Starting phenix.real_space_refine on Wed Sep 25 16:15:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofg_20045/09_2024/6ofg_20045.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofg_20045/09_2024/6ofg_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofg_20045/09_2024/6ofg_20045.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofg_20045/09_2024/6ofg_20045.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofg_20045/09_2024/6ofg_20045.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofg_20045/09_2024/6ofg_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-5461/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: 3.38, per 1000 atoms: 0.31 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: 2.98 Conformation dependent library (CDL) restraints added in 1.2 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: 1.08 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: 3.21 Time building geometry restraints manager: 3.44 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: 0.00 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: 0.680 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: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 23.860 Find NCS groups from input model: 0.410 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:12.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.020 ------------------------------------------------------------------------------- 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= 0.480 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 353 time to evaluate : 1.161 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: 0.9622 time to fit residues: 371.0295 Evaluate side-chains 242 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.250 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 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= 0.158 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 *********************** 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 fitting. rotamer outliers: 27 poor density : 268 time to evaluate : 1.244 Fit side-chains REVERT: P 59 ASN cc_start: 0.8261 (OUTLIER) cc_final: 0.7997 (t0) REVERT: Q 25 THR cc_start: 0.8535 (m) cc_final: 0.8271 (p) REVERT: Q 32 ASP cc_start: 0.7710 (m-30) cc_final: 0.7343 (m-30) REVERT: R 11 ASP cc_start: 0.8485 (m-30) cc_final: 0.8276 (m-30) REVERT: K 59 ASN cc_start: 0.8512 (OUTLIER) cc_final: 0.8177 (m-40) REVERT: K 69 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.7759 (tptm) REVERT: L 33 LYS cc_start: 0.8526 (mttt) cc_final: 0.8273 (mttm) REVERT: L 59 ASN cc_start: 0.8286 (OUTLIER) cc_final: 0.8081 (t0) REVERT: N 28 THR cc_start: 0.8823 (m) cc_final: 0.7940 (m) REVERT: N 29 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7361 (mt-10) REVERT: N 32 ASP cc_start: 0.7487 (m-30) cc_final: 0.7172 (m-30) REVERT: H 59 ASN cc_start: 0.8431 (OUTLIER) cc_final: 0.8182 (t0) REVERT: I 53 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7611 (mm-30) REVERT: I 59 ASN cc_start: 0.8334 (OUTLIER) cc_final: 0.7825 (t0) REVERT: J 59 ASN cc_start: 0.8393 (OUTLIER) cc_final: 0.7981 (t0) REVERT: A 37 LYS cc_start: 0.8381 (ttmt) cc_final: 0.7081 (tttp) REVERT: B 72 ASP cc_start: 0.8670 (m-30) cc_final: 0.8460 (m-30) REVERT: C 72 ASP cc_start: 0.8707 (m-30) cc_final: 0.8404 (m-30) REVERT: D 49 SER cc_start: 0.8845 (p) cc_final: 0.8633 (m) REVERT: D 72 ASP cc_start: 0.8701 (m-30) cc_final: 0.8491 (m-30) REVERT: E 15 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8165 (mtpt) REVERT: E 72 ASP cc_start: 0.8879 (m-30) cc_final: 0.8591 (m-30) outliers start: 27 outliers final: 6 residues processed: 271 average time/residue: 0.8890 time to fit residues: 266.0489 Evaluate side-chains 246 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 232 time to evaluate : 1.237 ------------------------------------------------------------------------------- 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 L residue 59 ASN 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 63 optimal weight: 0.0970 chunk 35 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 113 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 91 optimal weight: 0.3980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 E 77 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 11178 Z= 0.129 Angle : 0.422 3.537 15210 Z= 0.233 Chirality : 0.033 0.100 1728 Planarity : 0.003 0.023 1998 Dihedral : 3.788 18.436 1512 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.16 % Allowed : 14.44 % 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: 2.26 (0.21), residues: 1368 helix: 1.98 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.87 (0.49), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 5 PHE 0.004 0.001 PHE K 68 TYR 0.007 0.001 TYR E 57 ARG 0.001 0.000 ARG I 58 *********************** 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 304 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 267 time to evaluate : 1.237 Fit side-chains REVERT: P 15 LYS cc_start: 0.8760 (mtpp) cc_final: 0.8395 (mmtm) REVERT: P 57 TYR cc_start: 0.9053 (OUTLIER) cc_final: 0.8568 (t80) REVERT: P 59 ASN cc_start: 0.8236 (OUTLIER) cc_final: 0.8008 (t0) REVERT: Q 32 ASP cc_start: 0.7705 (m-30) cc_final: 0.7338 (m-30) REVERT: R 11 ASP cc_start: 0.8432 (m-30) cc_final: 0.8198 (m-30) REVERT: K 59 ASN cc_start: 0.8451 (OUTLIER) cc_final: 0.7980 (t0) REVERT: K 69 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.7883 (tptm) REVERT: L 15 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8475 (mmtm) REVERT: L 33 LYS cc_start: 0.8554 (mttt) cc_final: 0.8282 (mttm) REVERT: N 28 THR cc_start: 0.8854 (m) cc_final: 0.8078 (m) REVERT: N 29 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7386 (mt-10) REVERT: N 32 ASP cc_start: 0.7619 (m-30) cc_final: 0.7250 (m-30) REVERT: O 32 ASP cc_start: 0.7771 (m-30) cc_final: 0.7439 (m-30) REVERT: G 72 ASP cc_start: 0.8592 (m-30) cc_final: 0.8360 (m-30) REVERT: H 59 ASN cc_start: 0.8436 (OUTLIER) cc_final: 0.8209 (m-40) REVERT: I 59 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.7854 (t0) REVERT: J 59 ASN cc_start: 0.8389 (OUTLIER) cc_final: 0.8029 (t0) REVERT: J 69 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8343 (tttm) REVERT: A 37 LYS cc_start: 0.8413 (ttmt) cc_final: 0.7121 (tttp) REVERT: B 69 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8223 (tptm) REVERT: B 72 ASP cc_start: 0.8608 (m-30) cc_final: 0.8374 (m-30) REVERT: C 10 ASP cc_start: 0.8844 (m-30) cc_final: 0.8612 (m-30) REVERT: C 72 ASP cc_start: 0.8691 (m-30) cc_final: 0.8416 (m-30) REVERT: E 15 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8138 (mtpt) REVERT: E 59 ASN cc_start: 0.8268 (OUTLIER) cc_final: 0.7831 (t0) REVERT: E 72 ASP cc_start: 0.8880 (m-30) cc_final: 0.8610 (m-30) outliers start: 37 outliers final: 10 residues processed: 284 average time/residue: 0.8813 time to fit residues: 275.9851 Evaluate side-chains 262 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 240 time to evaluate : 1.151 ------------------------------------------------------------------------------- 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 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 H residue 59 ASN Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain J residue 32 ASP Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain E residue 15 LYS Chi-restraints excluded: chain E residue 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 113 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 109 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 D 77 GLN E 77 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2984 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= 0.160 Angle : 0.433 3.364 15210 Z= 0.237 Chirality : 0.034 0.104 1728 Planarity : 0.003 0.021 1998 Dihedral : 3.696 17.418 1512 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.59 % Allowed : 13.59 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.32 (0.21), residues: 1368 helix: 2.68 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.58 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 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 *********************** 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 296 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 254 time to evaluate : 1.296 Fit side-chains REVERT: P 15 LYS cc_start: 0.8743 (mtpp) cc_final: 0.8400 (mmtm) REVERT: P 57 TYR cc_start: 0.9106 (OUTLIER) cc_final: 0.8304 (t80) REVERT: P 59 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.8034 (t0) REVERT: Q 32 ASP cc_start: 0.7737 (m-30) cc_final: 0.7384 (m-30) REVERT: R 11 ASP cc_start: 0.8460 (m-30) cc_final: 0.8246 (m-30) REVERT: K 15 LYS cc_start: 0.8666 (ttmm) cc_final: 0.8047 (tttt) REVERT: K 53 GLU cc_start: 0.8411 (mm-30) cc_final: 0.7989 (mm-30) REVERT: K 59 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.7982 (t0) REVERT: K 69 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.7867 (tptm) REVERT: L 33 LYS cc_start: 0.8561 (mttt) cc_final: 0.8289 (mttm) REVERT: M 69 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.7913 (tptm) REVERT: N 28 THR cc_start: 0.8859 (m) cc_final: 0.8359 (m) REVERT: N 32 ASP cc_start: 0.7632 (m-30) cc_final: 0.7033 (m-30) REVERT: N 59 ASN cc_start: 0.8370 (t0) cc_final: 0.8089 (t0) REVERT: O 32 ASP cc_start: 0.7773 (m-30) cc_final: 0.7456 (m-30) REVERT: F 69 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8004 (tttm) REVERT: G 72 ASP cc_start: 0.8692 (m-30) cc_final: 0.8436 (m-30) REVERT: H 53 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8045 (mm-30) REVERT: H 59 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.8256 (m-40) REVERT: I 59 ASN cc_start: 0.8240 (OUTLIER) cc_final: 0.7760 (t0) REVERT: I 77 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7827 (tt0) REVERT: J 59 ASN cc_start: 0.8407 (OUTLIER) cc_final: 0.8063 (t0) REVERT: J 69 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8462 (tttm) REVERT: A 37 LYS cc_start: 0.8462 (ttmt) cc_final: 0.7167 (tttp) REVERT: B 69 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8273 (tptm) REVERT: C 18 THR cc_start: 0.8539 (p) cc_final: 0.8300 (m) REVERT: C 72 ASP cc_start: 0.8719 (m-30) cc_final: 0.8434 (m-30) REVERT: E 15 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7607 (mppt) REVERT: E 59 ASN cc_start: 0.8212 (OUTLIER) cc_final: 0.7787 (t0) REVERT: E 72 ASP cc_start: 0.8794 (m-30) cc_final: 0.8582 (m-30) outliers start: 42 outliers final: 11 residues processed: 279 average time/residue: 0.9714 time to fit residues: 297.1084 Evaluate side-chains 271 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 246 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 57 TYR Chi-restraints excluded: chain P residue 59 ASN Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain K residue 59 ASN Chi-restraints excluded: chain K residue 69 LYS Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 69 LYS Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain H residue 59 ASN 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 101 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3104 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= 0.147 Angle : 0.420 3.360 15210 Z= 0.230 Chirality : 0.034 0.102 1728 Planarity : 0.003 0.021 1998 Dihedral : 3.568 16.023 1512 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.93 % Allowed : 13.25 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.89 (0.22), residues: 1368 helix: 3.07 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.53 (0.52), 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 0.010 0.001 TYR J 57 ARG 0.001 0.000 ARG J 58 *********************** 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 fitting. rotamer outliers: 46 poor density : 255 time to evaluate : 1.250 Fit side-chains REVERT: P 15 LYS cc_start: 0.8707 (mtpp) cc_final: 0.8371 (mmtm) REVERT: P 57 TYR cc_start: 0.9108 (OUTLIER) cc_final: 0.8309 (t80) REVERT: P 59 ASN cc_start: 0.8332 (OUTLIER) cc_final: 0.8124 (t0) REVERT: Q 32 ASP cc_start: 0.7782 (m-30) cc_final: 0.7441 (m-30) REVERT: R 11 ASP cc_start: 0.8456 (m-30) cc_final: 0.8229 (m-30) REVERT: K 53 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7929 (mm-30) REVERT: K 59 ASN cc_start: 0.8450 (OUTLIER) cc_final: 0.7972 (t0) REVERT: K 69 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.7797 (tptm) REVERT: L 33 LYS cc_start: 0.8567 (mttt) cc_final: 0.8294 (mttm) REVERT: M 69 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.7855 (tptm) REVERT: N 28 THR cc_start: 0.8831 (m) cc_final: 0.7974 (m) REVERT: N 29 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7425 (mt-10) REVERT: N 32 ASP cc_start: 0.7620 (m-30) cc_final: 0.7235 (m-30) REVERT: N 59 ASN cc_start: 0.8364 (t0) cc_final: 0.8093 (t0) REVERT: N 69 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.7234 (tptm) REVERT: O 32 ASP cc_start: 0.7762 (m-30) cc_final: 0.7392 (m-30) REVERT: O 69 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8139 (tptm) REVERT: F 69 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.7982 (tttm) REVERT: G 72 ASP cc_start: 0.8692 (m-30) cc_final: 0.8436 (m-30) REVERT: H 53 GLU cc_start: 0.8321 (mm-30) cc_final: 0.8118 (mm-30) REVERT: H 69 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.7943 (tttm) REVERT: I 15 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8060 (tttt) REVERT: I 59 ASN cc_start: 0.8270 (OUTLIER) cc_final: 0.7807 (t0) REVERT: I 72 ASP cc_start: 0.8013 (m-30) cc_final: 0.7677 (m-30) REVERT: J 59 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.8071 (t0) REVERT: J 69 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8467 (tttm) REVERT: A 32 ASP cc_start: 0.7472 (m-30) cc_final: 0.6991 (m-30) REVERT: A 37 LYS cc_start: 0.8431 (ttmt) cc_final: 0.7158 (tttp) REVERT: B 69 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8242 (tptm) REVERT: C 18 THR cc_start: 0.8515 (p) cc_final: 0.8311 (m) REVERT: C 72 ASP cc_start: 0.8716 (m-30) cc_final: 0.8440 (m-30) REVERT: E 15 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7626 (mppt) REVERT: E 59 ASN cc_start: 0.8208 (OUTLIER) cc_final: 0.7810 (t0) outliers start: 46 outliers final: 14 residues processed: 284 average time/residue: 0.9014 time to fit residues: 281.7188 Evaluate side-chains 274 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 244 time to evaluate : 1.271 ------------------------------------------------------------------------------- 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 Q residue 59 ASN Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain K residue 59 ASN Chi-restraints excluded: chain K residue 69 LYS Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 33 LYS Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 69 LYS Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 69 LYS Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain 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 15 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 40 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 11178 Z= 0.197 Angle : 0.455 3.599 15210 Z= 0.246 Chirality : 0.035 0.104 1728 Planarity : 0.003 0.020 1998 Dihedral : 3.637 15.303 1512 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.76 % Allowed : 13.50 % 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: 4.06 (0.22), residues: 1368 helix: 3.19 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.56 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP O 5 PHE 0.007 0.001 PHE K 68 TYR 0.012 0.001 TYR H 57 ARG 0.002 0.000 ARG J 58 *********************** 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 296 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 252 time to evaluate : 1.283 Fit side-chains revert: symmetry clash REVERT: P 15 LYS cc_start: 0.8720 (mtpp) cc_final: 0.8371 (mmtm) REVERT: P 32 ASP cc_start: 0.7874 (m-30) cc_final: 0.7228 (m-30) REVERT: P 57 TYR cc_start: 0.9120 (OUTLIER) cc_final: 0.8137 (t80) REVERT: Q 32 ASP cc_start: 0.7780 (m-30) cc_final: 0.7432 (m-30) REVERT: K 15 LYS cc_start: 0.8722 (ttmm) cc_final: 0.8049 (tttt) REVERT: K 53 GLU cc_start: 0.8400 (mm-30) cc_final: 0.7971 (mm-30) REVERT: K 59 ASN cc_start: 0.8449 (OUTLIER) cc_final: 0.8127 (m-40) REVERT: K 69 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.7891 (tptm) REVERT: L 33 LYS cc_start: 0.8571 (mttt) cc_final: 0.8331 (mttm) REVERT: M 69 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.7862 (tptm) REVERT: N 28 THR cc_start: 0.8849 (m) cc_final: 0.7965 (m) REVERT: N 29 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7412 (mt-10) REVERT: N 32 ASP cc_start: 0.7570 (m-30) cc_final: 0.7164 (m-30) REVERT: N 59 ASN cc_start: 0.8398 (t0) cc_final: 0.8139 (t0) REVERT: N 69 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.7203 (tptm) REVERT: O 32 ASP cc_start: 0.7784 (m-30) cc_final: 0.7486 (m-30) REVERT: O 69 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8119 (tptm) REVERT: F 69 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8010 (tttm) REVERT: G 33 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8353 (mtmt) REVERT: G 72 ASP cc_start: 0.8672 (m-30) cc_final: 0.8410 (m-30) REVERT: H 53 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7897 (mm-30) REVERT: H 59 ASN cc_start: 0.8441 (m-40) cc_final: 0.8208 (t0) REVERT: H 69 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.7932 (tttm) REVERT: I 15 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8251 (mttt) REVERT: I 59 ASN cc_start: 0.8245 (OUTLIER) cc_final: 0.7798 (t0) REVERT: I 72 ASP cc_start: 0.8011 (m-30) cc_final: 0.7666 (m-30) REVERT: J 59 ASN cc_start: 0.8393 (OUTLIER) cc_final: 0.8060 (t0) REVERT: J 69 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8205 (tptm) REVERT: A 37 LYS cc_start: 0.8446 (ttmt) cc_final: 0.7148 (tttp) REVERT: B 69 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8314 (tptm) REVERT: C 18 THR cc_start: 0.8601 (p) cc_final: 0.8377 (m) REVERT: C 72 ASP cc_start: 0.8730 (m-30) cc_final: 0.8434 (m-30) REVERT: E 59 ASN cc_start: 0.8218 (OUTLIER) cc_final: 0.7810 (t0) outliers start: 44 outliers final: 15 residues processed: 279 average time/residue: 0.9671 time to fit residues: 295.3270 Evaluate side-chains 274 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 244 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 57 TYR Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain Q residue 59 ASN Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain K residue 59 ASN Chi-restraints excluded: chain K residue 69 LYS Chi-restraints excluded: chain L residue 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 G residue 33 LYS Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain I residue 15 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 69 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 13 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 77 GLN L 77 GLN G 77 GLN J 77 GLN D 77 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3237 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= 0.147 Angle : 0.425 3.501 15210 Z= 0.231 Chirality : 0.033 0.100 1728 Planarity : 0.003 0.022 1998 Dihedral : 3.487 14.483 1512 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.50 % Allowed : 13.68 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.36 (0.22), residues: 1368 helix: 3.40 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.60 (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 0.012 0.001 TYR J 57 ARG 0.006 0.000 ARG H 80 *********************** 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 299 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 258 time to evaluate : 1.310 Fit side-chains REVERT: P 15 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8336 (mmtm) REVERT: P 57 TYR cc_start: 0.9105 (OUTLIER) cc_final: 0.8192 (t80) REVERT: Q 32 ASP cc_start: 0.7778 (m-30) cc_final: 0.7415 (m-30) REVERT: K 53 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7964 (mm-30) REVERT: K 59 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.7995 (t0) REVERT: K 69 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.7845 (tptm) REVERT: L 33 LYS cc_start: 0.8547 (mttt) cc_final: 0.8301 (mttm) REVERT: M 69 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.7857 (tptm) REVERT: N 29 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7384 (mt-10) REVERT: N 32 ASP cc_start: 0.7631 (m-30) cc_final: 0.7112 (m-30) REVERT: N 59 ASN cc_start: 0.8394 (t0) cc_final: 0.8117 (t0) REVERT: N 69 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.7221 (tptm) REVERT: O 32 ASP cc_start: 0.7781 (m-30) cc_final: 0.7476 (m-30) REVERT: O 69 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8150 (tptm) REVERT: F 69 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.7940 (tttm) REVERT: G 72 ASP cc_start: 0.8675 (m-30) cc_final: 0.8410 (m-30) REVERT: H 53 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7925 (mm-30) REVERT: H 69 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.7916 (tttm) REVERT: I 15 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8064 (tttt) REVERT: I 59 ASN cc_start: 0.8253 (OUTLIER) cc_final: 0.7859 (t0) REVERT: I 72 ASP cc_start: 0.8021 (m-30) cc_final: 0.7648 (m-30) REVERT: J 59 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.8104 (t0) REVERT: J 69 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8218 (tptm) REVERT: A 37 LYS cc_start: 0.8437 (ttmt) cc_final: 0.7141 (tttp) REVERT: B 69 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8225 (tptm) REVERT: C 72 ASP cc_start: 0.8697 (m-30) cc_final: 0.8425 (m-30) REVERT: E 59 ASN cc_start: 0.8228 (OUTLIER) cc_final: 0.7807 (t0) outliers start: 41 outliers final: 16 residues processed: 286 average time/residue: 0.9535 time to fit residues: 298.9565 Evaluate side-chains 275 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 244 time to evaluate : 1.215 ------------------------------------------------------------------------------- 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 25 THR Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain Q residue 59 ASN Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain K residue 59 ASN Chi-restraints excluded: chain K residue 69 LYS Chi-restraints excluded: chain L residue 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 15 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 59 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 116 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 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 ** J 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 GLN D 77 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3289 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= 0.150 Angle : 0.431 3.612 15210 Z= 0.234 Chirality : 0.033 0.100 1728 Planarity : 0.003 0.025 1998 Dihedral : 3.419 13.692 1512 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.68 % Allowed : 13.93 % 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: 4.49 (0.22), residues: 1368 helix: 3.50 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.62 (0.51), 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 0.013 0.001 TYR H 57 ARG 0.007 0.000 ARG H 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 293 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 250 time to evaluate : 1.159 Fit side-chains REVERT: P 15 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8342 (mmtm) REVERT: P 57 TYR cc_start: 0.9108 (OUTLIER) cc_final: 0.8203 (t80) REVERT: Q 32 ASP cc_start: 0.7781 (m-30) cc_final: 0.7443 (m-30) REVERT: K 53 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7934 (mm-30) REVERT: K 59 ASN cc_start: 0.8441 (OUTLIER) cc_final: 0.8000 (t0) REVERT: K 69 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.7835 (tptm) REVERT: L 33 LYS cc_start: 0.8550 (mttt) cc_final: 0.8304 (mttm) REVERT: M 69 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.7834 (tptm) REVERT: N 29 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7439 (mt-10) REVERT: N 32 ASP cc_start: 0.7633 (m-30) cc_final: 0.7318 (m-30) REVERT: N 59 ASN cc_start: 0.8398 (t0) cc_final: 0.8124 (t0) REVERT: N 69 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.7226 (tptm) REVERT: O 32 ASP cc_start: 0.7786 (m-30) cc_final: 0.7497 (m-30) REVERT: O 69 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8159 (tptm) REVERT: F 10 ASP cc_start: 0.8885 (m-30) cc_final: 0.8580 (m-30) REVERT: F 69 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.7927 (tttm) REVERT: G 72 ASP cc_start: 0.8671 (m-30) cc_final: 0.8403 (m-30) REVERT: H 53 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7919 (mm-30) REVERT: H 69 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.7911 (tttm) REVERT: I 59 ASN cc_start: 0.8260 (OUTLIER) cc_final: 0.7860 (t0) REVERT: I 72 ASP cc_start: 0.8016 (m-30) cc_final: 0.7672 (m-30) REVERT: J 59 ASN cc_start: 0.8429 (OUTLIER) cc_final: 0.8100 (t0) REVERT: J 69 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8200 (tptm) REVERT: A 32 ASP cc_start: 0.7431 (m-30) cc_final: 0.6940 (m-30) REVERT: A 37 LYS cc_start: 0.8442 (ttmt) cc_final: 0.7154 (tttp) REVERT: B 69 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8212 (tptm) REVERT: C 72 ASP cc_start: 0.8720 (m-30) cc_final: 0.8447 (m-30) REVERT: E 53 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7787 (tp30) REVERT: E 59 ASN cc_start: 0.8230 (OUTLIER) cc_final: 0.7847 (t0) outliers start: 43 outliers final: 17 residues processed: 277 average time/residue: 0.9571 time to fit residues: 290.4862 Evaluate side-chains 272 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 241 time to evaluate : 1.269 ------------------------------------------------------------------------------- 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 25 THR Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain Q residue 59 ASN Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain K residue 15 LYS 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 B residue 57 TYR Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain E residue 59 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 102 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 112 optimal weight: 0.2980 chunk 74 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 77 GLN L 77 GLN G 77 GLN J 77 GLN D 77 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 11178 Z= 0.177 Angle : 0.451 4.001 15210 Z= 0.244 Chirality : 0.034 0.104 1728 Planarity : 0.003 0.025 1998 Dihedral : 3.438 12.984 1512 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.33 % Allowed : 14.62 % Favored : 82.05 % 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: 4.47 (0.22), residues: 1368 helix: 3.49 (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 0.006 0.001 TRP O 5 PHE 0.006 0.001 PHE K 68 TYR 0.011 0.001 TYR C 57 ARG 0.007 0.000 ARG H 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 290 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 251 time to evaluate : 1.292 Fit side-chains REVERT: P 15 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8338 (mmtm) REVERT: P 57 TYR cc_start: 0.9113 (OUTLIER) cc_final: 0.8222 (t80) REVERT: Q 32 ASP cc_start: 0.7777 (m-30) cc_final: 0.7436 (m-30) REVERT: K 53 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7934 (mm-30) REVERT: K 59 ASN cc_start: 0.8440 (OUTLIER) cc_final: 0.8091 (m-40) REVERT: K 69 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.7863 (tptm) REVERT: L 33 LYS cc_start: 0.8554 (mttt) cc_final: 0.8311 (mttm) REVERT: M 69 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.7842 (tptm) REVERT: N 29 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7433 (mt-10) REVERT: N 32 ASP cc_start: 0.7646 (m-30) cc_final: 0.7341 (m-30) REVERT: N 59 ASN cc_start: 0.8417 (t0) cc_final: 0.8141 (t0) REVERT: N 69 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.7229 (tptm) REVERT: O 32 ASP cc_start: 0.7788 (m-30) cc_final: 0.7487 (m-30) REVERT: O 69 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8151 (tptm) REVERT: F 10 ASP cc_start: 0.8899 (m-30) cc_final: 0.8584 (m-30) REVERT: F 69 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8049 (tttm) REVERT: G 72 ASP cc_start: 0.8673 (m-30) cc_final: 0.8411 (m-30) REVERT: H 53 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7884 (mm-30) REVERT: H 69 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.7916 (tttm) REVERT: I 59 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.7843 (t0) REVERT: I 72 ASP cc_start: 0.8013 (m-30) cc_final: 0.7671 (m-30) REVERT: J 59 ASN cc_start: 0.8427 (OUTLIER) cc_final: 0.8088 (t0) REVERT: J 69 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8192 (tptm) REVERT: A 32 ASP cc_start: 0.7439 (m-30) cc_final: 0.6897 (m-30) REVERT: A 37 LYS cc_start: 0.8483 (ttmt) cc_final: 0.7201 (tttp) REVERT: B 69 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8261 (tptm) REVERT: C 72 ASP cc_start: 0.8738 (m-30) cc_final: 0.8452 (m-30) REVERT: D 32 ASP cc_start: 0.7823 (m-30) cc_final: 0.7231 (m-30) REVERT: E 53 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7850 (tp30) REVERT: E 59 ASN cc_start: 0.8242 (OUTLIER) cc_final: 0.7846 (t0) outliers start: 39 outliers final: 18 residues processed: 277 average time/residue: 0.9485 time to fit residues: 287.7008 Evaluate side-chains 278 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 246 time to evaluate : 1.230 ------------------------------------------------------------------------------- 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 25 THR Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain Q residue 59 ASN Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain K residue 15 LYS Chi-restraints excluded: chain K residue 59 ASN Chi-restraints excluded: chain K residue 69 LYS Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 33 LYS Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 69 LYS Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 69 LYS Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain J residue 32 ASP Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain B residue 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 73 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 125 optimal weight: 0.8980 chunk 115 optimal weight: 0.5980 chunk 99 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 GLN A 77 GLN D 77 GLN E 77 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11178 Z= 0.148 Angle : 0.436 4.059 15210 Z= 0.237 Chirality : 0.033 0.114 1728 Planarity : 0.003 0.029 1998 Dihedral : 3.361 12.619 1512 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % 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: 4.62 (0.22), residues: 1368 helix: 3.59 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.63 (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 O 68 TYR 0.013 0.001 TYR H 57 ARG 0.007 0.000 ARG H 80 ********************** 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 280 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 246 time to evaluate : 1.262 Fit side-chains REVERT: P 15 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8322 (mmtm) REVERT: P 57 TYR cc_start: 0.9109 (OUTLIER) cc_final: 0.8206 (t80) REVERT: Q 32 ASP cc_start: 0.7779 (m-30) cc_final: 0.7432 (m-30) REVERT: K 53 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7936 (mm-30) REVERT: K 59 ASN cc_start: 0.8446 (OUTLIER) cc_final: 0.8022 (t0) REVERT: K 69 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.7818 (tptm) REVERT: L 33 LYS cc_start: 0.8559 (mttt) cc_final: 0.8317 (mttm) REVERT: M 69 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.7827 (tptm) REVERT: N 29 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7425 (mt-10) REVERT: N 32 ASP cc_start: 0.7650 (m-30) cc_final: 0.7335 (m-30) REVERT: N 59 ASN cc_start: 0.8396 (t0) cc_final: 0.8128 (t0) REVERT: N 69 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.7221 (tptm) REVERT: O 32 ASP cc_start: 0.7789 (m-30) cc_final: 0.7487 (m-30) REVERT: O 69 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8151 (tptm) REVERT: F 10 ASP cc_start: 0.8878 (m-30) cc_final: 0.8571 (m-30) REVERT: F 69 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8015 (tttm) REVERT: G 33 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8359 (mtmt) REVERT: G 72 ASP cc_start: 0.8582 (m-30) cc_final: 0.8367 (m-30) REVERT: H 53 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7857 (mm-30) REVERT: H 69 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.7908 (tttm) REVERT: I 59 ASN cc_start: 0.8246 (OUTLIER) cc_final: 0.7872 (t0) REVERT: I 72 ASP cc_start: 0.8014 (m-30) cc_final: 0.7666 (m-30) REVERT: J 59 ASN cc_start: 0.8425 (OUTLIER) cc_final: 0.8098 (t0) REVERT: J 69 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8202 (tptm) REVERT: A 32 ASP cc_start: 0.7454 (m-30) cc_final: 0.6986 (m-30) REVERT: A 37 LYS cc_start: 0.8454 (ttmt) cc_final: 0.7170 (tttp) REVERT: B 69 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8211 (tptm) REVERT: C 72 ASP cc_start: 0.8713 (m-30) cc_final: 0.8437 (m-30) REVERT: D 22 ASN cc_start: 0.7953 (p0) cc_final: 0.7096 (p0) REVERT: D 32 ASP cc_start: 0.7815 (m-30) cc_final: 0.7224 (m-30) REVERT: E 22 ASN cc_start: 0.7907 (p0) cc_final: 0.7528 (p0) REVERT: E 53 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7844 (tp30) REVERT: E 59 ASN cc_start: 0.8228 (OUTLIER) cc_final: 0.7867 (t0) outliers start: 34 outliers final: 16 residues processed: 267 average time/residue: 0.9537 time to fit residues: 278.8597 Evaluate side-chains 272 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 241 time to evaluate : 1.651 ------------------------------------------------------------------------------- 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 25 THR Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain Q residue 59 ASN Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain K residue 59 ASN Chi-restraints excluded: chain K residue 69 LYS Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 33 LYS Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 69 LYS Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 69 LYS Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain 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 30 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 87 optimal weight: 0.0980 chunk 5 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3331 r_free = 0.3331 target = 0.110062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.094494 restraints weight = 15622.338| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.71 r_work: 0.2982 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11178 Z= 0.151 Angle : 0.440 4.446 15210 Z= 0.239 Chirality : 0.033 0.107 1728 Planarity : 0.003 0.028 1998 Dihedral : 3.347 13.301 1512 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.08 % Allowed : 15.47 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.65 (0.22), residues: 1368 helix: 3.61 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.67 (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 R 68 TYR 0.013 0.001 TYR H 57 ARG 0.007 0.000 ARG H 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4574.70 seconds wall clock time: 80 minutes 46.86 seconds (4846.86 seconds total)