cc_final: 0.7417 (ttmt) REVERT: B 69 LYS cc_start: 0.8631 (tttm) cc_final: 0.8320 (tttm) REVERT: C 10 ASP cc_start: 0.8372 (m-30) cc_final: 0.7951 (m-30) REVERT: C 37 LYS cc_start: 0.8921 (ttmt) cc_final: 0.7559 (tptt) REVERT: C 69 LYS cc_start: 0.8826 (tmtt) cc_final: 0.8500 (tttm) REVERT: C 72 ASP cc_start: 0.8951 (m-30) cc_final: 0.8513 (m-30) REVERT: D 10 ASP cc_start: 0.8266 (m-30) cc_final: 0.7683 (m-30) REVERT: D 66 LYS cc_start: 0.8566 (tptp) cc_final: 0.7703 (ttmt) REVERT: D 69 LYS cc_start: 0.8693 (tmtt) cc_final: 0.8432 (tttm) REVERT: E 37 LYS cc_start: 0.9079 (ttmt) cc_final: 0.7911 (tptt) REVERT: E 66 LYS cc_start: 0.8415 (tptp) cc_final: 0.7573 (tppt) REVERT: F 10 ASP cc_start: 0.8270 (m-30) cc_final: 0.7921 (m-30) REVERT: F 37 LYS cc_start: 0.8908 (ttmt) cc_final: 0.7511 (tptt) REVERT: G 10 ASP cc_start: 0.8450 (m-30) cc_final: 0.8197 (m-30) REVERT: G 53 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7441 (mm-30) REVERT: H 72 ASP cc_start: 0.9057 (m-30) cc_final: 0.8629 (m-30) REVERT: I 8 TYR cc_start: 0.8557 (t80) cc_final: 0.8259 (t80) REVERT: I 53 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7332 (mt-10) REVERT: I 69 LYS cc_start: 0.8658 (tmtt) cc_final: 0.8188 (tttp) REVERT: L 39 SER cc_start: 0.8648 (m) cc_final: 0.7952 (m) REVERT: M 69 LYS cc_start: 0.9066 (tmtt) cc_final: 0.7788 (ttmt) REVERT: N 15 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.7482 (ttpt) REVERT: N 69 LYS cc_start: 0.8892 (tmtt) cc_final: 0.7851 (ttmt) REVERT: N 72 ASP cc_start: 0.7979 (m-30) cc_final: 0.7747 (m-30) REVERT: O 32 ASP cc_start: 0.7821 (m-30) cc_final: 0.7540 (m-30) REVERT: O 33 LYS cc_start: 0.8833 (mtmm) cc_final: 0.8630 (mtmt) REVERT: O 69 LYS cc_start: 0.9027 (tmtt) cc_final: 0.7927 (ttmt) REVERT: P 69 LYS cc_start: 0.8927 (tmtt) cc_final: 0.7848 (ttmt) REVERT: Q 15 LYS cc_start: 0.8724 (mttp) cc_final: 0.7593 (ttpt) REVERT: Q 25 THR cc_start: 0.9023 (m) cc_final: 0.8771 (p) REVERT: Q 32 ASP cc_start: 0.7816 (m-30) cc_final: 0.7484 (m-30) REVERT: Q 69 LYS cc_start: 0.8944 (tmtt) cc_final: 0.7506 (tttt) REVERT: R 15 LYS cc_start: 0.8486 (mttp) cc_final: 0.7450 (ttpt) REVERT: R 69 LYS cc_start: 0.9040 (tmtt) cc_final: 0.7813 (ttmt) outliers start: 12 outliers final: 7 residues processed: 318 average time/residue: 0.2134 time to fit residues: 96.2213 Evaluate side-chains 307 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 299 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain M residue 53 GLU Chi-restraints excluded: chain N residue 15 LYS Chi-restraints excluded: chain P residue 59 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 GLN D 55 ASN D 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 11214 Z= 0.236 Angle : 0.451 4.256 15264 Z= 0.240 Chirality : 0.036 0.106 1746 Planarity : 0.003 0.029 1998 Dihedral : 3.622 17.533 1512 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.01 % Allowed : 15.49 % Favored : 83.50 % 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: 3.49 (0.21), residues: 1368 helix: 2.84 (0.13), residues: 1206 sheet: None (None), residues: 0 loop : -2.26 (0.47), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 5 PHE 0.008 0.001 PHE O 68 TYR 0.014 0.001 TYR K 47 ARG 0.002 0.000 ARG G 58 *********************** 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 323 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 311 time to evaluate : 1.171 Fit side-chains revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8805 (tmtt) cc_final: 0.8602 (tttm) REVERT: B 37 LYS cc_start: 0.8944 (ttmt) cc_final: 0.7580 (tptt) REVERT: B 40 ASP cc_start: 0.8160 (t0) cc_final: 0.7775 (t0) REVERT: B 56 LEU cc_start: 0.9171 (mt) cc_final: 0.8783 (mt) REVERT: B 66 LYS cc_start: 0.8596 (tptp) cc_final: 0.7519 (ttmt) REVERT: C 10 ASP cc_start: 0.8490 (m-30) cc_final: 0.7989 (m-30) REVERT: C 37 LYS cc_start: 0.8969 (ttmt) cc_final: 0.7597 (tptt) REVERT: C 69 LYS cc_start: 0.8872 (tmtt) cc_final: 0.8539 (tttm) REVERT: C 72 ASP cc_start: 0.9057 (m-30) cc_final: 0.8649 (m-30) REVERT: D 10 ASP cc_start: 0.8407 (m-30) cc_final: 0.7741 (m-30) REVERT: D 66 LYS cc_start: 0.8582 (tptp) cc_final: 0.7755 (ttmt) REVERT: D 69 LYS cc_start: 0.8810 (tmtt) cc_final: 0.8500 (tttm) REVERT: E 37 LYS cc_start: 0.9099 (ttmt) cc_final: 0.7887 (tptt) REVERT: E 66 LYS cc_start: 0.8370 (tptp) cc_final: 0.7603 (tppt) REVERT: F 10 ASP cc_start: 0.8353 (m-30) cc_final: 0.7983 (m-30) REVERT: F 37 LYS cc_start: 0.8979 (ttmt) cc_final: 0.7507 (tptt) REVERT: G 10 ASP cc_start: 0.8455 (m-30) cc_final: 0.8222 (m-30) REVERT: G 32 ASP cc_start: 0.7886 (m-30) cc_final: 0.7405 (m-30) REVERT: H 72 ASP cc_start: 0.9125 (m-30) cc_final: 0.8766 (m-30) REVERT: I 8 TYR cc_start: 0.8681 (t80) cc_final: 0.8346 (t80) REVERT: I 53 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7214 (mt-10) REVERT: I 69 LYS cc_start: 0.8763 (tmtt) cc_final: 0.8279 (tttp) REVERT: L 39 SER cc_start: 0.8651 (m) cc_final: 0.8350 (p) REVERT: M 69 LYS cc_start: 0.9030 (tmtt) cc_final: 0.7799 (ttmt) REVERT: N 15 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.7488 (ttpt) REVERT: N 69 LYS cc_start: 0.8942 (tmtt) cc_final: 0.7898 (ttmt) REVERT: O 69 LYS cc_start: 0.8980 (tmtt) cc_final: 0.7890 (ttmt) REVERT: P 54 TYR cc_start: 0.9100 (t80) cc_final: 0.8818 (t80) REVERT: P 69 LYS cc_start: 0.8929 (tmtt) cc_final: 0.7789 (ttmt) REVERT: Q 25 THR cc_start: 0.9047 (m) cc_final: 0.8756 (p) REVERT: Q 32 ASP cc_start: 0.7823 (m-30) cc_final: 0.7472 (m-30) REVERT: Q 69 LYS cc_start: 0.8929 (tmtt) cc_final: 0.7496 (tttt) REVERT: R 69 LYS cc_start: 0.9055 (tmtt) cc_final: 0.7899 (ttmt) outliers start: 12 outliers final: 10 residues processed: 319 average time/residue: 0.2223 time to fit residues: 99.6595 Evaluate side-chains 314 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 303 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain M residue 53 GLU Chi-restraints excluded: chain N residue 15 LYS Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 59 ASN Chi-restraints excluded: chain R residue 49 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11214 Z= 0.156 Angle : 0.419 6.022 15264 Z= 0.222 Chirality : 0.034 0.104 1746 Planarity : 0.003 0.026 1998 Dihedral : 3.535 15.998 1512 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.09 % Allowed : 15.49 % Favored : 83.42 % 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: 3.76 (0.21), residues: 1368 helix: 3.04 (0.13), residues: 1206 sheet: None (None), residues: 0 loop : -2.43 (0.45), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 5 PHE 0.006 0.001 PHE N 68 TYR 0.018 0.001 TYR K 47 ARG 0.001 0.000 ARG O 80 *********************** 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 325 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 312 time to evaluate : 1.265 Fit side-chains revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8797 (tmtt) cc_final: 0.8414 (tttm) REVERT: B 37 LYS cc_start: 0.8903 (ttmt) cc_final: 0.7580 (tptt) REVERT: B 40 ASP cc_start: 0.8157 (t0) cc_final: 0.7774 (t0) REVERT: B 56 LEU cc_start: 0.9156 (mt) cc_final: 0.8757 (mt) REVERT: B 66 LYS cc_start: 0.8580 (tptp) cc_final: 0.7504 (ttmt) REVERT: C 10 ASP cc_start: 0.8417 (m-30) cc_final: 0.7936 (m-30) REVERT: C 37 LYS cc_start: 0.8964 (ttmt) cc_final: 0.7587 (tptt) REVERT: C 69 LYS cc_start: 0.8869 (tmtt) cc_final: 0.8549 (tttm) REVERT: C 72 ASP cc_start: 0.8977 (m-30) cc_final: 0.8549 (m-30) REVERT: D 10 ASP cc_start: 0.8337 (m-30) cc_final: 0.7695 (m-30) REVERT: D 66 LYS cc_start: 0.8610 (tptp) cc_final: 0.7764 (ttmt) REVERT: D 69 LYS cc_start: 0.8757 (tmtt) cc_final: 0.8469 (tttm) REVERT: E 37 LYS cc_start: 0.9076 (ttmt) cc_final: 0.7898 (tptt) REVERT: E 66 LYS cc_start: 0.8381 (tptp) cc_final: 0.7585 (tppt) REVERT: F 10 ASP cc_start: 0.8311 (m-30) cc_final: 0.7911 (m-30) REVERT: F 37 LYS cc_start: 0.8941 (ttmt) cc_final: 0.7521 (tptt) REVERT: G 10 ASP cc_start: 0.8498 (m-30) cc_final: 0.8254 (m-30) REVERT: H 72 ASP cc_start: 0.9099 (m-30) cc_final: 0.8749 (m-30) REVERT: I 8 TYR cc_start: 0.8623 (t80) cc_final: 0.8238 (t80) REVERT: I 53 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7172 (mt-10) REVERT: I 69 LYS cc_start: 0.8743 (tmtt) cc_final: 0.8257 (tttp) REVERT: J 10 ASP cc_start: 0.8631 (m-30) cc_final: 0.8343 (m-30) REVERT: M 69 LYS cc_start: 0.9053 (tmtt) cc_final: 0.7806 (ttmt) REVERT: N 15 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.7538 (ttpt) REVERT: N 69 LYS cc_start: 0.8913 (tmtt) cc_final: 0.7874 (ttmt) REVERT: O 69 LYS cc_start: 0.9029 (tmtt) cc_final: 0.7923 (ttmt) REVERT: P 54 TYR cc_start: 0.9104 (t80) cc_final: 0.8789 (t80) REVERT: P 69 LYS cc_start: 0.8923 (tmtt) cc_final: 0.7780 (ttmt) REVERT: Q 25 THR cc_start: 0.9035 (m) cc_final: 0.8777 (p) REVERT: Q 32 ASP cc_start: 0.7836 (m-30) cc_final: 0.7459 (m-30) REVERT: Q 69 LYS cc_start: 0.8920 (tmtt) cc_final: 0.7477 (tttt) REVERT: R 69 LYS cc_start: 0.9055 (tmtt) cc_final: 0.7882 (ttmt) outliers start: 13 outliers final: 10 residues processed: 321 average time/residue: 0.2196 time to fit residues: 99.4663 Evaluate side-chains 316 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 305 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain M residue 53 GLU Chi-restraints excluded: chain N residue 15 LYS Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain P residue 49 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 88 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 119 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11214 Z= 0.146 Angle : 0.417 5.624 15264 Z= 0.221 Chirality : 0.034 0.103 1746 Planarity : 0.003 0.030 1998 Dihedral : 3.513 15.197 1512 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.26 % Allowed : 15.82 % 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: 3.79 (0.21), residues: 1368 helix: 3.03 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.83 (0.50), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 5 PHE 0.005 0.001 PHE N 68 TYR 0.020 0.001 TYR K 47 ARG 0.001 0.000 ARG O 80 *********************** 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 324 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 309 time to evaluate : 1.234 Fit side-chains revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8809 (tmtt) cc_final: 0.8415 (tttm) REVERT: B 37 LYS cc_start: 0.8906 (ttmt) cc_final: 0.7564 (tptt) REVERT: B 40 ASP cc_start: 0.8137 (t0) cc_final: 0.7762 (t0) REVERT: B 56 LEU cc_start: 0.9160 (mt) cc_final: 0.8772 (mt) REVERT: B 66 LYS cc_start: 0.8573 (tptp) cc_final: 0.7502 (ttmt) REVERT: C 10 ASP cc_start: 0.8388 (m-30) cc_final: 0.7931 (m-30) REVERT: C 37 LYS cc_start: 0.8953 (ttmt) cc_final: 0.7578 (tptt) REVERT: C 69 LYS cc_start: 0.8841 (tmtt) cc_final: 0.8518 (tttm) REVERT: C 72 ASP cc_start: 0.8972 (m-30) cc_final: 0.8547 (m-30) REVERT: D 10 ASP cc_start: 0.8299 (m-30) cc_final: 0.7712 (m-30) REVERT: D 66 LYS cc_start: 0.8622 (tptp) cc_final: 0.7708 (ttmt) REVERT: D 69 LYS cc_start: 0.8731 (tmtt) cc_final: 0.8446 (tttm) REVERT: E 37 LYS cc_start: 0.9074 (ttmt) cc_final: 0.7896 (tptt) REVERT: E 66 LYS cc_start: 0.8402 (tptp) cc_final: 0.7562 (tppt) REVERT: F 10 ASP cc_start: 0.8291 (m-30) cc_final: 0.7884 (m-30) REVERT: F 37 LYS cc_start: 0.8930 (ttmt) cc_final: 0.7517 (tptt) REVERT: G 10 ASP cc_start: 0.8453 (m-30) cc_final: 0.8206 (m-30) REVERT: H 72 ASP cc_start: 0.9091 (m-30) cc_final: 0.8735 (m-30) REVERT: I 8 TYR cc_start: 0.8579 (t80) cc_final: 0.8185 (t80) REVERT: I 53 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7176 (mt-10) REVERT: I 69 LYS cc_start: 0.8744 (tmtt) cc_final: 0.8250 (tttp) REVERT: J 10 ASP cc_start: 0.8646 (m-30) cc_final: 0.8409 (m-30) REVERT: M 69 LYS cc_start: 0.9049 (tmtt) cc_final: 0.7795 (ttmt) REVERT: N 15 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.7529 (ttpt) REVERT: N 69 LYS cc_start: 0.8913 (tmtt) cc_final: 0.7866 (ttmt) REVERT: O 32 ASP cc_start: 0.7849 (m-30) cc_final: 0.7587 (m-30) REVERT: O 69 LYS cc_start: 0.9030 (tmtt) cc_final: 0.7917 (ttmt) REVERT: P 54 TYR cc_start: 0.9107 (t80) cc_final: 0.8791 (t80) REVERT: P 69 LYS cc_start: 0.8901 (tmtt) cc_final: 0.7709 (ttmt) REVERT: Q 25 THR cc_start: 0.9031 (m) cc_final: 0.8757 (p) REVERT: Q 32 ASP cc_start: 0.7799 (m-30) cc_final: 0.7463 (m-30) REVERT: Q 69 LYS cc_start: 0.8900 (tmtt) cc_final: 0.7471 (tttt) REVERT: R 15 LYS cc_start: 0.8466 (mttp) cc_final: 0.7442 (ttpt) REVERT: R 69 LYS cc_start: 0.9053 (tmtt) cc_final: 0.7882 (ttmt) outliers start: 15 outliers final: 11 residues processed: 318 average time/residue: 0.2186 time to fit residues: 97.8705 Evaluate side-chains 317 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 305 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain M residue 53 GLU Chi-restraints excluded: chain N residue 15 LYS Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain R residue 49 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11214 Z= 0.220 Angle : 0.457 5.005 15264 Z= 0.244 Chirality : 0.035 0.107 1746 Planarity : 0.003 0.021 1998 Dihedral : 3.637 16.972 1512 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.18 % Allowed : 16.33 % Favored : 82.49 % 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: 3.57 (0.21), residues: 1368 helix: 2.88 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.80 (0.50), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 5 PHE 0.007 0.001 PHE O 68 TYR 0.021 0.001 TYR K 47 ARG 0.001 0.000 ARG N 58 ********************** 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 315 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 301 time to evaluate : 1.258 Fit side-chains revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8822 (tmtt) cc_final: 0.8600 (tttm) REVERT: B 37 LYS cc_start: 0.8909 (ttmt) cc_final: 0.7527 (tptt) REVERT: B 40 ASP cc_start: 0.8209 (t0) cc_final: 0.7819 (t0) REVERT: B 56 LEU cc_start: 0.9177 (mt) cc_final: 0.8809 (mt) REVERT: B 66 LYS cc_start: 0.8569 (tptp) cc_final: 0.7463 (ttmt) REVERT: C 10 ASP cc_start: 0.8436 (m-30) cc_final: 0.8187 (m-30) REVERT: C 37 LYS cc_start: 0.8986 (ttmt) cc_final: 0.7596 (tptt) REVERT: C 69 LYS cc_start: 0.8871 (tmtt) cc_final: 0.8555 (tttm) REVERT: C 72 ASP cc_start: 0.9025 (m-30) cc_final: 0.8626 (m-30) REVERT: D 10 ASP cc_start: 0.8386 (m-30) cc_final: 0.7686 (m-30) REVERT: D 66 LYS cc_start: 0.8651 (tptp) cc_final: 0.7684 (tttt) REVERT: D 69 LYS cc_start: 0.8805 (tmtt) cc_final: 0.8490 (tttm) REVERT: E 37 LYS cc_start: 0.9095 (ttmt) cc_final: 0.7885 (tptt) REVERT: E 66 LYS cc_start: 0.8389 (tptp) cc_final: 0.7590 (tppt) REVERT: F 10 ASP cc_start: 0.8346 (m-30) cc_final: 0.7927 (m-30) REVERT: F 37 LYS cc_start: 0.8967 (ttmt) cc_final: 0.7539 (tptt) REVERT: G 10 ASP cc_start: 0.8490 (m-30) cc_final: 0.8272 (m-30) REVERT: H 72 ASP cc_start: 0.9128 (m-30) cc_final: 0.8767 (m-30) REVERT: I 8 TYR cc_start: 0.8658 (t80) cc_final: 0.8323 (t80) REVERT: I 69 LYS cc_start: 0.8758 (tmtt) cc_final: 0.8278 (tttp) REVERT: J 10 ASP cc_start: 0.8618 (m-30) cc_final: 0.8074 (m-30) REVERT: M 69 LYS cc_start: 0.9031 (tmtt) cc_final: 0.7788 (ttmt) REVERT: N 15 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.7498 (ttpt) REVERT: N 69 LYS cc_start: 0.8944 (tmtt) cc_final: 0.7904 (ttmt) REVERT: O 32 ASP cc_start: 0.7831 (m-30) cc_final: 0.7368 (m-30) REVERT: O 69 LYS cc_start: 0.8999 (tmtt) cc_final: 0.7882 (ttmt) REVERT: P 54 TYR cc_start: 0.9116 (t80) cc_final: 0.8807 (t80) REVERT: P 69 LYS cc_start: 0.8908 (tmtt) cc_final: 0.7717 (ttmt) REVERT: Q 25 THR cc_start: 0.9044 (m) cc_final: 0.8735 (p) REVERT: Q 32 ASP cc_start: 0.7791 (m-30) cc_final: 0.7348 (m-30) REVERT: Q 69 LYS cc_start: 0.8932 (tmtt) cc_final: 0.7486 (tttt) REVERT: R 69 LYS cc_start: 0.9056 (tmtt) cc_final: 0.7898 (ttmt) outliers start: 14 outliers final: 13 residues processed: 310 average time/residue: 0.2209 time to fit residues: 96.8774 Evaluate side-chains 310 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 296 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain M residue 53 GLU Chi-restraints excluded: chain N residue 15 LYS Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain R residue 49 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 87 optimal weight: 0.3980 chunk 5 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.091994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.082044 restraints weight = 18706.985| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.80 r_work: 0.2872 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11214 Z= 0.156 Angle : 0.427 4.344 15264 Z= 0.228 Chirality : 0.034 0.103 1746 Planarity : 0.003 0.021 1998 Dihedral : 3.581 15.034 1512 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.93 % Allowed : 16.67 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.78 (0.21), residues: 1368 helix: 3.02 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.75 (0.50), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 5 PHE 0.006 0.001 PHE N 68 TYR 0.018 0.001 TYR K 47 ARG 0.001 0.000 ARG O 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2519.48 seconds wall clock time: 45 minutes 41.65 seconds (2741.65 seconds total)