Starting phenix.real_space_refine on Sun Aug 24 04:25:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gtb_34248/08_2025/8gtb_34248.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gtb_34248/08_2025/8gtb_34248.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gtb_34248/08_2025/8gtb_34248.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gtb_34248/08_2025/8gtb_34248.map" model { file = "/net/cci-nas-00/data/ceres_data/8gtb_34248/08_2025/8gtb_34248.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gtb_34248/08_2025/8gtb_34248.cif" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.097 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 10548 2.51 5 N 2898 2.21 5 O 3636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17136 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 952 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Restraints were copied for chains: A, C, D, E, F, I, G, K, M, O, Q, J, H, L, N, P, R Time building chain proxies: 1.77, per 1000 atoms: 0.10 Number of scatterers: 17136 At special positions: 0 Unit cell: (104.904, 104.904, 142.128, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 3636 8.00 N 2898 7.00 C 10548 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: 1.20 Conformation dependent library (CDL) restraints added in 828.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4068 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 3 sheets defined 0.0% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 8 through 11 removed outlier: 3.706A pdb=" N ASP B 16 " --> pdb=" O ASN B 11 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 16 through 17 current: chain 'B' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 44 through 59 current: chain 'B' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN B 116 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR B 101 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR B 114 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLU B 103 " --> pdb=" O MET B 112 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET B 112 " --> pdb=" O GLU B 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 112 through 119 current: chain 'A' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 16 through 17 current: chain 'A' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 44 through 59 current: chain 'A' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN A 116 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR A 101 " --> pdb=" O THR A 114 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR A 114 " --> pdb=" O THR A 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU A 103 " --> pdb=" O MET A 112 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET A 112 " --> pdb=" O GLU A 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 112 through 119 current: chain 'C' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 16 through 17 current: chain 'C' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 44 through 59 current: chain 'C' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN C 116 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR C 101 " --> pdb=" O THR C 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR C 114 " --> pdb=" O THR C 101 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLU C 103 " --> pdb=" O MET C 112 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET C 112 " --> pdb=" O GLU C 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 112 through 119 current: chain 'D' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 16 through 17 current: chain 'D' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 44 through 59 current: chain 'D' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN D 116 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR D 101 " --> pdb=" O THR D 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR D 114 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLU D 103 " --> pdb=" O MET D 112 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET D 112 " --> pdb=" O GLU D 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 112 through 119 current: chain 'E' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 16 through 17 current: chain 'E' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 44 through 59 current: chain 'E' and resid 91 through 104 removed outlier: 6.940A pdb=" N ASN E 116 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR E 101 " --> pdb=" O THR E 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR E 114 " --> pdb=" O THR E 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU E 103 " --> pdb=" O MET E 112 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET E 112 " --> pdb=" O GLU E 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 112 through 119 current: chain 'F' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 16 through 17 current: chain 'F' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 44 through 59 current: chain 'F' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN F 116 " --> pdb=" O LEU F 99 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR F 101 " --> pdb=" O THR F 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR F 114 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU F 103 " --> pdb=" O MET F 112 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N MET F 112 " --> pdb=" O GLU F 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 8 through 11 removed outlier: 3.706A pdb=" N ASP I 16 " --> pdb=" O ASN I 11 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 16 through 17 current: chain 'I' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 44 through 59 current: chain 'I' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN I 116 " --> pdb=" O LEU I 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR I 101 " --> pdb=" O THR I 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR I 114 " --> pdb=" O THR I 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU I 103 " --> pdb=" O MET I 112 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N MET I 112 " --> pdb=" O GLU I 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 112 through 119 current: chain 'G' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 16 through 17 current: chain 'G' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 44 through 59 current: chain 'G' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN G 116 " --> pdb=" O LEU G 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR G 101 " --> pdb=" O THR G 114 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR G 114 " --> pdb=" O THR G 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU G 103 " --> pdb=" O MET G 112 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET G 112 " --> pdb=" O GLU G 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 112 through 119 current: chain 'K' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 16 through 17 current: chain 'K' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 44 through 59 current: chain 'K' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN K 116 " --> pdb=" O LEU K 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR K 101 " --> pdb=" O THR K 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR K 114 " --> pdb=" O THR K 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU K 103 " --> pdb=" O MET K 112 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N MET K 112 " --> pdb=" O GLU K 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 112 through 119 current: chain 'M' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 16 through 17 current: chain 'M' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 44 through 59 current: chain 'M' and resid 91 through 106 removed outlier: 6.940A pdb=" N ASN M 116 " --> pdb=" O LEU M 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR M 101 " --> pdb=" O THR M 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR M 114 " --> pdb=" O THR M 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU M 103 " --> pdb=" O MET M 112 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET M 112 " --> pdb=" O GLU M 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 112 through 119 current: chain 'O' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 16 through 17 current: chain 'O' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 44 through 59 current: chain 'O' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN O 116 " --> pdb=" O LEU O 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR O 101 " --> pdb=" O THR O 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR O 114 " --> pdb=" O THR O 101 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLU O 103 " --> pdb=" O MET O 112 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET O 112 " --> pdb=" O GLU O 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 112 through 119 current: chain 'Q' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 16 through 17 current: chain 'Q' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 44 through 59 current: chain 'Q' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN Q 116 " --> pdb=" O LEU Q 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR Q 101 " --> pdb=" O THR Q 114 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR Q 114 " --> pdb=" O THR Q 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU Q 103 " --> pdb=" O MET Q 112 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N MET Q 112 " --> pdb=" O GLU Q 103 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 8 through 11 removed outlier: 3.707A pdb=" N ASP J 16 " --> pdb=" O ASN J 11 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 16 through 17 current: chain 'J' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 44 through 59 current: chain 'J' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN J 116 " --> pdb=" O LEU J 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR J 101 " --> pdb=" O THR J 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR J 114 " --> pdb=" O THR J 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU J 103 " --> pdb=" O MET J 112 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N MET J 112 " --> pdb=" O GLU J 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 112 through 119 current: chain 'H' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 16 through 17 current: chain 'H' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 44 through 59 current: chain 'H' and resid 91 through 104 removed outlier: 6.940A pdb=" N ASN H 116 " --> pdb=" O LEU H 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR H 101 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR H 114 " --> pdb=" O THR H 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU H 103 " --> pdb=" O MET H 112 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N MET H 112 " --> pdb=" O GLU H 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 112 through 119 current: chain 'L' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 16 through 17 current: chain 'L' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 44 through 59 current: chain 'L' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN L 116 " --> pdb=" O LEU L 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR L 101 " --> pdb=" O THR L 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR L 114 " --> pdb=" O THR L 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU L 103 " --> pdb=" O MET L 112 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET L 112 " --> pdb=" O GLU L 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 112 through 119 current: chain 'N' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 16 through 17 current: chain 'N' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 44 through 59 current: chain 'N' and resid 91 through 106 removed outlier: 6.941A pdb=" N ASN N 116 " --> pdb=" O LEU N 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR N 101 " --> pdb=" O THR N 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR N 114 " --> pdb=" O THR N 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU N 103 " --> pdb=" O MET N 112 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET N 112 " --> pdb=" O GLU N 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 112 through 119 current: chain 'P' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 16 through 17 current: chain 'P' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 44 through 59 current: chain 'P' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN P 116 " --> pdb=" O LEU P 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR P 101 " --> pdb=" O THR P 114 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR P 114 " --> pdb=" O THR P 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU P 103 " --> pdb=" O MET P 112 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N MET P 112 " --> pdb=" O GLU P 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 112 through 119 current: chain 'R' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 16 through 17 current: chain 'R' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 44 through 59 current: chain 'R' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN R 116 " --> pdb=" O LEU R 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR R 101 " --> pdb=" O THR R 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR R 114 " --> pdb=" O THR R 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU R 103 " --> pdb=" O MET R 112 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET R 112 " --> pdb=" O GLU R 103 " (cutoff:3.500A) 57 hydrogen bonds defined for protein. 171 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.04 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5904 1.34 - 1.45: 3242 1.45 - 1.57: 8188 1.57 - 1.68: 0 1.68 - 1.80: 108 Bond restraints: 17442 Sorted by residual: bond pdb=" CA GLY R 19 " pdb=" C GLY R 19 " ideal model delta sigma weight residual 1.524 1.507 0.017 1.20e-02 6.94e+03 2.10e+00 bond pdb=" CA GLY J 19 " pdb=" C GLY J 19 " ideal model delta sigma weight residual 1.524 1.507 0.017 1.20e-02 6.94e+03 2.09e+00 bond pdb=" CA GLY D 19 " pdb=" C GLY D 19 " ideal model delta sigma weight residual 1.524 1.507 0.017 1.20e-02 6.94e+03 2.06e+00 bond pdb=" CA GLY K 19 " pdb=" C GLY K 19 " ideal model delta sigma weight residual 1.524 1.507 0.017 1.20e-02 6.94e+03 2.05e+00 bond pdb=" CA GLY N 19 " pdb=" C GLY N 19 " ideal model delta sigma weight residual 1.524 1.507 0.017 1.20e-02 6.94e+03 2.01e+00 ... (remaining 17437 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.94: 20428 0.94 - 1.89: 2690 1.89 - 2.83: 385 2.83 - 3.77: 130 3.77 - 4.71: 55 Bond angle restraints: 23688 Sorted by residual: angle pdb=" C ARG J 51 " pdb=" CA ARG J 51 " pdb=" CB ARG J 51 " ideal model delta sigma weight residual 113.19 108.89 4.30 2.37e+00 1.78e-01 3.29e+00 angle pdb=" C ARG E 51 " pdb=" CA ARG E 51 " pdb=" CB ARG E 51 " ideal model delta sigma weight residual 113.19 108.89 4.30 2.37e+00 1.78e-01 3.29e+00 angle pdb=" C ARG B 51 " pdb=" CA ARG B 51 " pdb=" CB ARG B 51 " ideal model delta sigma weight residual 113.19 108.90 4.29 2.37e+00 1.78e-01 3.28e+00 angle pdb=" C ARG P 51 " pdb=" CA ARG P 51 " pdb=" CB ARG P 51 " ideal model delta sigma weight residual 113.19 108.91 4.28 2.37e+00 1.78e-01 3.27e+00 angle pdb=" C ARG K 51 " pdb=" CA ARG K 51 " pdb=" CB ARG K 51 " ideal model delta sigma weight residual 113.19 108.91 4.28 2.37e+00 1.78e-01 3.26e+00 ... (remaining 23683 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.61: 9155 15.61 - 31.21: 975 31.21 - 46.82: 148 46.82 - 62.43: 0 62.43 - 78.03: 18 Dihedral angle restraints: 10296 sinusoidal: 3852 harmonic: 6444 Sorted by residual: dihedral pdb=" CA LYS P 10 " pdb=" C LYS P 10 " pdb=" N ASN P 11 " pdb=" CA ASN P 11 " ideal model delta harmonic sigma weight residual 180.00 163.70 16.30 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA LYS J 10 " pdb=" C LYS J 10 " pdb=" N ASN J 11 " pdb=" CA ASN J 11 " ideal model delta harmonic sigma weight residual 180.00 163.71 16.29 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA LYS A 10 " pdb=" C LYS A 10 " pdb=" N ASN A 11 " pdb=" CA ASN A 11 " ideal model delta harmonic sigma weight residual 180.00 163.72 16.28 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 10293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1285 0.025 - 0.049: 865 0.049 - 0.074: 198 0.074 - 0.099: 146 0.099 - 0.123: 134 Chirality restraints: 2628 Sorted by residual: chirality pdb=" CA VAL O 33 " pdb=" N VAL O 33 " pdb=" C VAL O 33 " pdb=" CB VAL O 33 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 chirality pdb=" CA VAL J 33 " pdb=" N VAL J 33 " pdb=" C VAL J 33 " pdb=" CB VAL J 33 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 chirality pdb=" CA VAL M 33 " pdb=" N VAL M 33 " pdb=" C VAL M 33 " pdb=" CB VAL M 33 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.74e-01 ... (remaining 2625 not shown) Planarity restraints: 3150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP R 64 " 0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO R 65 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO R 65 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO R 65 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 64 " 0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO E 65 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO E 65 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 65 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP H 64 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.79e+00 pdb=" N PRO H 65 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO H 65 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO H 65 " -0.019 5.00e-02 4.00e+02 ... (remaining 3147 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2724 2.75 - 3.29: 15622 3.29 - 3.83: 26022 3.83 - 4.36: 30477 4.36 - 4.90: 57153 Nonbonded interactions: 131998 Sorted by model distance: nonbonded pdb=" OE2 GLU J 43 " pdb=" NH2 ARG R 118 " model vdw 2.213 3.120 nonbonded pdb=" NH2 ARG A 118 " pdb=" OE2 GLU C 43 " model vdw 2.268 3.120 nonbonded pdb=" O SER F 120 " pdb=" OG SER F 120 " model vdw 2.269 3.040 nonbonded pdb=" O SER R 120 " pdb=" OG SER R 120 " model vdw 2.269 3.040 nonbonded pdb=" O SER P 120 " pdb=" OG SER P 120 " model vdw 2.270 3.040 ... (remaining 131993 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: 0.07 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'G' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'J' selection = chain 'H' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.720 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: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 13.050 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2580 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 : 0.007 0.027 17442 Z= 0.336 Angle : 0.714 4.714 23688 Z= 0.411 Chirality : 0.042 0.123 2628 Planarity : 0.004 0.034 3150 Dihedral : 12.850 78.033 6228 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.27 (0.14), residues: 2304 helix: None (None), residues: 0 sheet: -2.06 (0.13), residues: 1260 loop : -2.13 (0.13), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG M 30 TYR 0.007 0.001 TYR O 90 PHE 0.007 0.002 PHE L 56 TRP 0.006 0.001 TRP I 24 HIS 0.002 0.001 HIS M 20 Details of bonding type rmsd covalent geometry : bond 0.00701 (17442) covalent geometry : angle 0.71433 (23688) hydrogen bonds : bond 0.16112 ( 57) hydrogen bonds : angle 12.18361 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 420 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 ASN cc_start: 0.6859 (t0) cc_final: 0.6630 (t0) REVERT: A 76 ASP cc_start: 0.6058 (m-30) cc_final: 0.5710 (p0) REVERT: C 18 ILE cc_start: 0.4028 (mm) cc_final: 0.3571 (mm) REVERT: G 93 VAL cc_start: 0.3844 (t) cc_final: 0.3612 (t) REVERT: K 1 MET cc_start: 0.3647 (ttm) cc_final: 0.3159 (tmm) REVERT: K 80 TYR cc_start: 0.2891 (m-80) cc_final: 0.2337 (m-80) REVERT: H 11 ASN cc_start: 0.6636 (t0) cc_final: 0.6373 (t0) REVERT: H 93 VAL cc_start: 0.3150 (t) cc_final: 0.2908 (t) REVERT: H 112 MET cc_start: 0.1221 (mtt) cc_final: 0.0605 (mtm) REVERT: H 113 LEU cc_start: 0.5032 (tp) cc_final: 0.4647 (tp) REVERT: L 80 TYR cc_start: 0.5061 (m-80) cc_final: 0.4062 (m-80) REVERT: L 81 PRO cc_start: 0.3394 (Cg_exo) cc_final: 0.2822 (Cg_endo) REVERT: P 38 MET cc_start: 0.3380 (mtp) cc_final: 0.2607 (ttt) REVERT: R 38 MET cc_start: 0.4885 (mtp) cc_final: 0.2711 (tmm) outliers start: 0 outliers final: 0 residues processed: 420 average time/residue: 0.1540 time to fit residues: 92.5134 Evaluate side-chains 206 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN A 125 GLN D 22 GLN D 125 GLN E 125 GLN I 125 GLN G 125 GLN K 125 GLN O 125 GLN H 125 GLN L 125 GLN P 125 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.106347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.094257 restraints weight = 32180.905| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.77 r_work: 0.3385 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4248 moved from start: 0.6377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17442 Z= 0.197 Angle : 0.831 15.084 23688 Z= 0.410 Chirality : 0.048 0.171 2628 Planarity : 0.006 0.084 3150 Dihedral : 4.960 24.144 2466 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.69 % Allowed : 13.09 % Favored : 83.22 % 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 aren not related in a simple way. whole: -1.92 (0.16), residues: 2304 helix: None (None), residues: 0 sheet: -1.24 (0.13), residues: 1260 loop : -1.13 (0.16), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 51 TYR 0.034 0.003 TYR D 59 PHE 0.028 0.003 PHE N 56 TRP 0.021 0.002 TRP A 36 HIS 0.008 0.002 HIS D 20 Details of bonding type rmsd covalent geometry : bond 0.00416 (17442) covalent geometry : angle 0.83135 (23688) hydrogen bonds : bond 0.03475 ( 57) hydrogen bonds : angle 5.76468 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 399 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 1 MET cc_start: 0.5034 (pmm) cc_final: 0.4337 (ptp) REVERT: I 38 MET cc_start: 0.5614 (ttp) cc_final: 0.5257 (ttm) REVERT: K 78 GLU cc_start: 0.5606 (pt0) cc_final: 0.5038 (pt0) REVERT: M 1 MET cc_start: 0.4630 (tmm) cc_final: -0.2320 (mpp) REVERT: O 21 LEU cc_start: 0.7774 (mt) cc_final: 0.7457 (mp) REVERT: H 11 ASN cc_start: 0.7008 (t0) cc_final: 0.6806 (t0) REVERT: H 69 LEU cc_start: 0.4412 (mt) cc_final: 0.4168 (mp) REVERT: N 1 MET cc_start: 0.4401 (tmm) cc_final: 0.4149 (tpp) REVERT: P 38 MET cc_start: 0.4863 (mtp) cc_final: 0.3316 (tmm) REVERT: P 112 MET cc_start: 0.5839 (mmt) cc_final: 0.5597 (mmm) REVERT: R 38 MET cc_start: 0.6693 (mtp) cc_final: 0.4018 (tmm) outliers start: 67 outliers final: 20 residues processed: 434 average time/residue: 0.1406 time to fit residues: 90.0417 Evaluate side-chains 294 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 274 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain O residue 40 ASP Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain P residue 67 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 154 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 145 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 127 optimal weight: 0.0010 chunk 18 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 192 optimal weight: 5.9990 chunk 182 optimal weight: 0.4980 chunk 203 optimal weight: 0.0870 overall best weight: 0.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 125 GLN P 11 ASN R 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.104503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.091653 restraints weight = 33549.568| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 3.34 r_work: 0.3334 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4836 moved from start: 0.8029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17442 Z= 0.108 Angle : 0.633 11.228 23688 Z= 0.299 Chirality : 0.042 0.159 2628 Planarity : 0.004 0.044 3150 Dihedral : 3.988 22.794 2466 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.70 % Allowed : 17.88 % Favored : 79.43 % 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 aren not related in a simple way. whole: -1.13 (0.16), residues: 2304 helix: None (None), residues: 0 sheet: -0.52 (0.14), residues: 1242 loop : -0.89 (0.17), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 118 TYR 0.021 0.001 TYR C 80 PHE 0.030 0.002 PHE N 56 TRP 0.024 0.001 TRP L 24 HIS 0.010 0.001 HIS K 20 Details of bonding type rmsd covalent geometry : bond 0.00237 (17442) covalent geometry : angle 0.63320 (23688) hydrogen bonds : bond 0.02256 ( 57) hydrogen bonds : angle 5.35561 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 345 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 ASN cc_start: 0.7312 (t0) cc_final: 0.7025 (t0) REVERT: A 40 ASP cc_start: 0.4448 (m-30) cc_final: 0.4247 (p0) REVERT: A 76 ASP cc_start: 0.6906 (m-30) cc_final: 0.6314 (p0) REVERT: C 9 VAL cc_start: 0.2867 (OUTLIER) cc_final: 0.2664 (m) REVERT: G 90 TYR cc_start: 0.7134 (p90) cc_final: 0.6524 (p90) REVERT: K 91 ARG cc_start: 0.5653 (OUTLIER) cc_final: 0.5348 (mtt-85) REVERT: M 1 MET cc_start: 0.5334 (tmm) cc_final: 0.5103 (tmm) REVERT: Q 74 LEU cc_start: 0.5667 (tt) cc_final: 0.5386 (tt) REVERT: H 11 ASN cc_start: 0.6702 (t0) cc_final: 0.6378 (t0) REVERT: H 84 GLU cc_start: 0.7745 (tt0) cc_final: 0.7160 (tp30) REVERT: H 90 TYR cc_start: 0.7280 (p90) cc_final: 0.6761 (p90) REVERT: N 9 VAL cc_start: 0.2364 (m) cc_final: 0.1935 (m) REVERT: N 32 GLU cc_start: 0.6547 (pm20) cc_final: 0.6271 (pm20) REVERT: P 38 MET cc_start: 0.5212 (mtp) cc_final: 0.3272 (ttp) REVERT: R 29 GLN cc_start: 0.5435 (OUTLIER) cc_final: 0.5195 (pm20) REVERT: R 38 MET cc_start: 0.7006 (mtp) cc_final: 0.4191 (tmm) outliers start: 49 outliers final: 27 residues processed: 370 average time/residue: 0.1149 time to fit residues: 66.3508 Evaluate side-chains 305 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 275 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 80 TYR Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain K residue 40 ASP Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 53 SER Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 91 ARG Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain O residue 123 LEU Chi-restraints excluded: chain Q residue 14 THR Chi-restraints excluded: chain Q residue 21 LEU Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain P residue 11 ASN Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain R residue 29 GLN Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 123 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 204 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 154 optimal weight: 0.7980 chunk 206 optimal weight: 2.9990 chunk 93 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 186 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 20 HIS C 22 GLN E 11 ASN ** F 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 HIS M 20 HIS O 20 HIS O 22 GLN L 22 GLN N 22 GLN P 11 ASN R 20 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.109380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.096399 restraints weight = 36533.119| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 3.48 r_work: 0.3440 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 1.8506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 17442 Z= 0.291 Angle : 1.019 20.202 23688 Z= 0.520 Chirality : 0.054 0.312 2628 Planarity : 0.007 0.070 3150 Dihedral : 6.648 46.816 2466 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.68 % Allowed : 19.25 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 aren not related in a simple way. whole: -2.20 (0.16), residues: 2304 helix: None (None), residues: 0 sheet: -1.32 (0.14), residues: 1220 loop : -1.49 (0.16), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 118 TYR 0.041 0.003 TYR D 59 PHE 0.030 0.003 PHE D 56 TRP 0.051 0.003 TRP C 24 HIS 0.007 0.002 HIS G 20 Details of bonding type rmsd covalent geometry : bond 0.00635 (17442) covalent geometry : angle 1.01944 (23688) hydrogen bonds : bond 0.04147 ( 57) hydrogen bonds : angle 7.27510 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 625 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 LYS cc_start: 0.7810 (mmmt) cc_final: 0.7484 (mmtm) REVERT: B 11 ASN cc_start: 0.7113 (t0) cc_final: 0.6793 (t0) REVERT: B 31 ASP cc_start: 0.8300 (m-30) cc_final: 0.7931 (m-30) REVERT: B 113 LEU cc_start: 0.8026 (pt) cc_final: 0.7737 (pt) REVERT: B 125 GLN cc_start: 0.8379 (tp-100) cc_final: 0.7781 (tm-30) REVERT: B 126 LYS cc_start: 0.7929 (tmtt) cc_final: 0.7689 (ttmt) REVERT: A 90 TYR cc_start: 0.8414 (p90) cc_final: 0.8169 (p90) REVERT: A 110 ILE cc_start: 0.8939 (mp) cc_final: 0.8693 (mm) REVERT: A 112 MET cc_start: 0.8568 (mtt) cc_final: 0.8360 (mmm) REVERT: C 68 ASP cc_start: 0.7748 (m-30) cc_final: 0.7176 (p0) REVERT: C 91 ARG cc_start: 0.7846 (mpt90) cc_final: 0.7566 (mtt90) REVERT: C 125 GLN cc_start: 0.8054 (pm20) cc_final: 0.7847 (mp10) REVERT: D 43 GLU cc_start: 0.8045 (pp20) cc_final: 0.7723 (pp20) REVERT: D 78 GLU cc_start: 0.8338 (pt0) cc_final: 0.7703 (pp20) REVERT: E 38 MET cc_start: 0.7642 (mmm) cc_final: 0.7440 (mtp) REVERT: E 70 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8068 (mt-10) REVERT: E 79 LEU cc_start: 0.8354 (mp) cc_final: 0.8123 (mp) REVERT: F 13 SER cc_start: 0.7433 (m) cc_final: 0.7209 (p) REVERT: F 27 ASP cc_start: 0.7795 (t70) cc_final: 0.6745 (t70) REVERT: F 125 GLN cc_start: 0.8105 (tm-30) cc_final: 0.7459 (tm-30) REVERT: I 11 ASN cc_start: 0.7232 (t0) cc_final: 0.6977 (t0) REVERT: I 27 ASP cc_start: 0.7907 (t70) cc_final: 0.6686 (t70) REVERT: I 28 THR cc_start: 0.6658 (OUTLIER) cc_final: 0.6359 (m) REVERT: I 29 GLN cc_start: 0.7810 (mt0) cc_final: 0.7535 (mp10) REVERT: I 73 ASP cc_start: 0.8849 (OUTLIER) cc_final: 0.8465 (t0) REVERT: I 78 GLU cc_start: 0.6058 (mt-10) cc_final: 0.5673 (mt-10) REVERT: I 107 LYS cc_start: 0.8255 (pttm) cc_final: 0.6521 (tptt) REVERT: I 108 ASP cc_start: 0.8776 (t0) cc_final: 0.8505 (t0) REVERT: G 22 GLN cc_start: 0.8620 (tp40) cc_final: 0.8160 (tp40) REVERT: G 70 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7738 (mm-30) REVERT: G 78 GLU cc_start: 0.8017 (tt0) cc_final: 0.7754 (tm-30) REVERT: G 80 TYR cc_start: 0.8287 (m-80) cc_final: 0.7830 (m-80) REVERT: G 112 MET cc_start: 0.7850 (mtp) cc_final: 0.7436 (mtt) REVERT: K 40 ASP cc_start: 0.6910 (OUTLIER) cc_final: 0.6575 (p0) REVERT: K 76 ASP cc_start: 0.8150 (m-30) cc_final: 0.7656 (p0) REVERT: M 1 MET cc_start: 0.6442 (tmm) cc_final: 0.6221 (tmm) REVERT: M 38 MET cc_start: 0.6467 (mmp) cc_final: 0.5567 (mtt) REVERT: M 43 GLU cc_start: 0.7593 (pp20) cc_final: 0.6866 (pp20) REVERT: M 76 ASP cc_start: 0.7919 (m-30) cc_final: 0.7697 (t0) REVERT: M 125 GLN cc_start: 0.7720 (pm20) cc_final: 0.7354 (mp10) REVERT: O 27 ASP cc_start: 0.7470 (t70) cc_final: 0.7144 (t70) REVERT: O 29 GLN cc_start: 0.8377 (mp10) cc_final: 0.7896 (mp10) REVERT: O 115 VAL cc_start: 0.8057 (t) cc_final: 0.7823 (m) REVERT: Q 27 ASP cc_start: 0.7096 (t70) cc_final: 0.6392 (t70) REVERT: Q 29 GLN cc_start: 0.7480 (pm20) cc_final: 0.6919 (pm20) REVERT: Q 70 GLU cc_start: 0.8328 (mp0) cc_final: 0.7935 (mp0) REVERT: J 93 VAL cc_start: 0.8216 (t) cc_final: 0.7811 (m) REVERT: J 125 GLN cc_start: 0.8540 (tp-100) cc_final: 0.7967 (tm-30) REVERT: J 126 LYS cc_start: 0.8565 (tptp) cc_final: 0.7879 (ttpt) REVERT: H 11 ASN cc_start: 0.6914 (t0) cc_final: 0.6484 (t0) REVERT: H 31 ASP cc_start: 0.8369 (m-30) cc_final: 0.8057 (m-30) REVERT: H 84 GLU cc_start: 0.8494 (tt0) cc_final: 0.8093 (tt0) REVERT: L 27 ASP cc_start: 0.7870 (t70) cc_final: 0.7643 (t0) REVERT: L 90 TYR cc_start: 0.8616 (p90) cc_final: 0.8278 (p90) REVERT: L 125 GLN cc_start: 0.8052 (mm-40) cc_final: 0.7632 (mm110) REVERT: N 29 GLN cc_start: 0.8522 (mt0) cc_final: 0.8264 (mp10) REVERT: N 76 ASP cc_start: 0.8190 (m-30) cc_final: 0.7824 (t0) REVERT: N 84 GLU cc_start: 0.7775 (mp0) cc_final: 0.6989 (mt-10) REVERT: P 27 ASP cc_start: 0.7212 (t70) cc_final: 0.6345 (t0) REVERT: P 29 GLN cc_start: 0.8529 (pm20) cc_final: 0.7727 (pm20) REVERT: P 70 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7607 (mm-30) outliers start: 85 outliers final: 27 residues processed: 685 average time/residue: 0.1225 time to fit residues: 125.7259 Evaluate side-chains 461 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 431 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain K residue 40 ASP Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 68 ASP Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain Q residue 14 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain R residue 20 HIS Chi-restraints excluded: chain R residue 74 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 175 optimal weight: 7.9990 chunk 179 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 147 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 202 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 GLN D 20 HIS E 20 HIS E 22 GLN E 125 GLN ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 22 GLN J 29 GLN N 22 GLN R 20 HIS R 22 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.078769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.065505 restraints weight = 37532.522| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.41 r_work: 0.2867 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 2.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 17442 Z= 0.314 Angle : 0.898 10.363 23688 Z= 0.448 Chirality : 0.050 0.244 2628 Planarity : 0.006 0.053 3150 Dihedral : 5.838 28.050 2466 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 6.11 % Allowed : 24.37 % Favored : 69.53 % 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 aren not related in a simple way. whole: -2.17 (0.16), residues: 2304 helix: None (None), residues: 0 sheet: -1.25 (0.14), residues: 1242 loop : -1.53 (0.16), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 91 TYR 0.038 0.003 TYR D 59 PHE 0.018 0.003 PHE D 46 TRP 0.031 0.002 TRP N 36 HIS 0.027 0.002 HIS R 20 Details of bonding type rmsd covalent geometry : bond 0.00702 (17442) covalent geometry : angle 0.89823 (23688) hydrogen bonds : bond 0.02779 ( 57) hydrogen bonds : angle 7.04025 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 451 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: B 29 GLN cc_start: 0.9059 (pt0) cc_final: 0.8821 (pt0) REVERT: B 57 GLU cc_start: 0.8465 (pt0) cc_final: 0.8201 (pt0) REVERT: B 112 MET cc_start: 0.8378 (mtp) cc_final: 0.8107 (mmm) REVERT: B 125 GLN cc_start: 0.8671 (tp-100) cc_final: 0.7613 (tm-30) REVERT: A 22 GLN cc_start: 0.8769 (tp40) cc_final: 0.8534 (mm-40) REVERT: A 44 ARG cc_start: 0.8566 (mpt-90) cc_final: 0.8327 (mmm-85) REVERT: A 112 MET cc_start: 0.8930 (mtt) cc_final: 0.8714 (mtt) REVERT: A 125 GLN cc_start: 0.8387 (mm-40) cc_final: 0.7697 (mm-40) REVERT: C 51 ARG cc_start: 0.8761 (ptp-170) cc_final: 0.8548 (ptp90) REVERT: D 29 GLN cc_start: 0.8392 (pm20) cc_final: 0.8189 (pm20) REVERT: D 78 GLU cc_start: 0.8709 (pt0) cc_final: 0.8447 (pt0) REVERT: E 6 ASP cc_start: 0.9079 (t0) cc_final: 0.8769 (t0) REVERT: E 27 ASP cc_start: 0.8158 (t70) cc_final: 0.7841 (t0) REVERT: E 29 GLN cc_start: 0.8725 (mt0) cc_final: 0.8504 (mt0) REVERT: E 70 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8294 (mt-10) REVERT: E 126 LYS cc_start: 0.8771 (mtmm) cc_final: 0.8520 (mtpp) REVERT: F 40 ASP cc_start: 0.8791 (m-30) cc_final: 0.8479 (m-30) REVERT: F 125 GLN cc_start: 0.8366 (tm-30) cc_final: 0.8068 (tm-30) REVERT: I 11 ASN cc_start: 0.7398 (t0) cc_final: 0.6930 (t0) REVERT: I 79 LEU cc_start: 0.9066 (mt) cc_final: 0.8778 (tp) REVERT: G 40 ASP cc_start: 0.8209 (m-30) cc_final: 0.8008 (m-30) REVERT: G 76 ASP cc_start: 0.8700 (t0) cc_final: 0.8316 (t0) REVERT: K 1 MET cc_start: 0.8251 (ttm) cc_final: 0.8006 (ttp) REVERT: M 43 GLU cc_start: 0.8426 (pp20) cc_final: 0.8099 (pt0) REVERT: O 78 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7688 (pt0) REVERT: O 125 GLN cc_start: 0.7507 (pm20) cc_final: 0.7076 (pm20) REVERT: Q 16 ASP cc_start: 0.7676 (p0) cc_final: 0.7464 (p0) REVERT: Q 27 ASP cc_start: 0.8272 (t70) cc_final: 0.7681 (t0) REVERT: Q 29 GLN cc_start: 0.8729 (pm20) cc_final: 0.8240 (pm20) REVERT: J 22 GLN cc_start: 0.8967 (mm110) cc_final: 0.8690 (mm-40) REVERT: J 125 GLN cc_start: 0.8834 (tp-100) cc_final: 0.8161 (tm-30) REVERT: J 126 LYS cc_start: 0.8558 (tptp) cc_final: 0.8313 (ttpt) REVERT: H 11 ASN cc_start: 0.7825 (t0) cc_final: 0.7524 (t0) REVERT: H 27 ASP cc_start: 0.8786 (OUTLIER) cc_final: 0.8494 (p0) REVERT: H 31 ASP cc_start: 0.8644 (m-30) cc_final: 0.8415 (m-30) REVERT: H 40 ASP cc_start: 0.8104 (m-30) cc_final: 0.7846 (m-30) REVERT: H 112 MET cc_start: 0.8827 (mmm) cc_final: 0.8541 (mmt) REVERT: L 3 LYS cc_start: 0.9013 (tppt) cc_final: 0.8808 (tppt) REVERT: L 31 ASP cc_start: 0.8573 (m-30) cc_final: 0.8339 (m-30) REVERT: L 125 GLN cc_start: 0.8471 (mm-40) cc_final: 0.8237 (mm110) REVERT: N 57 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8404 (tm-30) REVERT: R 29 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8608 (pm20) REVERT: R 46 PHE cc_start: 0.6563 (OUTLIER) cc_final: 0.6319 (t80) outliers start: 111 outliers final: 52 residues processed: 534 average time/residue: 0.1302 time to fit residues: 102.7566 Evaluate side-chains 399 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 343 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 104 SER Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 55 ASN Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 55 ASN Chi-restraints excluded: chain O residue 78 GLU Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain P residue 3 LYS Chi-restraints excluded: chain R residue 20 HIS Chi-restraints excluded: chain R residue 29 GLN Chi-restraints excluded: chain R residue 46 PHE Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 128 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 86 optimal weight: 0.5980 chunk 142 optimal weight: 0.0020 chunk 3 optimal weight: 7.9990 chunk 232 optimal weight: 4.9990 chunk 205 optimal weight: 8.9990 chunk 144 optimal weight: 3.9990 chunk 98 optimal weight: 0.0670 chunk 146 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 101 optimal weight: 8.9990 overall best weight: 1.5330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 GLN P 11 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.077913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.064660 restraints weight = 36610.066| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.41 r_work: 0.2847 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 2.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17442 Z= 0.141 Angle : 0.663 9.589 23688 Z= 0.322 Chirality : 0.043 0.146 2628 Planarity : 0.005 0.044 3150 Dihedral : 4.450 23.516 2466 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.52 % Allowed : 27.89 % Favored : 68.59 % 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 aren not related in a simple way. whole: -1.68 (0.16), residues: 2304 helix: None (None), residues: 0 sheet: -0.89 (0.14), residues: 1260 loop : -1.26 (0.17), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 51 TYR 0.023 0.001 TYR K 90 PHE 0.016 0.002 PHE M 56 TRP 0.014 0.001 TRP L 24 HIS 0.013 0.001 HIS R 20 Details of bonding type rmsd covalent geometry : bond 0.00324 (17442) covalent geometry : angle 0.66264 (23688) hydrogen bonds : bond 0.01713 ( 57) hydrogen bonds : angle 5.96289 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 375 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 103 GLU cc_start: 0.8340 (mp0) cc_final: 0.7818 (mp0) REVERT: B 112 MET cc_start: 0.8449 (mtp) cc_final: 0.8210 (mmm) REVERT: B 125 GLN cc_start: 0.8713 (tp-100) cc_final: 0.7777 (tm-30) REVERT: A 22 GLN cc_start: 0.8837 (tp40) cc_final: 0.8606 (mm-40) REVERT: A 27 ASP cc_start: 0.8875 (p0) cc_final: 0.8415 (p0) REVERT: A 31 ASP cc_start: 0.8717 (m-30) cc_final: 0.8384 (m-30) REVERT: A 44 ARG cc_start: 0.8613 (mpt-90) cc_final: 0.8307 (mmm-85) REVERT: A 68 ASP cc_start: 0.8815 (m-30) cc_final: 0.8372 (p0) REVERT: A 125 GLN cc_start: 0.8524 (mm-40) cc_final: 0.7860 (mm-40) REVERT: C 125 GLN cc_start: 0.8614 (mp10) cc_final: 0.8305 (mp10) REVERT: D 11 ASN cc_start: 0.8650 (m-40) cc_final: 0.8421 (t0) REVERT: D 59 TYR cc_start: 0.7628 (OUTLIER) cc_final: 0.7077 (t80) REVERT: E 3 LYS cc_start: 0.8574 (mmtm) cc_final: 0.8136 (mmmt) REVERT: E 27 ASP cc_start: 0.8082 (t70) cc_final: 0.7596 (t0) REVERT: E 91 ARG cc_start: 0.8842 (mpt90) cc_final: 0.8531 (mpt180) REVERT: F 84 GLU cc_start: 0.8529 (tt0) cc_final: 0.8324 (tt0) REVERT: F 103 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7958 (mp0) REVERT: F 112 MET cc_start: 0.9006 (mmt) cc_final: 0.8713 (mmt) REVERT: F 125 GLN cc_start: 0.8466 (tm-30) cc_final: 0.8184 (tm-30) REVERT: I 1 MET cc_start: 0.8980 (ptp) cc_final: 0.8712 (ptp) REVERT: I 11 ASN cc_start: 0.7708 (t0) cc_final: 0.7397 (t0) REVERT: I 79 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8729 (tp) REVERT: G 44 ARG cc_start: 0.8464 (mmm-85) cc_final: 0.8108 (mmm-85) REVERT: G 70 GLU cc_start: 0.8313 (mm-30) cc_final: 0.8056 (mm-30) REVERT: K 103 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7972 (tm-30) REVERT: M 43 GLU cc_start: 0.8307 (pp20) cc_final: 0.7949 (pt0) REVERT: O 112 MET cc_start: 0.8958 (mmm) cc_final: 0.8720 (mmt) REVERT: Q 27 ASP cc_start: 0.8380 (t70) cc_final: 0.7762 (t70) REVERT: Q 29 GLN cc_start: 0.8759 (pm20) cc_final: 0.8121 (pm20) REVERT: J 125 GLN cc_start: 0.8733 (tp-100) cc_final: 0.8324 (tm-30) REVERT: H 84 GLU cc_start: 0.8417 (tt0) cc_final: 0.8082 (tt0) REVERT: H 125 GLN cc_start: 0.8428 (mm-40) cc_final: 0.8203 (mm110) REVERT: L 112 MET cc_start: 0.8847 (mmm) cc_final: 0.8647 (mmm) REVERT: L 125 GLN cc_start: 0.8533 (mm-40) cc_final: 0.8300 (mm110) REVERT: N 57 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8417 (tm-30) REVERT: P 27 ASP cc_start: 0.8288 (t0) cc_final: 0.7022 (t70) REVERT: P 29 GLN cc_start: 0.8599 (pm20) cc_final: 0.7871 (pm20) REVERT: P 43 GLU cc_start: 0.8415 (pp20) cc_final: 0.8052 (pt0) REVERT: R 29 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8154 (pm20) outliers start: 64 outliers final: 50 residues processed: 420 average time/residue: 0.1225 time to fit residues: 76.7672 Evaluate side-chains 388 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 335 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain E residue 20 HIS Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain G residue 67 ASP Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain K residue 20 HIS Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain K residue 104 SER Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 103 GLU Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain N residue 29 GLN Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 91 ARG Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain R residue 29 GLN Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 128 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 93 optimal weight: 4.9990 chunk 191 optimal weight: 9.9990 chunk 144 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 65 optimal weight: 0.0870 chunk 72 optimal weight: 5.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 ASN ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 GLN P 22 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.073420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.060432 restraints weight = 37222.782| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 3.40 r_work: 0.2749 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 2.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 17442 Z= 0.226 Angle : 0.711 9.088 23688 Z= 0.348 Chirality : 0.044 0.145 2628 Planarity : 0.005 0.043 3150 Dihedral : 4.989 22.473 2466 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.90 % Allowed : 26.90 % Favored : 68.21 % 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 aren not related in a simple way. whole: -1.78 (0.16), residues: 2304 helix: None (None), residues: 0 sheet: -1.02 (0.14), residues: 1296 loop : -1.21 (0.17), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 44 TYR 0.020 0.002 TYR D 59 PHE 0.013 0.002 PHE M 56 TRP 0.016 0.001 TRP C 24 HIS 0.004 0.001 HIS K 20 Details of bonding type rmsd covalent geometry : bond 0.00517 (17442) covalent geometry : angle 0.71084 (23688) hydrogen bonds : bond 0.01836 ( 57) hydrogen bonds : angle 6.34700 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 337 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 MET cc_start: 0.8554 (mtp) cc_final: 0.8225 (mmm) REVERT: B 125 GLN cc_start: 0.8827 (tp-100) cc_final: 0.7897 (tm-30) REVERT: A 22 GLN cc_start: 0.8952 (tp40) cc_final: 0.8751 (mm-40) REVERT: A 27 ASP cc_start: 0.9011 (OUTLIER) cc_final: 0.8532 (p0) REVERT: A 31 ASP cc_start: 0.8689 (m-30) cc_final: 0.8402 (m-30) REVERT: A 68 ASP cc_start: 0.8985 (m-30) cc_final: 0.8241 (p0) REVERT: A 70 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7518 (mp0) REVERT: D 2 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8584 (mt) REVERT: D 59 TYR cc_start: 0.7835 (OUTLIER) cc_final: 0.7049 (t80) REVERT: E 1 MET cc_start: 0.8680 (ttp) cc_final: 0.8371 (ptm) REVERT: E 3 LYS cc_start: 0.8781 (mmtm) cc_final: 0.8041 (mmmt) REVERT: F 112 MET cc_start: 0.8981 (mmt) cc_final: 0.8691 (mmt) REVERT: F 125 GLN cc_start: 0.8369 (tm-30) cc_final: 0.8037 (tm-30) REVERT: I 11 ASN cc_start: 0.7877 (t0) cc_final: 0.7541 (t0) REVERT: I 31 ASP cc_start: 0.8634 (m-30) cc_final: 0.8412 (m-30) REVERT: I 79 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8939 (mt) REVERT: G 44 ARG cc_start: 0.8390 (mmm-85) cc_final: 0.7959 (mmm-85) REVERT: G 70 GLU cc_start: 0.8273 (mm-30) cc_final: 0.8052 (mm-30) REVERT: M 125 GLN cc_start: 0.8631 (pm20) cc_final: 0.8264 (mp10) REVERT: O 57 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8542 (tm-30) REVERT: O 103 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7422 (tm-30) REVERT: O 112 MET cc_start: 0.8979 (mmm) cc_final: 0.8372 (mmt) REVERT: Q 27 ASP cc_start: 0.8665 (t70) cc_final: 0.8011 (t70) REVERT: Q 29 GLN cc_start: 0.8817 (pm20) cc_final: 0.7717 (pm20) REVERT: Q 123 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8992 (mp) REVERT: J 125 GLN cc_start: 0.8780 (tp-100) cc_final: 0.8268 (tm-30) REVERT: H 57 GLU cc_start: 0.8645 (pt0) cc_final: 0.8319 (pt0) REVERT: H 103 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7662 (mp0) REVERT: H 125 GLN cc_start: 0.8352 (mm-40) cc_final: 0.7930 (mm110) REVERT: L 125 GLN cc_start: 0.8606 (mm-40) cc_final: 0.8317 (mm110) REVERT: N 57 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8461 (tm-30) REVERT: N 125 GLN cc_start: 0.8484 (pm20) cc_final: 0.8151 (mp10) REVERT: P 27 ASP cc_start: 0.8383 (t0) cc_final: 0.8164 (t70) REVERT: R 1 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.7843 (ppp) REVERT: R 29 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8062 (pm20) outliers start: 89 outliers final: 68 residues processed: 403 average time/residue: 0.1312 time to fit residues: 77.5356 Evaluate side-chains 397 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 322 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 20 HIS Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain K residue 20 HIS Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 32 GLU Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 103 GLU Chi-restraints excluded: chain Q residue 123 LEU Chi-restraints excluded: chain Q residue 128 THR Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain N residue 29 GLN Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 91 ARG Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain P residue 3 LYS Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 104 SER Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 29 GLN Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 128 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 69 optimal weight: 6.9990 chunk 32 optimal weight: 0.0010 chunk 24 optimal weight: 4.9990 chunk 136 optimal weight: 0.0470 chunk 94 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.6090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.073957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.061153 restraints weight = 38222.173| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 3.36 r_work: 0.2779 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 2.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17442 Z= 0.138 Angle : 0.622 8.598 23688 Z= 0.302 Chirality : 0.042 0.137 2628 Planarity : 0.004 0.041 3150 Dihedral : 4.335 21.357 2466 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.80 % Allowed : 28.11 % Favored : 68.10 % 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 aren not related in a simple way. whole: -1.41 (0.17), residues: 2304 helix: None (None), residues: 0 sheet: -0.70 (0.14), residues: 1260 loop : -1.09 (0.17), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 44 TYR 0.015 0.001 TYR D 59 PHE 0.014 0.002 PHE N 56 TRP 0.012 0.001 TRP E 24 HIS 0.003 0.001 HIS E 20 Details of bonding type rmsd covalent geometry : bond 0.00319 (17442) covalent geometry : angle 0.62241 (23688) hydrogen bonds : bond 0.01485 ( 57) hydrogen bonds : angle 5.92170 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 338 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 MET cc_start: 0.8494 (mtp) cc_final: 0.8159 (mmm) REVERT: B 125 GLN cc_start: 0.8756 (tp-100) cc_final: 0.7853 (tm-30) REVERT: A 22 GLN cc_start: 0.8898 (tp40) cc_final: 0.8590 (mm-40) REVERT: A 27 ASP cc_start: 0.8916 (p0) cc_final: 0.8524 (p0) REVERT: A 68 ASP cc_start: 0.8960 (m-30) cc_final: 0.8278 (p0) REVERT: A 70 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7486 (mp0) REVERT: A 125 GLN cc_start: 0.8398 (mm-40) cc_final: 0.8189 (mm110) REVERT: C 43 GLU cc_start: 0.8257 (pm20) cc_final: 0.7521 (pt0) REVERT: C 125 GLN cc_start: 0.8588 (mp10) cc_final: 0.8345 (mp10) REVERT: D 11 ASN cc_start: 0.8593 (m-40) cc_final: 0.8392 (t0) REVERT: D 59 TYR cc_start: 0.7903 (OUTLIER) cc_final: 0.7098 (t80) REVERT: E 1 MET cc_start: 0.8712 (ttp) cc_final: 0.8434 (ptm) REVERT: E 3 LYS cc_start: 0.8779 (mmtm) cc_final: 0.8281 (mmmt) REVERT: F 112 MET cc_start: 0.9036 (mmt) cc_final: 0.8750 (mmt) REVERT: F 125 GLN cc_start: 0.8396 (tm-30) cc_final: 0.8109 (tm-30) REVERT: I 11 ASN cc_start: 0.8016 (t0) cc_final: 0.7671 (t0) REVERT: G 103 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7477 (mp0) REVERT: G 112 MET cc_start: 0.8662 (mtt) cc_final: 0.8389 (mtt) REVERT: M 125 GLN cc_start: 0.8550 (pm20) cc_final: 0.8227 (mp10) REVERT: O 57 GLU cc_start: 0.8969 (tm-30) cc_final: 0.8652 (tm-30) REVERT: O 103 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7579 (tm-30) REVERT: O 112 MET cc_start: 0.8927 (mmm) cc_final: 0.8385 (mmt) REVERT: Q 27 ASP cc_start: 0.8641 (t70) cc_final: 0.8363 (t70) REVERT: Q 126 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8108 (ttmt) REVERT: J 125 GLN cc_start: 0.8814 (tp-100) cc_final: 0.8359 (tm-30) REVERT: H 57 GLU cc_start: 0.8585 (pt0) cc_final: 0.8287 (pt0) REVERT: H 103 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7856 (mp0) REVERT: H 125 GLN cc_start: 0.8406 (mm-40) cc_final: 0.8036 (mm110) REVERT: L 125 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8520 (mm110) REVERT: N 57 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8491 (tt0) REVERT: N 125 GLN cc_start: 0.8429 (pm20) cc_final: 0.8111 (mp10) REVERT: P 27 ASP cc_start: 0.8178 (t0) cc_final: 0.7858 (t70) REVERT: R 1 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.7905 (ppp) outliers start: 69 outliers final: 51 residues processed: 384 average time/residue: 0.1576 time to fit residues: 86.8169 Evaluate side-chains 376 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 322 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain E residue 20 HIS Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 103 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 103 GLU Chi-restraints excluded: chain Q residue 126 LYS Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 32 GLU Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain N residue 29 GLN Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 91 ARG Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 5 LYS Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 128 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 140 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 229 optimal weight: 8.9990 chunk 197 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 194 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 226 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN D 29 GLN Q 22 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.070195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.057631 restraints weight = 39076.257| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 3.30 r_work: 0.2695 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 2.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 17442 Z= 0.313 Angle : 0.751 8.670 23688 Z= 0.369 Chirality : 0.045 0.152 2628 Planarity : 0.005 0.041 3150 Dihedral : 5.289 25.427 2466 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.62 % Allowed : 27.72 % Favored : 67.66 % 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 aren not related in a simple way. whole: -1.79 (0.17), residues: 2304 helix: None (None), residues: 0 sheet: -1.07 (0.14), residues: 1296 loop : -1.16 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 118 TYR 0.026 0.003 TYR E 80 PHE 0.015 0.002 PHE J 56 TRP 0.016 0.002 TRP E 24 HIS 0.004 0.001 HIS E 20 Details of bonding type rmsd covalent geometry : bond 0.00713 (17442) covalent geometry : angle 0.75084 (23688) hydrogen bonds : bond 0.01948 ( 57) hydrogen bonds : angle 6.50377 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 309 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 112 MET cc_start: 0.8617 (mtp) cc_final: 0.8277 (mmm) REVERT: B 125 GLN cc_start: 0.8732 (tp-100) cc_final: 0.7860 (tm-30) REVERT: A 22 GLN cc_start: 0.9025 (tp40) cc_final: 0.8777 (mm-40) REVERT: A 27 ASP cc_start: 0.8957 (OUTLIER) cc_final: 0.8668 (p0) REVERT: A 68 ASP cc_start: 0.9008 (m-30) cc_final: 0.8382 (p0) REVERT: C 1 MET cc_start: 0.7594 (tpp) cc_final: 0.7305 (tpt) REVERT: C 43 GLU cc_start: 0.8449 (pm20) cc_final: 0.7994 (pt0) REVERT: C 125 GLN cc_start: 0.8564 (mp10) cc_final: 0.8304 (mp10) REVERT: D 29 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8456 (pm20) REVERT: D 59 TYR cc_start: 0.8128 (OUTLIER) cc_final: 0.7066 (t80) REVERT: E 1 MET cc_start: 0.8727 (ttp) cc_final: 0.8498 (ptm) REVERT: E 76 ASP cc_start: 0.8417 (t0) cc_final: 0.8033 (p0) REVERT: F 44 ARG cc_start: 0.8463 (mtp85) cc_final: 0.8186 (mtp180) REVERT: F 112 MET cc_start: 0.9072 (mmt) cc_final: 0.8764 (mmt) REVERT: F 125 GLN cc_start: 0.8366 (tm-30) cc_final: 0.8060 (tm-30) REVERT: I 11 ASN cc_start: 0.8342 (t0) cc_final: 0.7996 (t0) REVERT: G 103 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7542 (mp0) REVERT: M 103 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7990 (tm-30) REVERT: M 125 GLN cc_start: 0.8464 (pm20) cc_final: 0.8180 (mp10) REVERT: O 57 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8467 (tm-30) REVERT: O 112 MET cc_start: 0.8907 (mmm) cc_final: 0.8326 (mmt) REVERT: Q 27 ASP cc_start: 0.8788 (t70) cc_final: 0.8519 (t0) REVERT: Q 126 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8302 (ttmt) REVERT: J 125 GLN cc_start: 0.8850 (tp-100) cc_final: 0.8155 (tm-30) REVERT: H 57 GLU cc_start: 0.8667 (pt0) cc_final: 0.8413 (pt0) REVERT: H 103 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8015 (mp0) REVERT: L 103 GLU cc_start: 0.8619 (pt0) cc_final: 0.8201 (pm20) REVERT: L 125 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8240 (mm110) REVERT: N 57 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8168 (tm-30) REVERT: N 103 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8225 (tm-30) REVERT: N 125 GLN cc_start: 0.8370 (pm20) cc_final: 0.8123 (mp10) REVERT: R 1 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.7637 (ppp) REVERT: R 46 PHE cc_start: 0.6478 (OUTLIER) cc_final: 0.6158 (t80) outliers start: 84 outliers final: 69 residues processed: 364 average time/residue: 0.1545 time to fit residues: 80.5540 Evaluate side-chains 373 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 298 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain E residue 20 HIS Chi-restraints excluded: chain E residue 29 GLN Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 103 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 32 GLU Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain K residue 104 SER Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain M residue 29 GLN Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 103 GLU Chi-restraints excluded: chain Q residue 126 LYS Chi-restraints excluded: chain Q residue 128 THR Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain N residue 29 GLN Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 91 ARG Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain P residue 3 LYS Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 5 LYS Chi-restraints excluded: chain R residue 46 PHE Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 128 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 116 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 188 optimal weight: 5.9990 chunk 214 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 175 optimal weight: 0.0060 overall best weight: 2.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN D 29 GLN F 20 HIS H 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.072021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.059404 restraints weight = 38292.559| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 3.34 r_work: 0.2735 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 2.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17442 Z= 0.175 Angle : 0.646 8.662 23688 Z= 0.316 Chirality : 0.043 0.138 2628 Planarity : 0.004 0.045 3150 Dihedral : 4.713 23.534 2466 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.91 % Allowed : 28.27 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.17), residues: 2304 helix: None (None), residues: 0 sheet: -0.95 (0.14), residues: 1296 loop : -1.02 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 91 TYR 0.019 0.002 TYR D 59 PHE 0.014 0.002 PHE M 56 TRP 0.017 0.001 TRP M 24 HIS 0.003 0.001 HIS E 20 Details of bonding type rmsd covalent geometry : bond 0.00403 (17442) covalent geometry : angle 0.64604 (23688) hydrogen bonds : bond 0.01567 ( 57) hydrogen bonds : angle 6.22958 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 320 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 MET cc_start: 0.8547 (mtp) cc_final: 0.8214 (mmm) REVERT: B 125 GLN cc_start: 0.8764 (tp-100) cc_final: 0.8071 (tm-30) REVERT: A 22 GLN cc_start: 0.8990 (tp40) cc_final: 0.8750 (mm-40) REVERT: A 27 ASP cc_start: 0.8951 (p0) cc_final: 0.8610 (p0) REVERT: A 68 ASP cc_start: 0.8806 (m-30) cc_final: 0.8373 (p0) REVERT: C 1 MET cc_start: 0.7667 (tpp) cc_final: 0.7368 (tpt) REVERT: C 43 GLU cc_start: 0.8362 (pm20) cc_final: 0.7942 (pt0) REVERT: C 125 GLN cc_start: 0.8588 (mp10) cc_final: 0.8336 (mp10) REVERT: D 29 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8351 (pm20) REVERT: D 59 TYR cc_start: 0.8019 (OUTLIER) cc_final: 0.6918 (t80) REVERT: E 1 MET cc_start: 0.8714 (ttp) cc_final: 0.8453 (ptm) REVERT: E 3 LYS cc_start: 0.8838 (mmtm) cc_final: 0.8556 (mmtm) REVERT: E 103 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7908 (mp0) REVERT: F 84 GLU cc_start: 0.8490 (tt0) cc_final: 0.8217 (tt0) REVERT: F 112 MET cc_start: 0.9065 (mmt) cc_final: 0.8775 (mmt) REVERT: F 125 GLN cc_start: 0.8361 (tm-30) cc_final: 0.8092 (tm-30) REVERT: G 103 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7654 (mp0) REVERT: G 112 MET cc_start: 0.8708 (mtt) cc_final: 0.8439 (mtt) REVERT: K 11 ASN cc_start: 0.8738 (m-40) cc_final: 0.8044 (t0) REVERT: M 125 GLN cc_start: 0.8441 (pm20) cc_final: 0.8227 (mp10) REVERT: O 57 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8507 (tm-30) REVERT: O 103 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7569 (tm-30) REVERT: O 112 MET cc_start: 0.8864 (mmm) cc_final: 0.8335 (mmt) REVERT: Q 27 ASP cc_start: 0.8692 (t70) cc_final: 0.8435 (t70) REVERT: J 125 GLN cc_start: 0.8911 (tp-100) cc_final: 0.8220 (tm-30) REVERT: H 57 GLU cc_start: 0.8593 (pt0) cc_final: 0.8351 (pt0) REVERT: H 103 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7956 (mp0) REVERT: H 125 GLN cc_start: 0.8496 (mm-40) cc_final: 0.8125 (mm110) REVERT: L 103 GLU cc_start: 0.8573 (pt0) cc_final: 0.8158 (pm20) REVERT: L 125 GLN cc_start: 0.8732 (mm-40) cc_final: 0.8275 (mm110) REVERT: N 57 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8272 (tm-30) REVERT: N 103 GLU cc_start: 0.8283 (tm-30) cc_final: 0.8000 (tm-30) REVERT: N 125 GLN cc_start: 0.8308 (pm20) cc_final: 0.8068 (mp10) REVERT: R 1 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.7814 (ppp) REVERT: R 46 PHE cc_start: 0.6367 (OUTLIER) cc_final: 0.6076 (t80) outliers start: 71 outliers final: 62 residues processed: 364 average time/residue: 0.1543 time to fit residues: 80.7303 Evaluate side-chains 378 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 311 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 20 HIS Chi-restraints excluded: chain E residue 29 GLN Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 103 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 32 GLU Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain K residue 104 SER Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 29 GLN Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 91 ARG Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 103 GLU Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 32 GLU Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain N residue 29 GLN Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 91 ARG Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain P residue 3 LYS Chi-restraints excluded: chain P residue 104 SER Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 5 LYS Chi-restraints excluded: chain R residue 46 PHE Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 128 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 5 optimal weight: 0.3980 chunk 0 optimal weight: 6.9990 chunk 51 optimal weight: 0.0570 chunk 102 optimal weight: 0.9980 chunk 216 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 178 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.8902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN D 29 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.074329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.061488 restraints weight = 38044.494| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 3.36 r_work: 0.2781 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 2.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17442 Z= 0.103 Angle : 0.602 9.879 23688 Z= 0.292 Chirality : 0.041 0.141 2628 Planarity : 0.004 0.043 3150 Dihedral : 4.179 21.765 2466 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.36 % Allowed : 28.93 % Favored : 67.71 % 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 aren not related in a simple way. whole: -1.20 (0.17), residues: 2304 helix: None (None), residues: 0 sheet: -0.54 (0.15), residues: 1242 loop : -0.97 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 91 TYR 0.014 0.001 TYR D 59 PHE 0.015 0.002 PHE N 56 TRP 0.018 0.001 TRP M 24 HIS 0.002 0.000 HIS E 20 Details of bonding type rmsd covalent geometry : bond 0.00242 (17442) covalent geometry : angle 0.60226 (23688) hydrogen bonds : bond 0.01432 ( 57) hydrogen bonds : angle 5.93876 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3105.23 seconds wall clock time: 54 minutes 14.28 seconds (3254.28 seconds total)