Starting phenix.real_space_refine on Tue Aug 4 16:00:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/24um_69827/08_2026/24um_69827.cif Found real_map, /net/cci-nas-00/data/ceres_data/24um_69827/08_2026/24um_69827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/24um_69827/08_2026/24um_69827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/24um_69827/08_2026/24um_69827.map" model { file = "/net/cci-nas-00/data/ceres_data/24um_69827/08_2026/24um_69827.cif" } default_model = "/net/cci-nas-00/data/ceres_data/24um_69827/08_2026/24um_69827.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.002 sd= 0.006 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 2980 2.51 5 N 800 2.21 5 O 800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4580 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 229 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "B" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 229 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Restraints were copied for chains: C, E, G, I, K, M, O, Q, S, D, F, H, J, L, N, P, R, T Time building chain proxies: 0.77, per 1000 atoms: 0.17 Number of scatterers: 4580 At special positions: 0 Unit cell: (88.54, 135.14, 43.804, 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 800 8.00 N 800 7.00 C 2980 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.34 Conformation dependent library (CDL) restraints added in 144.3 milliseconds 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1000 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 46.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 13 removed outlier: 6.594A pdb=" N TRP A 7 " --> pdb=" O GLN E 8 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL E 10 " --> pdb=" O TRP A 7 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLN A 9 " --> pdb=" O VAL E 10 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ASN E 12 " --> pdb=" O GLN A 9 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU A 11 " --> pdb=" O ASN E 12 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TRP E 7 " --> pdb=" O GLN I 8 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL I 10 " --> pdb=" O TRP E 7 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLN E 9 " --> pdb=" O VAL I 10 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ASN I 12 " --> pdb=" O GLN E 9 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU E 11 " --> pdb=" O ASN I 12 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TRP I 7 " --> pdb=" O GLN M 8 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL M 10 " --> pdb=" O TRP I 7 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLN I 9 " --> pdb=" O VAL M 10 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ASN M 12 " --> pdb=" O GLN I 9 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU I 11 " --> pdb=" O ASN M 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TRP M 7 " --> pdb=" O GLN Q 8 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL Q 10 " --> pdb=" O TRP M 7 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLN M 9 " --> pdb=" O VAL Q 10 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ASN Q 12 " --> pdb=" O GLN M 9 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU M 11 " --> pdb=" O ASN Q 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 21 Processing sheet with id=AA3, first strand: chain 'A' and resid 24 through 32 removed outlier: 6.365A pdb=" N HIS A 24 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N GLU E 27 " --> pdb=" O HIS A 24 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLN A 26 " --> pdb=" O GLU E 27 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N LEU E 29 " --> pdb=" O GLN A 26 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL A 28 " --> pdb=" O LEU E 29 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ARG E 31 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE A 30 " --> pdb=" O ARG E 31 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N HIS E 24 " --> pdb=" O GLY I 25 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N GLU I 27 " --> pdb=" O HIS E 24 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLN E 26 " --> pdb=" O GLU I 27 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N LEU I 29 " --> pdb=" O GLN E 26 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL E 28 " --> pdb=" O LEU I 29 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ARG I 31 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE E 30 " --> pdb=" O ARG I 31 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N HIS I 24 " --> pdb=" O GLY M 25 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N GLU M 27 " --> pdb=" O HIS I 24 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLN I 26 " --> pdb=" O GLU M 27 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N LEU M 29 " --> pdb=" O GLN I 26 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL I 28 " --> pdb=" O LEU M 29 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ARG M 31 " --> pdb=" O VAL I 28 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE I 30 " --> pdb=" O ARG M 31 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N HIS M 24 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N GLU Q 27 " --> pdb=" O HIS M 24 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN M 26 " --> pdb=" O GLU Q 27 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N LEU Q 29 " --> pdb=" O GLN M 26 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL M 28 " --> pdb=" O LEU Q 29 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ARG Q 31 " --> pdb=" O VAL M 28 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE M 30 " --> pdb=" O ARG Q 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 8 through 10 removed outlier: 6.491A pdb=" N GLN B 9 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLN F 9 " --> pdb=" O VAL J 10 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLN J 9 " --> pdb=" O VAL N 10 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLN N 9 " --> pdb=" O VAL R 10 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 20 through 22 Processing sheet with id=AA6, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.385A pdb=" N GLU B 27 " --> pdb=" O VAL F 28 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLU F 27 " --> pdb=" O VAL J 28 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLU J 27 " --> pdb=" O VAL N 28 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLU N 27 " --> pdb=" O VAL R 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 31 through 32 removed outlier: 6.470A pdb=" N ARG B 31 " --> pdb=" O LEU F 32 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ARG F 31 " --> pdb=" O LEU J 32 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ARG J 31 " --> pdb=" O LEU N 32 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ARG N 31 " --> pdb=" O LEU R 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 7 through 13 removed outlier: 6.595A pdb=" N TRP C 7 " --> pdb=" O GLN G 8 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL G 10 " --> pdb=" O TRP C 7 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLN C 9 " --> pdb=" O VAL G 10 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ASN G 12 " --> pdb=" O GLN C 9 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU C 11 " --> pdb=" O ASN G 12 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TRP G 7 " --> pdb=" O GLN K 8 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL K 10 " --> pdb=" O TRP G 7 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLN G 9 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ASN K 12 " --> pdb=" O GLN G 9 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU G 11 " --> pdb=" O ASN K 12 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TRP K 7 " --> pdb=" O GLN O 8 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N VAL O 10 " --> pdb=" O TRP K 7 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLN K 9 " --> pdb=" O VAL O 10 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ASN O 12 " --> pdb=" O GLN K 9 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU K 11 " --> pdb=" O ASN O 12 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TRP O 7 " --> pdb=" O GLN S 8 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL S 10 " --> pdb=" O TRP O 7 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLN O 9 " --> pdb=" O VAL S 10 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ASN S 12 " --> pdb=" O GLN O 9 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU O 11 " --> pdb=" O ASN S 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 16 through 21 Processing sheet with id=AB1, first strand: chain 'C' and resid 24 through 32 removed outlier: 6.365A pdb=" N HIS C 24 " --> pdb=" O GLY G 25 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N GLU G 27 " --> pdb=" O HIS C 24 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLN C 26 " --> pdb=" O GLU G 27 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N LEU G 29 " --> pdb=" O GLN C 26 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL C 28 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ARG G 31 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE C 30 " --> pdb=" O ARG G 31 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N HIS G 24 " --> pdb=" O GLY K 25 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N GLU K 27 " --> pdb=" O HIS G 24 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLN G 26 " --> pdb=" O GLU K 27 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N LEU K 29 " --> pdb=" O GLN G 26 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL G 28 " --> pdb=" O LEU K 29 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ARG K 31 " --> pdb=" O VAL G 28 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE G 30 " --> pdb=" O ARG K 31 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N HIS K 24 " --> pdb=" O GLY O 25 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N GLU O 27 " --> pdb=" O HIS K 24 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN K 26 " --> pdb=" O GLU O 27 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N LEU O 29 " --> pdb=" O GLN K 26 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL K 28 " --> pdb=" O LEU O 29 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ARG O 31 " --> pdb=" O VAL K 28 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE K 30 " --> pdb=" O ARG O 31 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N HIS O 24 " --> pdb=" O GLY S 25 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N GLU S 27 " --> pdb=" O HIS O 24 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN O 26 " --> pdb=" O GLU S 27 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N LEU S 29 " --> pdb=" O GLN O 26 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL O 28 " --> pdb=" O LEU S 29 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ARG S 31 " --> pdb=" O VAL O 28 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE O 30 " --> pdb=" O ARG S 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 8 through 10 removed outlier: 6.491A pdb=" N GLN D 9 " --> pdb=" O VAL H 10 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLN H 9 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLN L 9 " --> pdb=" O VAL P 10 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLN P 9 " --> pdb=" O VAL T 10 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 20 through 22 Processing sheet with id=AB4, first strand: chain 'D' and resid 26 through 28 removed outlier: 6.385A pdb=" N GLU D 27 " --> pdb=" O VAL H 28 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLU H 27 " --> pdb=" O VAL L 28 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLU L 27 " --> pdb=" O VAL P 28 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLU P 27 " --> pdb=" O VAL T 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 31 through 32 removed outlier: 6.470A pdb=" N ARG D 31 " --> pdb=" O LEU H 32 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ARG H 31 " --> pdb=" O LEU L 32 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ARG L 31 " --> pdb=" O LEU P 32 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ARG P 31 " --> pdb=" O LEU T 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 56 hydrogen bonds defined for protein. 168 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: 0.60 Time building geometry restraints manager: 0.47 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: 800 1.29 - 1.35: 727 1.35 - 1.42: 533 1.42 - 1.48: 620 1.48 - 1.55: 2000 Bond restraints: 4680 Sorted by residual: bond pdb=" CB LEU N 29 " pdb=" CG LEU N 29 " ideal model delta sigma weight residual 1.530 1.546 -0.016 2.00e-02 2.50e+03 6.44e-01 bond pdb=" CB LEU B 29 " pdb=" CG LEU B 29 " ideal model delta sigma weight residual 1.530 1.546 -0.016 2.00e-02 2.50e+03 6.42e-01 bond pdb=" CB LEU J 29 " pdb=" CG LEU J 29 " ideal model delta sigma weight residual 1.530 1.546 -0.016 2.00e-02 2.50e+03 6.37e-01 bond pdb=" CB LEU D 29 " pdb=" CG LEU D 29 " ideal model delta sigma weight residual 1.530 1.546 -0.016 2.00e-02 2.50e+03 6.14e-01 bond pdb=" CB LEU H 29 " pdb=" CG LEU H 29 " ideal model delta sigma weight residual 1.530 1.545 -0.015 2.00e-02 2.50e+03 5.86e-01 ... (remaining 4675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 6206 1.95 - 3.90: 94 3.90 - 5.85: 20 5.85 - 7.80: 10 7.80 - 9.76: 10 Bond angle restraints: 6340 Sorted by residual: angle pdb=" CA LEU L 29 " pdb=" CB LEU L 29 " pdb=" CG LEU L 29 " ideal model delta sigma weight residual 116.30 126.06 -9.76 3.50e+00 8.16e-02 7.77e+00 angle pdb=" CA LEU T 29 " pdb=" CB LEU T 29 " pdb=" CG LEU T 29 " ideal model delta sigma weight residual 116.30 126.05 -9.75 3.50e+00 8.16e-02 7.76e+00 angle pdb=" CA LEU J 29 " pdb=" CB LEU J 29 " pdb=" CG LEU J 29 " ideal model delta sigma weight residual 116.30 126.04 -9.74 3.50e+00 8.16e-02 7.75e+00 angle pdb=" CA LEU B 29 " pdb=" CB LEU B 29 " pdb=" CG LEU B 29 " ideal model delta sigma weight residual 116.30 126.03 -9.73 3.50e+00 8.16e-02 7.72e+00 angle pdb=" CA LEU R 29 " pdb=" CB LEU R 29 " pdb=" CG LEU R 29 " ideal model delta sigma weight residual 116.30 126.02 -9.72 3.50e+00 8.16e-02 7.72e+00 ... (remaining 6335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 2120 17.96 - 35.92: 329 35.92 - 53.88: 131 53.88 - 71.84: 10 71.84 - 89.80: 10 Dihedral angle restraints: 2600 sinusoidal: 1060 harmonic: 1540 Sorted by residual: dihedral pdb=" N LEU R 11 " pdb=" CA LEU R 11 " pdb=" CB LEU R 11 " pdb=" CG LEU R 11 " ideal model delta sinusoidal sigma weight residual -60.00 -117.83 57.83 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" N LEU D 11 " pdb=" CA LEU D 11 " pdb=" CB LEU D 11 " pdb=" CG LEU D 11 " ideal model delta sinusoidal sigma weight residual -60.00 -117.81 57.81 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" N LEU H 11 " pdb=" CA LEU H 11 " pdb=" CB LEU H 11 " pdb=" CG LEU H 11 " ideal model delta sinusoidal sigma weight residual -60.00 -117.81 57.81 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 2597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 322 0.028 - 0.056: 208 0.056 - 0.084: 40 0.084 - 0.112: 50 0.112 - 0.140: 60 Chirality restraints: 680 Sorted by residual: chirality pdb=" CG LEU P 29 " pdb=" CB LEU P 29 " pdb=" CD1 LEU P 29 " pdb=" CD2 LEU P 29 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CG LEU L 29 " pdb=" CB LEU L 29 " pdb=" CD1 LEU L 29 " pdb=" CD2 LEU L 29 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CG LEU N 29 " pdb=" CB LEU N 29 " pdb=" CD1 LEU N 29 " pdb=" CD2 LEU N 29 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 677 not shown) Planarity restraints: 800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU T 29 " 0.007 2.00e-02 2.50e+03 1.33e-02 1.78e+00 pdb=" C LEU T 29 " -0.023 2.00e-02 2.50e+03 pdb=" O LEU T 29 " 0.009 2.00e-02 2.50e+03 pdb=" N ILE T 30 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 29 " 0.007 2.00e-02 2.50e+03 1.33e-02 1.76e+00 pdb=" C LEU R 29 " -0.023 2.00e-02 2.50e+03 pdb=" O LEU R 29 " 0.009 2.00e-02 2.50e+03 pdb=" N ILE R 30 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU N 29 " 0.007 2.00e-02 2.50e+03 1.32e-02 1.75e+00 pdb=" C LEU N 29 " -0.023 2.00e-02 2.50e+03 pdb=" O LEU N 29 " 0.009 2.00e-02 2.50e+03 pdb=" N ILE N 30 " 0.008 2.00e-02 2.50e+03 ... (remaining 797 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 2024 2.94 - 3.43: 3641 3.43 - 3.92: 7500 3.92 - 4.41: 8502 4.41 - 4.90: 17830 Nonbonded interactions: 39497 Sorted by model distance: nonbonded pdb=" OE1 GLN I 26 " pdb=" O HIS N 24 " model vdw 2.452 3.040 nonbonded pdb=" OE1 GLN A 26 " pdb=" O HIS F 24 " model vdw 2.452 3.040 nonbonded pdb=" OE1 GLN G 26 " pdb=" O HIS L 24 " model vdw 2.453 3.040 nonbonded pdb=" OE1 GLN E 26 " pdb=" O HIS J 24 " model vdw 2.453 3.040 nonbonded pdb=" OE1 GLN M 26 " pdb=" O HIS R 24 " model vdw 2.453 3.040 ... (remaining 39492 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' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.190 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: 0.020 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.630 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:7.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 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 : 0.004 0.017 4680 Z= 0.173 Angle : 0.796 9.756 6340 Z= 0.364 Chirality : 0.054 0.140 680 Planarity : 0.002 0.013 800 Dihedral : 19.978 89.796 1600 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.54 % Favored : 88.46 % Rotamer: Outliers : 0.00 % Allowed : 50.00 % Favored : 50.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.38 (0.31), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG S 31 PHE 0.002 0.000 PHE J 33 TRP 0.011 0.001 TRP F 7 HIS 0.003 0.001 HIS F 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 ( 4680) covalent geometry : angle 0.79585 / 0.36 ( 6340) hydrogen bonds : bond 0.09316 / 5.94 ( 56) hydrogen bonds : angle 6.30070 / 4.38 ( 168) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.206 Fit side-chains REVERT: B 27 GLU cc_start: 0.8339 (tt0) cc_final: 0.7914 (tm-30) REVERT: F 27 GLU cc_start: 0.8568 (tt0) cc_final: 0.7919 (tm-30) REVERT: H 27 GLU cc_start: 0.8500 (tt0) cc_final: 0.8190 (tm-30) REVERT: H 31 ARG cc_start: 0.7001 (mmm-85) cc_final: 0.6578 (mtt180) REVERT: J 27 GLU cc_start: 0.8483 (tt0) cc_final: 0.7997 (tm-30) REVERT: L 27 GLU cc_start: 0.8638 (tt0) cc_final: 0.8065 (tm-30) REVERT: N 18 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7544 (mp0) REVERT: P 27 GLU cc_start: 0.8485 (tt0) cc_final: 0.7863 (tm-30) REVERT: R 16 LYS cc_start: 0.8564 (ttmm) cc_final: 0.7583 (pmtt) REVERT: R 18 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7945 (mp0) REVERT: T 18 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7950 (mp0) REVERT: T 27 GLU cc_start: 0.8526 (tt0) cc_final: 0.8117 (tm-30) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.6329 time to fit residues: 98.5396 Evaluate side-chains 111 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 30.0000 chunk 25 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 chunk 22 optimal weight: 7.9990 chunk 37 optimal weight: 20.0000 overall best weight: 6.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 GLN C 12 ASN D 26 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 HIS G 9 GLN G 12 ASN ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 HIS ** N 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 12 ASN ** P 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.127042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.117630 restraints weight = 8868.636| |-----------------------------------------------------------------------------| r_work (start): 0.4310 rms_B_bonded: 2.42 r_work: 0.4221 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.4109 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4680 Z= 0.174 Angle : 0.678 6.954 6340 Z= 0.326 Chirality : 0.052 0.182 680 Planarity : 0.002 0.009 800 Dihedral : 6.333 13.360 560 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 12.17 % Allowed : 38.04 % Favored : 49.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.18 (0.31), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.23), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG T 31 PHE 0.002 0.001 PHE S 33 TRP 0.008 0.001 TRP R 7 HIS 0.002 0.001 HIS J 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 ( 4680) covalent geometry : angle 0.67759 / 0.33 ( 6340) hydrogen bonds : bond 0.01201 / 0.74 ( 56) hydrogen bonds : angle 4.55400 / 3.13 ( 168) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 117 time to evaluate : 0.193 Fit side-chains REVERT: A 31 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7469 (mtm-85) REVERT: B 16 LYS cc_start: 0.8451 (ttpt) cc_final: 0.8234 (tttt) REVERT: B 27 GLU cc_start: 0.8477 (tt0) cc_final: 0.7653 (tm-30) REVERT: D 16 LYS cc_start: 0.8491 (ttpt) cc_final: 0.8137 (tttt) REVERT: D 17 VAL cc_start: 0.8713 (OUTLIER) cc_final: 0.8503 (t) REVERT: D 18 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.8018 (mp0) REVERT: F 17 VAL cc_start: 0.8625 (OUTLIER) cc_final: 0.8393 (t) REVERT: F 18 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7621 (mp0) REVERT: F 27 GLU cc_start: 0.8664 (tt0) cc_final: 0.7712 (tm-30) REVERT: G 31 ARG cc_start: 0.6876 (OUTLIER) cc_final: 0.6397 (ttm170) REVERT: H 17 VAL cc_start: 0.8588 (OUTLIER) cc_final: 0.8368 (t) REVERT: J 17 VAL cc_start: 0.8671 (OUTLIER) cc_final: 0.8363 (t) REVERT: J 27 GLU cc_start: 0.8615 (tt0) cc_final: 0.7858 (tm-30) REVERT: K 9 GLN cc_start: 0.8633 (tt0) cc_final: 0.8370 (tt0) REVERT: K 31 ARG cc_start: 0.6812 (OUTLIER) cc_final: 0.6449 (ttm170) REVERT: L 6 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7170 (tt0) REVERT: L 27 GLU cc_start: 0.8820 (tt0) cc_final: 0.7752 (tm-30) REVERT: M 31 ARG cc_start: 0.6792 (OUTLIER) cc_final: 0.6105 (ttm170) REVERT: N 17 VAL cc_start: 0.8568 (OUTLIER) cc_final: 0.8229 (t) REVERT: O 31 ARG cc_start: 0.6834 (OUTLIER) cc_final: 0.6259 (ttm170) REVERT: P 27 GLU cc_start: 0.8637 (tt0) cc_final: 0.7613 (tm-30) REVERT: Q 8 GLN cc_start: 0.8817 (mp10) cc_final: 0.8615 (mp10) REVERT: R 16 LYS cc_start: 0.8667 (ttmm) cc_final: 0.7535 (pmtt) REVERT: R 17 VAL cc_start: 0.8657 (OUTLIER) cc_final: 0.8279 (t) REVERT: R 18 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7934 (mp0) REVERT: S 31 ARG cc_start: 0.6908 (OUTLIER) cc_final: 0.6425 (ttm170) REVERT: T 16 LYS cc_start: 0.8440 (ttmm) cc_final: 0.7352 (pmtt) REVERT: T 17 VAL cc_start: 0.8690 (OUTLIER) cc_final: 0.8402 (t) REVERT: T 18 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7812 (mp0) REVERT: T 27 GLU cc_start: 0.8791 (tt0) cc_final: 0.8109 (tm-30) outliers start: 56 outliers final: 6 residues processed: 147 average time/residue: 0.6738 time to fit residues: 101.9688 Evaluate side-chains 116 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain G residue 31 ARG Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 31 ARG Chi-restraints excluded: chain M residue 31 ARG Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain R residue 17 VAL Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain S residue 16 LYS Chi-restraints excluded: chain S residue 31 ARG Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 18 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 7.9990 chunk 17 optimal weight: 30.0000 chunk 4 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 chunk 29 optimal weight: 40.0000 chunk 20 optimal weight: 7.9990 chunk 23 optimal weight: 30.0000 chunk 18 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 21 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 overall best weight: 9.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 12 ASN ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 ASN ** N 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 24 HIS ** R 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.124296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.114370 restraints weight = 8847.415| |-----------------------------------------------------------------------------| r_work (start): 0.4264 rms_B_bonded: 2.44 r_work: 0.4179 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.4067 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 4680 Z= 0.245 Angle : 0.680 7.155 6340 Z= 0.332 Chirality : 0.052 0.177 680 Planarity : 0.002 0.010 800 Dihedral : 6.373 14.112 560 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 13.91 % Allowed : 34.57 % Favored : 51.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.36 (0.30), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.23), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 31 PHE 0.003 0.001 PHE B 33 TRP 0.008 0.001 TRP R 7 HIS 0.003 0.001 HIS R 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.25 ( 4680) covalent geometry : angle 0.67955 / 0.33 ( 6340) hydrogen bonds : bond 0.01399 / 0.89 ( 56) hydrogen bonds : angle 4.18156 / 2.87 ( 168) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 99 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: A 31 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7439 (mtm-85) REVERT: B 27 GLU cc_start: 0.8442 (tt0) cc_final: 0.7646 (tm-30) REVERT: D 17 VAL cc_start: 0.8792 (OUTLIER) cc_final: 0.8503 (t) REVERT: F 17 VAL cc_start: 0.8737 (OUTLIER) cc_final: 0.8471 (t) REVERT: F 18 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7655 (mp0) REVERT: F 27 GLU cc_start: 0.8700 (tt0) cc_final: 0.7828 (tm-30) REVERT: G 31 ARG cc_start: 0.6876 (OUTLIER) cc_final: 0.6363 (ttm170) REVERT: H 17 VAL cc_start: 0.8639 (OUTLIER) cc_final: 0.8417 (t) REVERT: J 17 VAL cc_start: 0.8653 (OUTLIER) cc_final: 0.8367 (t) REVERT: J 18 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7563 (pm20) REVERT: J 27 GLU cc_start: 0.8636 (tt0) cc_final: 0.7856 (tm-30) REVERT: K 9 GLN cc_start: 0.8662 (tt0) cc_final: 0.8424 (tt0) REVERT: K 31 ARG cc_start: 0.6862 (OUTLIER) cc_final: 0.6454 (ttm170) REVERT: L 27 GLU cc_start: 0.8805 (tt0) cc_final: 0.8269 (tm-30) REVERT: M 31 ARG cc_start: 0.6842 (OUTLIER) cc_final: 0.6153 (ttm170) REVERT: N 17 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8279 (t) REVERT: N 18 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7535 (pm20) REVERT: O 31 ARG cc_start: 0.6856 (OUTLIER) cc_final: 0.6264 (ttm170) REVERT: P 18 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7521 (mp0) REVERT: P 27 GLU cc_start: 0.8652 (tt0) cc_final: 0.8015 (tm-30) REVERT: R 16 LYS cc_start: 0.8747 (ttmm) cc_final: 0.7733 (pmtt) REVERT: R 17 VAL cc_start: 0.8657 (OUTLIER) cc_final: 0.8244 (t) REVERT: R 18 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7834 (mp0) REVERT: S 31 ARG cc_start: 0.6988 (OUTLIER) cc_final: 0.6410 (ttm170) REVERT: T 16 LYS cc_start: 0.8439 (ttmm) cc_final: 0.7463 (pmtt) REVERT: T 17 VAL cc_start: 0.8796 (OUTLIER) cc_final: 0.8551 (t) REVERT: T 18 GLU cc_start: 0.8431 (mt-10) cc_final: 0.7762 (mp0) REVERT: T 27 GLU cc_start: 0.8844 (tt0) cc_final: 0.8147 (tm-30) outliers start: 64 outliers final: 14 residues processed: 140 average time/residue: 0.6268 time to fit residues: 90.3898 Evaluate side-chains 115 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain G residue 31 ARG Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain K residue 31 ARG Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain M residue 31 ARG Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 18 GLU Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 31 ARG Chi-restraints excluded: chain R residue 17 VAL Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain S residue 16 LYS Chi-restraints excluded: chain S residue 31 ARG Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 30 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 5 optimal weight: 20.0000 chunk 19 optimal weight: 40.0000 chunk 12 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 37 optimal weight: 30.0000 chunk 29 optimal weight: 20.0000 overall best weight: 9.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 HIS ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.123742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.113954 restraints weight = 8951.567| |-----------------------------------------------------------------------------| r_work (start): 0.4263 rms_B_bonded: 2.45 r_work: 0.4176 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.4066 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 4680 Z= 0.248 Angle : 0.710 8.808 6340 Z= 0.338 Chirality : 0.052 0.171 680 Planarity : 0.002 0.010 800 Dihedral : 6.287 13.351 560 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 13.48 % Allowed : 35.00 % Favored : 51.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.48 (0.29), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.22), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 31 PHE 0.003 0.001 PHE B 33 TRP 0.007 0.001 TRP D 7 HIS 0.003 0.001 HIS R 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.25 ( 4680) covalent geometry : angle 0.71005 / 0.34 ( 6340) hydrogen bonds : bond 0.01370 / 0.86 ( 56) hydrogen bonds : angle 4.04465 / 2.76 ( 168) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 98 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: B 18 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7709 (mp0) REVERT: B 27 GLU cc_start: 0.8427 (tt0) cc_final: 0.7687 (tm-30) REVERT: C 27 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8477 (tm-30) REVERT: D 6 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7663 (tt0) REVERT: D 17 VAL cc_start: 0.8812 (OUTLIER) cc_final: 0.8484 (t) REVERT: D 18 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7976 (mp0) REVERT: F 17 VAL cc_start: 0.8730 (OUTLIER) cc_final: 0.8432 (t) REVERT: F 18 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7551 (mp0) REVERT: F 27 GLU cc_start: 0.8684 (tt0) cc_final: 0.7772 (tm-30) REVERT: G 27 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8429 (tm-30) REVERT: H 31 ARG cc_start: 0.7005 (mtp180) cc_final: 0.6767 (mtp-110) REVERT: I 27 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.7862 (tm-30) REVERT: I 29 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7738 (mp) REVERT: J 17 VAL cc_start: 0.8708 (OUTLIER) cc_final: 0.8386 (t) REVERT: J 18 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7465 (mp0) REVERT: J 27 GLU cc_start: 0.8630 (tt0) cc_final: 0.7808 (tm-30) REVERT: K 9 GLN cc_start: 0.8683 (tt0) cc_final: 0.8430 (tt0) REVERT: K 31 ARG cc_start: 0.6961 (OUTLIER) cc_final: 0.6564 (ttm170) REVERT: L 27 GLU cc_start: 0.8818 (tt0) cc_final: 0.8294 (tm-30) REVERT: M 27 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8438 (tm-30) REVERT: M 29 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8072 (mp) REVERT: N 17 VAL cc_start: 0.8617 (OUTLIER) cc_final: 0.8236 (t) REVERT: N 18 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7461 (mp0) REVERT: O 31 ARG cc_start: 0.6846 (OUTLIER) cc_final: 0.6264 (ttm170) REVERT: P 27 GLU cc_start: 0.8645 (tt0) cc_final: 0.8006 (tm-30) REVERT: R 16 LYS cc_start: 0.8730 (ttmm) cc_final: 0.7697 (pmtt) REVERT: R 17 VAL cc_start: 0.8715 (OUTLIER) cc_final: 0.8300 (t) REVERT: R 18 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7823 (mp0) REVERT: T 16 LYS cc_start: 0.8504 (ttmm) cc_final: 0.7716 (pmtt) REVERT: T 17 VAL cc_start: 0.8819 (OUTLIER) cc_final: 0.8596 (t) REVERT: T 18 GLU cc_start: 0.8424 (mt-10) cc_final: 0.7802 (mp0) REVERT: T 27 GLU cc_start: 0.8835 (tt0) cc_final: 0.8092 (tm-30) outliers start: 62 outliers final: 18 residues processed: 137 average time/residue: 0.4573 time to fit residues: 64.7181 Evaluate side-chains 125 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 89 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain G residue 27 GLU Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 27 GLU Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain K residue 31 ARG Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain M residue 16 LYS Chi-restraints excluded: chain M residue 27 GLU Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 18 GLU Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 31 ARG Chi-restraints excluded: chain Q residue 16 LYS Chi-restraints excluded: chain R residue 17 VAL Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain S residue 16 LYS Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 30 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 8.9990 chunk 11 optimal weight: 0.6980 chunk 39 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 5 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 34 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 overall best weight: 7.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.125344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.115627 restraints weight = 8804.391| |-----------------------------------------------------------------------------| r_work (start): 0.4280 rms_B_bonded: 2.46 r_work: 0.4193 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.4079 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4680 Z= 0.197 Angle : 0.718 9.510 6340 Z= 0.336 Chirality : 0.052 0.161 680 Planarity : 0.002 0.012 800 Dihedral : 6.222 16.829 560 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 10.65 % Allowed : 36.52 % Favored : 52.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.43 (0.29), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.22), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 31 PHE 0.003 0.001 PHE I 33 TRP 0.007 0.001 TRP H 14 HIS 0.002 0.001 HIS R 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.20 ( 4680) covalent geometry : angle 0.71823 / 0.34 ( 6340) hydrogen bonds : bond 0.01237 / 0.78 ( 56) hydrogen bonds : angle 3.92067 / 2.68 ( 168) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 103 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: B 16 LYS cc_start: 0.8538 (ttpt) cc_final: 0.8235 (ttmm) REVERT: B 27 GLU cc_start: 0.8389 (tt0) cc_final: 0.7604 (tm-30) REVERT: C 27 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8251 (tm-30) REVERT: D 6 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7643 (tt0) REVERT: D 17 VAL cc_start: 0.8747 (OUTLIER) cc_final: 0.8376 (t) REVERT: D 18 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7817 (mp0) REVERT: F 17 VAL cc_start: 0.8769 (OUTLIER) cc_final: 0.8514 (t) REVERT: F 18 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7576 (mp0) REVERT: F 27 GLU cc_start: 0.8649 (tt0) cc_final: 0.7688 (tm-30) REVERT: G 27 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8467 (tm-30) REVERT: H 31 ARG cc_start: 0.6999 (mtp180) cc_final: 0.6776 (mtp-110) REVERT: J 17 VAL cc_start: 0.8632 (OUTLIER) cc_final: 0.8310 (t) REVERT: J 18 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7569 (mp0) REVERT: J 27 GLU cc_start: 0.8662 (tt0) cc_final: 0.7813 (tm-30) REVERT: K 9 GLN cc_start: 0.8694 (tt0) cc_final: 0.8474 (tt0) REVERT: K 31 ARG cc_start: 0.6958 (OUTLIER) cc_final: 0.6546 (ttm170) REVERT: L 27 GLU cc_start: 0.8774 (tt0) cc_final: 0.7769 (tm-30) REVERT: M 29 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8050 (mp) REVERT: N 17 VAL cc_start: 0.8595 (OUTLIER) cc_final: 0.8288 (t) REVERT: O 31 ARG cc_start: 0.6781 (OUTLIER) cc_final: 0.6187 (ttm170) REVERT: P 27 GLU cc_start: 0.8624 (tt0) cc_final: 0.7853 (tm-30) REVERT: R 16 LYS cc_start: 0.8685 (ttmm) cc_final: 0.7733 (pmtt) REVERT: R 17 VAL cc_start: 0.8678 (OUTLIER) cc_final: 0.8294 (t) REVERT: R 18 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7920 (mp0) REVERT: T 16 LYS cc_start: 0.8402 (ttmm) cc_final: 0.7553 (pmtt) REVERT: T 17 VAL cc_start: 0.8789 (OUTLIER) cc_final: 0.8546 (t) REVERT: T 18 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7768 (mp0) REVERT: T 27 GLU cc_start: 0.8787 (tt0) cc_final: 0.8025 (tm-30) outliers start: 49 outliers final: 18 residues processed: 131 average time/residue: 0.6011 time to fit residues: 81.3720 Evaluate side-chains 120 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 87 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain G residue 27 GLU Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 31 ARG Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain M residue 16 LYS Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 18 GLU Chi-restraints excluded: chain O residue 16 LYS Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain Q residue 16 LYS Chi-restraints excluded: chain R residue 17 VAL Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain S residue 16 LYS Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 18 GLU Chi-restraints excluded: chain T residue 30 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 5 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 29 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 14 optimal weight: 4.9990 chunk 11 optimal weight: 40.0000 chunk 24 optimal weight: 20.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.124859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.115260 restraints weight = 8916.084| |-----------------------------------------------------------------------------| r_work (start): 0.4288 rms_B_bonded: 2.46 r_work: 0.4201 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.4086 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 4680 Z= 0.206 Angle : 0.742 9.939 6340 Z= 0.343 Chirality : 0.052 0.171 680 Planarity : 0.002 0.013 800 Dihedral : 6.243 17.373 560 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 10.00 % Allowed : 36.30 % Favored : 53.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.49 (0.29), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.22), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 31 PHE 0.003 0.001 PHE I 33 TRP 0.007 0.001 TRP H 14 HIS 0.002 0.001 HIS R 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.21 ( 4680) covalent geometry : angle 0.74224 / 0.34 ( 6340) hydrogen bonds : bond 0.01284 / 0.81 ( 56) hydrogen bonds : angle 3.82174 / 2.60 ( 168) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 97 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: B 27 GLU cc_start: 0.8377 (tt0) cc_final: 0.7603 (tm-30) REVERT: D 6 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7672 (tt0) REVERT: D 17 VAL cc_start: 0.8768 (OUTLIER) cc_final: 0.8408 (t) REVERT: D 18 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7826 (mp0) REVERT: F 17 VAL cc_start: 0.8782 (OUTLIER) cc_final: 0.8518 (t) REVERT: F 18 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7631 (mp0) REVERT: F 27 GLU cc_start: 0.8669 (tt0) cc_final: 0.7747 (tm-30) REVERT: H 31 ARG cc_start: 0.7060 (mtp180) cc_final: 0.6833 (mtp-110) REVERT: J 17 VAL cc_start: 0.8659 (OUTLIER) cc_final: 0.8323 (t) REVERT: J 18 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7559 (mp0) REVERT: J 27 GLU cc_start: 0.8714 (tt0) cc_final: 0.7852 (tm-30) REVERT: K 9 GLN cc_start: 0.8682 (tt0) cc_final: 0.8453 (tt0) REVERT: K 31 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.6580 (ttm170) REVERT: L 27 GLU cc_start: 0.8781 (tt0) cc_final: 0.7778 (tm-30) REVERT: M 29 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8136 (mp) REVERT: N 17 VAL cc_start: 0.8579 (OUTLIER) cc_final: 0.8218 (t) REVERT: N 18 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7431 (mp0) REVERT: O 31 ARG cc_start: 0.6852 (OUTLIER) cc_final: 0.6290 (ttm170) REVERT: P 27 GLU cc_start: 0.8646 (tt0) cc_final: 0.7621 (tm-30) REVERT: R 16 LYS cc_start: 0.8689 (ttmm) cc_final: 0.7699 (pmtt) REVERT: R 17 VAL cc_start: 0.8685 (OUTLIER) cc_final: 0.8295 (t) REVERT: R 18 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7814 (mp0) REVERT: T 16 LYS cc_start: 0.8433 (ttmm) cc_final: 0.7448 (pmtt) REVERT: T 17 VAL cc_start: 0.8797 (OUTLIER) cc_final: 0.8561 (t) REVERT: T 18 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: T 27 GLU cc_start: 0.8829 (tt0) cc_final: 0.8070 (tm-30) REVERT: T 31 ARG cc_start: 0.7762 (mmm-85) cc_final: 0.5615 (pmt-80) outliers start: 46 outliers final: 16 residues processed: 121 average time/residue: 0.5668 time to fit residues: 70.9264 Evaluate side-chains 119 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 89 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 31 ARG Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain M residue 16 LYS Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 18 GLU Chi-restraints excluded: chain O residue 16 LYS Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain Q residue 16 LYS Chi-restraints excluded: chain R residue 17 VAL Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain S residue 16 LYS Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 18 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 5 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 chunk 31 optimal weight: 30.0000 chunk 19 optimal weight: 40.0000 chunk 14 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 26 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.124891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.115286 restraints weight = 8804.987| |-----------------------------------------------------------------------------| r_work (start): 0.4290 rms_B_bonded: 2.46 r_work: 0.4206 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.4092 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4680 Z= 0.194 Angle : 0.763 11.349 6340 Z= 0.347 Chirality : 0.052 0.162 680 Planarity : 0.002 0.013 800 Dihedral : 6.241 19.044 560 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 9.57 % Allowed : 36.09 % Favored : 54.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.50 (0.29), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.22), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 31 PHE 0.002 0.001 PHE I 33 TRP 0.007 0.001 TRP T 14 HIS 0.002 0.001 HIS R 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 ( 4680) covalent geometry : angle 0.76283 / 0.35 ( 6340) hydrogen bonds : bond 0.01245 / 0.78 ( 56) hydrogen bonds : angle 3.78196 / 2.58 ( 168) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 97 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 18 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7820 (mp0) REVERT: B 27 GLU cc_start: 0.8379 (tt0) cc_final: 0.7598 (tm-30) REVERT: D 6 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7701 (tt0) REVERT: D 17 VAL cc_start: 0.8770 (OUTLIER) cc_final: 0.8395 (t) REVERT: D 18 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7860 (mp0) REVERT: F 17 VAL cc_start: 0.8710 (OUTLIER) cc_final: 0.8473 (t) REVERT: F 18 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7588 (mp0) REVERT: F 27 GLU cc_start: 0.8660 (tt0) cc_final: 0.7740 (tm-30) REVERT: H 16 LYS cc_start: 0.8699 (ttpt) cc_final: 0.8386 (ttpp) REVERT: H 31 ARG cc_start: 0.7121 (mtp180) cc_final: 0.6885 (mtp-110) REVERT: J 17 VAL cc_start: 0.8658 (OUTLIER) cc_final: 0.8320 (t) REVERT: J 18 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7555 (mp0) REVERT: J 27 GLU cc_start: 0.8704 (tt0) cc_final: 0.8097 (tm-30) REVERT: K 9 GLN cc_start: 0.8685 (tt0) cc_final: 0.8450 (tt0) REVERT: K 31 ARG cc_start: 0.6964 (OUTLIER) cc_final: 0.6545 (ttm170) REVERT: L 16 LYS cc_start: 0.8755 (ttmm) cc_final: 0.8232 (tttt) REVERT: L 18 GLU cc_start: 0.8393 (mp0) cc_final: 0.8169 (mp0) REVERT: L 27 GLU cc_start: 0.8750 (tt0) cc_final: 0.7743 (tm-30) REVERT: M 27 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8127 (tm-30) REVERT: M 29 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8073 (mp) REVERT: N 17 VAL cc_start: 0.8597 (OUTLIER) cc_final: 0.8209 (t) REVERT: N 18 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7427 (mp0) REVERT: O 29 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7975 (mp) REVERT: O 31 ARG cc_start: 0.6851 (OUTLIER) cc_final: 0.6288 (ttm170) REVERT: P 27 GLU cc_start: 0.8636 (tt0) cc_final: 0.7881 (tm-30) REVERT: R 16 LYS cc_start: 0.8680 (ttmm) cc_final: 0.7719 (pmtt) REVERT: R 17 VAL cc_start: 0.8682 (OUTLIER) cc_final: 0.8283 (t) REVERT: R 18 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7840 (mp0) REVERT: R 31 ARG cc_start: 0.7773 (mmm-85) cc_final: 0.5620 (ppt170) REVERT: T 16 LYS cc_start: 0.8399 (ttmm) cc_final: 0.7443 (pmtt) REVERT: T 17 VAL cc_start: 0.8822 (OUTLIER) cc_final: 0.8588 (t) REVERT: T 18 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7794 (mp0) REVERT: T 27 GLU cc_start: 0.8820 (tt0) cc_final: 0.8065 (tm-30) REVERT: T 31 ARG cc_start: 0.7789 (mmm-85) cc_final: 0.5615 (pmt170) outliers start: 44 outliers final: 16 residues processed: 120 average time/residue: 0.6001 time to fit residues: 74.3882 Evaluate side-chains 123 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 31 ARG Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain M residue 16 LYS Chi-restraints excluded: chain M residue 27 GLU Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 18 GLU Chi-restraints excluded: chain O residue 16 LYS Chi-restraints excluded: chain O residue 29 LEU Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain Q residue 16 LYS Chi-restraints excluded: chain R residue 17 VAL Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain S residue 16 LYS Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 18 GLU Chi-restraints excluded: chain T residue 30 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 17 optimal weight: 30.0000 chunk 39 optimal weight: 7.9990 chunk 21 optimal weight: 30.0000 chunk 12 optimal weight: 4.9990 chunk 31 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 13 optimal weight: 8.9990 chunk 10 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 6 optimal weight: 8.9990 chunk 15 optimal weight: 30.0000 overall best weight: 10.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 HIS ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 HIS ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 HIS ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.131490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.123166 restraints weight = 8008.272| |-----------------------------------------------------------------------------| r_work (start): 0.4399 rms_B_bonded: 2.22 r_work: 0.4302 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.4199 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 4680 Z= 0.263 Angle : 0.811 11.769 6340 Z= 0.371 Chirality : 0.053 0.202 680 Planarity : 0.002 0.012 800 Dihedral : 6.332 19.948 560 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 10.22 % Allowed : 35.00 % Favored : 54.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.63 (0.28), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.22), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 31 PHE 0.003 0.001 PHE I 33 TRP 0.006 0.001 TRP N 14 HIS 0.003 0.001 HIS R 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.26 ( 4680) covalent geometry : angle 0.81079 / 0.37 ( 6340) hydrogen bonds : bond 0.01460 / 0.92 ( 56) hydrogen bonds : angle 3.76675 / 2.57 ( 168) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 96 time to evaluate : 0.242 Fit side-chains REVERT: B 27 GLU cc_start: 0.8394 (tt0) cc_final: 0.7711 (tm-30) REVERT: C 8 GLN cc_start: 0.9199 (mp10) cc_final: 0.8928 (mp10) REVERT: D 6 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7675 (tt0) REVERT: D 17 VAL cc_start: 0.8821 (OUTLIER) cc_final: 0.8475 (t) REVERT: D 18 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7842 (mp0) REVERT: F 17 VAL cc_start: 0.8766 (OUTLIER) cc_final: 0.8532 (t) REVERT: F 18 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7615 (mp0) REVERT: F 27 GLU cc_start: 0.8614 (tt0) cc_final: 0.7766 (tm-30) REVERT: H 31 ARG cc_start: 0.7211 (mtp180) cc_final: 0.6957 (mtp-110) REVERT: J 17 VAL cc_start: 0.8712 (OUTLIER) cc_final: 0.8405 (t) REVERT: J 18 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7592 (mp0) REVERT: J 27 GLU cc_start: 0.8670 (tt0) cc_final: 0.7815 (tm-30) REVERT: K 9 GLN cc_start: 0.8798 (tt0) cc_final: 0.8526 (tt0) REVERT: K 31 ARG cc_start: 0.6919 (OUTLIER) cc_final: 0.6472 (ttm170) REVERT: L 16 LYS cc_start: 0.8738 (ttmm) cc_final: 0.8208 (tttt) REVERT: L 18 GLU cc_start: 0.8368 (mp0) cc_final: 0.7965 (mp0) REVERT: L 27 GLU cc_start: 0.8761 (tt0) cc_final: 0.7727 (tm-30) REVERT: M 29 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8233 (mp) REVERT: N 17 VAL cc_start: 0.8644 (OUTLIER) cc_final: 0.8263 (t) REVERT: N 18 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7465 (mp0) REVERT: O 29 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8025 (mp) REVERT: O 31 ARG cc_start: 0.6820 (OUTLIER) cc_final: 0.6265 (ttm170) REVERT: P 27 GLU cc_start: 0.8569 (tt0) cc_final: 0.7821 (tm-30) REVERT: P 31 ARG cc_start: 0.6823 (mmm-85) cc_final: 0.6610 (mtp85) REVERT: R 16 LYS cc_start: 0.8655 (ttmm) cc_final: 0.7724 (pmtt) REVERT: R 17 VAL cc_start: 0.8745 (OUTLIER) cc_final: 0.8346 (t) REVERT: R 18 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7873 (mp0) REVERT: R 31 ARG cc_start: 0.7819 (mmm-85) cc_final: 0.5773 (ppt170) REVERT: T 16 LYS cc_start: 0.8413 (ttmm) cc_final: 0.7656 (pmtt) REVERT: T 17 VAL cc_start: 0.8847 (OUTLIER) cc_final: 0.8639 (t) REVERT: T 18 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7781 (mp0) REVERT: T 27 GLU cc_start: 0.8743 (tt0) cc_final: 0.7992 (tm-30) REVERT: T 31 ARG cc_start: 0.7839 (mmm-85) cc_final: 0.5737 (pmt170) outliers start: 47 outliers final: 19 residues processed: 122 average time/residue: 0.6038 time to fit residues: 76.1924 Evaluate side-chains 128 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 94 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 31 ARG Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain M residue 16 LYS Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 18 GLU Chi-restraints excluded: chain O residue 16 LYS Chi-restraints excluded: chain O residue 29 LEU Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain Q residue 16 LYS Chi-restraints excluded: chain R residue 17 VAL Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain S residue 16 LYS Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 18 GLU Chi-restraints excluded: chain T residue 30 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 18 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 25 optimal weight: 30.0000 chunk 6 optimal weight: 9.9990 chunk 21 optimal weight: 30.0000 chunk 29 optimal weight: 20.0000 chunk 4 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.125732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.116593 restraints weight = 8494.391| |-----------------------------------------------------------------------------| r_work (start): 0.4310 rms_B_bonded: 2.37 r_work: 0.4222 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.4112 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 4680 Z= 0.230 Angle : 0.835 13.239 6340 Z= 0.374 Chirality : 0.053 0.169 680 Planarity : 0.002 0.012 800 Dihedral : 6.343 20.427 560 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 8.26 % Allowed : 36.52 % Favored : 55.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.64 (0.29), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.22), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 31 PHE 0.003 0.001 PHE S 33 TRP 0.007 0.001 TRP B 14 HIS 0.002 0.001 HIS R 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.23 ( 4680) covalent geometry : angle 0.83535 / 0.37 ( 6340) hydrogen bonds : bond 0.01389 / 0.87 ( 56) hydrogen bonds : angle 3.77381 / 2.57 ( 168) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 98 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: B 18 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7694 (mp0) REVERT: B 27 GLU cc_start: 0.8432 (tt0) cc_final: 0.7682 (tm-30) REVERT: C 8 GLN cc_start: 0.9174 (mp10) cc_final: 0.8942 (mp10) REVERT: D 6 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7670 (tt0) REVERT: D 17 VAL cc_start: 0.8839 (OUTLIER) cc_final: 0.8497 (t) REVERT: D 18 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7884 (mp0) REVERT: F 17 VAL cc_start: 0.8771 (OUTLIER) cc_final: 0.8538 (t) REVERT: F 18 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7484 (mp0) REVERT: F 27 GLU cc_start: 0.8638 (tt0) cc_final: 0.7747 (tm-30) REVERT: H 31 ARG cc_start: 0.7176 (mtp180) cc_final: 0.6932 (mtp-110) REVERT: J 17 VAL cc_start: 0.8708 (OUTLIER) cc_final: 0.8399 (t) REVERT: J 18 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7572 (mp0) REVERT: J 27 GLU cc_start: 0.8686 (tt0) cc_final: 0.8103 (tm-30) REVERT: K 9 GLN cc_start: 0.8724 (tt0) cc_final: 0.8469 (tt0) REVERT: K 31 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.6469 (ttm170) REVERT: L 16 LYS cc_start: 0.8706 (ttmm) cc_final: 0.8152 (tttt) REVERT: L 18 GLU cc_start: 0.8278 (mp0) cc_final: 0.7919 (mp0) REVERT: L 27 GLU cc_start: 0.8754 (tt0) cc_final: 0.7713 (tm-30) REVERT: M 29 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8180 (mp) REVERT: N 17 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8239 (t) REVERT: N 18 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7550 (mp0) REVERT: O 29 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.8008 (mp) REVERT: O 31 ARG cc_start: 0.6684 (OUTLIER) cc_final: 0.6133 (ttm170) REVERT: P 18 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7622 (mp0) REVERT: P 27 GLU cc_start: 0.8575 (tt0) cc_final: 0.7774 (tm-30) REVERT: P 31 ARG cc_start: 0.6758 (mmm-85) cc_final: 0.6539 (mtp85) REVERT: R 16 LYS cc_start: 0.8660 (ttmm) cc_final: 0.7753 (pmtt) REVERT: R 17 VAL cc_start: 0.8730 (OUTLIER) cc_final: 0.8332 (t) REVERT: R 18 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7906 (mp0) REVERT: R 31 ARG cc_start: 0.7829 (mmm-85) cc_final: 0.5730 (ppt170) REVERT: T 16 LYS cc_start: 0.8435 (ttmm) cc_final: 0.7624 (pmtt) REVERT: T 17 VAL cc_start: 0.8820 (OUTLIER) cc_final: 0.8592 (t) REVERT: T 18 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7737 (mp0) REVERT: T 27 GLU cc_start: 0.8778 (tt0) cc_final: 0.7933 (tm-30) REVERT: T 31 ARG cc_start: 0.7845 (mmm-85) cc_final: 0.5714 (pmt170) outliers start: 38 outliers final: 18 residues processed: 117 average time/residue: 0.6408 time to fit residues: 77.3903 Evaluate side-chains 128 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 95 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 31 ARG Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain M residue 16 LYS Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 18 GLU Chi-restraints excluded: chain O residue 16 LYS Chi-restraints excluded: chain O residue 29 LEU Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain Q residue 16 LYS Chi-restraints excluded: chain R residue 17 VAL Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain S residue 16 LYS Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 18 GLU Chi-restraints excluded: chain T residue 30 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 10 optimal weight: 5.9990 chunk 37 optimal weight: 30.0000 chunk 27 optimal weight: 30.0000 chunk 6 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 9 optimal weight: 20.0000 chunk 13 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.126443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.117310 restraints weight = 8469.542| |-----------------------------------------------------------------------------| r_work (start): 0.4334 rms_B_bonded: 2.38 r_work: 0.4243 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.4133 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4680 Z= 0.202 Angle : 0.852 14.115 6340 Z= 0.375 Chirality : 0.053 0.164 680 Planarity : 0.002 0.012 800 Dihedral : 6.301 20.941 560 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 8.04 % Allowed : 36.52 % Favored : 55.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.63 (0.29), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.22), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 31 PHE 0.003 0.001 PHE I 33 TRP 0.007 0.001 TRP T 14 HIS 0.002 0.001 HIS R 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 ( 4680) covalent geometry : angle 0.85154 / 0.37 ( 6340) hydrogen bonds : bond 0.01296 / 0.81 ( 56) hydrogen bonds : angle 3.74271 / 2.55 ( 168) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 104 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 18 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7743 (mp0) REVERT: B 27 GLU cc_start: 0.8417 (tt0) cc_final: 0.7660 (tm-30) REVERT: C 8 GLN cc_start: 0.9170 (mp10) cc_final: 0.8940 (mp10) REVERT: D 6 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7697 (tt0) REVERT: D 17 VAL cc_start: 0.8826 (OUTLIER) cc_final: 0.8477 (t) REVERT: D 18 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7871 (mp0) REVERT: F 17 VAL cc_start: 0.8726 (OUTLIER) cc_final: 0.8491 (t) REVERT: F 18 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7585 (mp0) REVERT: F 27 GLU cc_start: 0.8668 (tt0) cc_final: 0.7753 (tm-30) REVERT: H 26 GLN cc_start: 0.9042 (tt0) cc_final: 0.8836 (tt0) REVERT: H 31 ARG cc_start: 0.7233 (mtp180) cc_final: 0.6986 (mtp-110) REVERT: J 17 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8377 (t) REVERT: J 18 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7625 (mp0) REVERT: J 27 GLU cc_start: 0.8724 (tt0) cc_final: 0.7849 (tm-30) REVERT: K 9 GLN cc_start: 0.8701 (tt0) cc_final: 0.8444 (tt0) REVERT: K 31 ARG cc_start: 0.6959 (OUTLIER) cc_final: 0.6512 (ttm170) REVERT: L 16 LYS cc_start: 0.8696 (ttmm) cc_final: 0.8161 (tttt) REVERT: L 18 GLU cc_start: 0.8235 (mp0) cc_final: 0.8024 (mp0) REVERT: L 27 GLU cc_start: 0.8764 (tt0) cc_final: 0.7724 (tm-30) REVERT: M 29 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8077 (mp) REVERT: N 17 VAL cc_start: 0.8607 (OUTLIER) cc_final: 0.8305 (t) REVERT: O 29 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7957 (mp) REVERT: O 31 ARG cc_start: 0.6726 (OUTLIER) cc_final: 0.6207 (ttm170) REVERT: P 27 GLU cc_start: 0.8567 (tt0) cc_final: 0.7770 (tm-30) REVERT: P 31 ARG cc_start: 0.6792 (mmm-85) cc_final: 0.6579 (mtp85) REVERT: R 16 LYS cc_start: 0.8655 (ttmm) cc_final: 0.7754 (pmtt) REVERT: R 17 VAL cc_start: 0.8694 (OUTLIER) cc_final: 0.8308 (t) REVERT: R 18 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7930 (mp0) REVERT: R 31 ARG cc_start: 0.7850 (mmm-85) cc_final: 0.5760 (pmt170) REVERT: T 16 LYS cc_start: 0.8363 (ttmm) cc_final: 0.7599 (pmtt) REVERT: T 17 VAL cc_start: 0.8793 (OUTLIER) cc_final: 0.8559 (t) REVERT: T 18 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7760 (mp0) REVERT: T 27 GLU cc_start: 0.8790 (tt0) cc_final: 0.7922 (tm-30) REVERT: T 31 ARG cc_start: 0.7860 (mmm-85) cc_final: 0.5726 (pmt170) outliers start: 37 outliers final: 16 residues processed: 122 average time/residue: 0.6226 time to fit residues: 78.3367 Evaluate side-chains 127 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 31 ARG Chi-restraints excluded: chain M residue 16 LYS Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain O residue 16 LYS Chi-restraints excluded: chain O residue 29 LEU Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain Q residue 16 LYS Chi-restraints excluded: chain R residue 17 VAL Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain S residue 16 LYS Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 18 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 36 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 35 optimal weight: 30.0000 chunk 3 optimal weight: 40.0000 chunk 17 optimal weight: 30.0000 chunk 24 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 33 optimal weight: 30.0000 chunk 21 optimal weight: 30.0000 chunk 8 optimal weight: 10.0000 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.125582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.116353 restraints weight = 8548.667| |-----------------------------------------------------------------------------| r_work (start): 0.4306 rms_B_bonded: 2.40 r_work: 0.4216 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.4106 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4680 Z= 0.232 Angle : 0.881 14.033 6340 Z= 0.390 Chirality : 0.054 0.245 680 Planarity : 0.002 0.015 800 Dihedral : 6.366 23.750 560 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 7.39 % Allowed : 37.17 % Favored : 55.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.68 (0.29), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.22), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 31 PHE 0.003 0.001 PHE I 33 TRP 0.007 0.001 TRP N 14 HIS 0.003 0.001 HIS R 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.23 ( 4680) covalent geometry : angle 0.88135 / 0.39 ( 6340) hydrogen bonds : bond 0.01400 / 0.87 ( 56) hydrogen bonds : angle 3.74848 / 2.55 ( 168) =============================================================================== Job complete usr+sys time: 2237.10 seconds wall clock time: 38 minutes 49.65 seconds (2329.65 seconds total)