Starting phenix.real_space_refine on Sun May 18 12:00:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gtb_34248/05_2025/8gtb_34248.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gtb_34248/05_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_34248/05_2025/8gtb_34248.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gtb_34248/05_2025/8gtb_34248.map" model { file = "/net/cci-nas-00/data/ceres_data/8gtb_34248/05_2025/8gtb_34248.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gtb_34248/05_2025/8gtb_34248.cif" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17136 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" 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: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, R Time building chain proxies: 4.59, per 1000 atoms: 0.27 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: 3.92 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 1.51 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: 3.85 Time building geometry restraints manager: 4.58 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: 0.18 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 32.030 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.900 ------------------------------------------------------------------------------- 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 : 7.43 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (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 TRP 0.006 0.001 TRP I 24 HIS 0.002 0.001 HIS M 20 PHE 0.007 0.002 PHE L 56 TYR 0.007 0.001 TYR O 90 ARG 0.001 0.000 ARG M 30 Details of bonding type rmsd hydrogen bonds : bond 0.16112 ( 57) hydrogen bonds : angle 12.18361 ( 171) covalent geometry : bond 0.00701 (17442) covalent geometry : angle 0.71433 (23688) *********************** 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 : 1.619 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: 0.6631 (t0) REVERT: A 76 ASP cc_start: 0.6058 (m-30) cc_final: 0.5723 (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: 0.2336 (m-80) REVERT: H 11 ASN cc_start: 0.6636 (t0) cc_final: 0.6372 (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: 0.0606 (mtm) REVERT: H 113 LEU cc_start: 0.5032 (tp) cc_final: 0.4649 (tp) REVERT: L 81 PRO cc_start: 0.3394 (Cg_exo) cc_final: 0.2815 (Cg_endo) REVERT: P 38 MET cc_start: 0.3380 (mtp) cc_final: 0.2608 (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: 0.3186 time to fit residues: 190.7272 Evaluate side-chains 205 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 2.9990 chunk 177 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 60 optimal weight: 0.0170 chunk 119 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 111 optimal weight: 0.3980 chunk 136 optimal weight: 0.3980 chunk 212 optimal weight: 0.9990 overall best weight: 0.5620 ------------------------------------------------------------------------------- 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 125 GLN E 125 GLN F 20 HIS ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 GLN I 125 GLN G 125 GLN K 125 GLN O 125 GLN Q 125 GLN H 125 GLN L 125 GLN P 125 GLN R 125 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.102211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.089938 restraints weight = 31901.597| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.82 r_work: 0.3297 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3358 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17442 Z= 0.130 Angle : 0.671 11.508 23688 Z= 0.324 Chirality : 0.043 0.182 2628 Planarity : 0.004 0.042 3150 Dihedral : 4.169 20.454 2466 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.81 % Allowed : 12.60 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.15), residues: 2304 helix: None (None), residues: 0 sheet: -1.17 (0.13), residues: 1242 loop : -1.12 (0.16), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 36 HIS 0.005 0.001 HIS F 20 PHE 0.046 0.002 PHE N 56 TYR 0.017 0.002 TYR D 59 ARG 0.005 0.001 ARG N 91 Details of bonding type rmsd hydrogen bonds : bond 0.02592 ( 57) hydrogen bonds : angle 6.53913 ( 171) covalent geometry : bond 0.00276 (17442) covalent geometry : angle 0.67138 (23688) *********************** 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 348 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 297 time to evaluate : 1.628 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 1 MET cc_start: 0.5996 (pmm) cc_final: 0.5585 (mtp) REVERT: F 1 MET cc_start: 0.1427 (pmm) cc_final: 0.1086 (ptm) REVERT: K 1 MET cc_start: 0.3649 (ttm) cc_final: 0.3002 (tmm) REVERT: K 38 MET cc_start: 0.0107 (mtp) cc_final: -0.0334 (ttm) REVERT: K 112 MET cc_start: 0.6063 (pmm) cc_final: 0.5780 (pmm) REVERT: J 1 MET cc_start: 0.4700 (pmm) cc_final: 0.4137 (ptm) REVERT: H 93 VAL cc_start: 0.4691 (t) cc_final: 0.4481 (t) REVERT: N 1 MET cc_start: 0.4494 (tmm) cc_final: 0.4148 (tpp) REVERT: P 38 MET cc_start: 0.4002 (mtp) cc_final: 0.2981 (tmm) REVERT: R 38 MET cc_start: 0.5801 (mtp) cc_final: 0.3159 (tmm) outliers start: 51 outliers final: 27 residues processed: 325 average time/residue: 0.2849 time to fit residues: 139.1131 Evaluate side-chains 236 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 209 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 LEU 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 C residue 112 MET Chi-restraints excluded: chain D residue 5 LYS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain F residue 21 LEU 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 26 LEU Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain Q residue 14 THR Chi-restraints excluded: chain Q residue 119 THR 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 58 VAL Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain P residue 58 VAL 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 161 optimal weight: 0.7980 chunk 207 optimal weight: 0.6980 chunk 146 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 208 optimal weight: 6.9990 chunk 213 optimal weight: 0.7980 chunk 171 optimal weight: 0.5980 chunk 104 optimal weight: 6.9990 chunk 201 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 22 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3650 r_free = 0.3650 target = 0.106346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.093325 restraints weight = 33202.095| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 3.37 r_work: 0.3351 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5122 moved from start: 0.8701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 17442 Z= 0.199 Angle : 0.776 13.230 23688 Z= 0.382 Chirality : 0.045 0.227 2628 Planarity : 0.006 0.073 3150 Dihedral : 4.449 21.372 2466 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.80 % Allowed : 15.95 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.16), residues: 2304 helix: None (None), residues: 0 sheet: -0.68 (0.14), residues: 1242 loop : -0.93 (0.17), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 24 HIS 0.004 0.001 HIS J 20 PHE 0.036 0.003 PHE N 56 TYR 0.031 0.002 TYR D 59 ARG 0.009 0.001 ARG L 51 Details of bonding type rmsd hydrogen bonds : bond 0.02949 ( 57) hydrogen bonds : angle 5.93726 ( 171) covalent geometry : bond 0.00441 (17442) covalent geometry : angle 0.77649 (23688) *********************** 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 487 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 418 time to evaluate : 1.695 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: B 11 ASN cc_start: 0.7157 (t0) cc_final: 0.6877 (t0) REVERT: A 75 VAL cc_start: 0.3747 (OUTLIER) cc_final: 0.3515 (p) REVERT: C 99 LEU cc_start: 0.7802 (tt) cc_final: 0.7246 (tp) REVERT: I 1 MET cc_start: 0.5777 (pmm) cc_final: 0.4592 (ptp) REVERT: M 1 MET cc_start: 0.4890 (tmm) cc_final: -0.1800 (mmt) REVERT: M 18 ILE cc_start: 0.5383 (mm) cc_final: 0.5021 (mm) REVERT: M 74 LEU cc_start: 0.6862 (pp) cc_final: 0.6642 (pp) REVERT: J 24 TRP cc_start: 0.4700 (p-90) cc_final: 0.4226 (p90) REVERT: J 112 MET cc_start: 0.3663 (OUTLIER) cc_final: 0.3407 (mmm) REVERT: J 125 GLN cc_start: 0.7393 (tp-100) cc_final: 0.6591 (tm-30) REVERT: H 47 THR cc_start: 0.6151 (p) cc_final: 0.5834 (p) REVERT: H 84 GLU cc_start: 0.7868 (tt0) cc_final: 0.7363 (tp30) REVERT: H 106 SER cc_start: 0.6831 (OUTLIER) cc_final: 0.6589 (t) REVERT: N 119 THR cc_start: 0.6392 (t) cc_final: 0.6145 (t) REVERT: P 38 MET cc_start: 0.5583 (mtp) cc_final: 0.3429 (ttp) outliers start: 69 outliers final: 27 residues processed: 453 average time/residue: 0.2777 time to fit residues: 187.7440 Evaluate side-chains 338 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 308 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain E residue 21 LEU 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 86 THR Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain Q residue 14 THR Chi-restraints excluded: chain Q residue 112 MET Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 112 MET Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain P residue 67 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 13 optimal weight: 0.0970 chunk 49 optimal weight: 2.9990 chunk 213 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 6 optimal weight: 0.4980 chunk 99 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 221 optimal weight: 0.8980 chunk 110 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN C 20 HIS ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 125 GLN ** R 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.105966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.092919 restraints weight = 34150.556| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 3.40 r_work: 0.3358 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5778 moved from start: 1.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 17442 Z= 0.126 Angle : 0.665 12.211 23688 Z= 0.314 Chirality : 0.043 0.225 2628 Planarity : 0.005 0.073 3150 Dihedral : 3.996 21.580 2466 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.63 % Allowed : 19.80 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.17), residues: 2304 helix: None (None), residues: 0 sheet: -0.33 (0.14), residues: 1260 loop : -0.65 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 24 HIS 0.005 0.001 HIS N 20 PHE 0.022 0.002 PHE Q 46 TYR 0.028 0.001 TYR D 59 ARG 0.006 0.001 ARG O 51 Details of bonding type rmsd hydrogen bonds : bond 0.01907 ( 57) hydrogen bonds : angle 5.29698 ( 171) covalent geometry : bond 0.00273 (17442) covalent geometry : angle 0.66500 (23688) *********************** 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 482 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 416 time to evaluate : 1.866 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: B 11 ASN cc_start: 0.6961 (t0) cc_final: 0.6670 (t0) REVERT: A 103 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6802 (mt-10) REVERT: C 99 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8022 (tp) REVERT: F 123 LEU cc_start: 0.6023 (pt) cc_final: 0.5628 (tp) REVERT: I 1 MET cc_start: 0.6185 (pmm) cc_final: 0.5185 (ptt) REVERT: I 112 MET cc_start: 0.2035 (tpp) cc_final: 0.1820 (mmt) REVERT: M 79 LEU cc_start: 0.3131 (OUTLIER) cc_final: 0.2750 (mt) REVERT: J 73 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.8071 (t70) REVERT: J 123 LEU cc_start: 0.6278 (pt) cc_final: 0.5809 (tp) REVERT: J 125 GLN cc_start: 0.7744 (tp-100) cc_final: 0.6985 (tm-30) REVERT: H 60 LEU cc_start: 0.6584 (mp) cc_final: 0.6330 (mp) REVERT: H 80 TYR cc_start: 0.7842 (OUTLIER) cc_final: 0.7124 (t80) REVERT: L 16 ASP cc_start: 0.7850 (p0) cc_final: 0.7610 (p0) REVERT: L 91 ARG cc_start: 0.6739 (ptp90) cc_final: 0.6519 (mtt-85) REVERT: P 27 ASP cc_start: 0.7504 (p0) cc_final: 0.7036 (p0) outliers start: 66 outliers final: 33 residues processed: 445 average time/residue: 0.2723 time to fit residues: 183.5205 Evaluate side-chains 373 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 336 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 24 TRP Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 120 SER Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 53 SER 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 Q residue 21 LEU Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 112 MET Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain P residue 11 ASN Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain R residue 21 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 134 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 197 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 209 optimal weight: 0.0010 chunk 24 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 chunk 188 optimal weight: 0.0030 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 20 HIS E 22 GLN I 22 GLN ** K 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 22 GLN P 22 GLN ** R 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.104511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.091016 restraints weight = 35815.885| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 3.53 r_work: 0.3357 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 1.6793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 17442 Z= 0.211 Angle : 0.867 14.769 23688 Z= 0.427 Chirality : 0.049 0.264 2628 Planarity : 0.006 0.113 3150 Dihedral : 5.117 28.448 2466 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.35 % Allowed : 22.28 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.17), residues: 2304 helix: None (None), residues: 0 sheet: -0.50 (0.14), residues: 1278 loop : -0.96 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP L 24 HIS 0.016 0.002 HIS F 20 PHE 0.031 0.003 PHE Q 46 TYR 0.035 0.003 TYR J 80 ARG 0.012 0.001 ARG Q 118 Details of bonding type rmsd hydrogen bonds : bond 0.03529 ( 57) hydrogen bonds : angle 6.14629 ( 171) covalent geometry : bond 0.00479 (17442) covalent geometry : angle 0.86669 (23688) *********************** 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 633 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 554 time to evaluate : 1.941 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: B 29 GLN cc_start: 0.8384 (mt0) cc_final: 0.7711 (mp10) REVERT: B 31 ASP cc_start: 0.8241 (m-30) cc_final: 0.7839 (m-30) REVERT: B 48 THR cc_start: 0.7713 (p) cc_final: 0.7347 (p) REVERT: B 49 VAL cc_start: 0.8854 (t) cc_final: 0.8472 (m) REVERT: B 108 ASP cc_start: 0.8800 (t0) cc_final: 0.8413 (t0) REVERT: A 90 TYR cc_start: 0.8354 (p90) cc_final: 0.7824 (p90) REVERT: A 112 MET cc_start: 0.7946 (mtt) cc_final: 0.7485 (mtt) REVERT: A 125 GLN cc_start: 0.7893 (mm-40) cc_final: 0.7324 (mm-40) REVERT: C 76 ASP cc_start: 0.7664 (m-30) cc_final: 0.7443 (m-30) REVERT: C 90 TYR cc_start: 0.8510 (p90) cc_final: 0.8201 (p90) REVERT: C 112 MET cc_start: 0.8573 (mmt) cc_final: 0.8274 (mmm) REVERT: D 43 GLU cc_start: 0.7627 (pp20) cc_final: 0.6570 (pp20) REVERT: D 59 TYR cc_start: 0.7121 (t80) cc_final: 0.6323 (t80) REVERT: D 76 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7605 (t0) REVERT: D 84 GLU cc_start: 0.7159 (pm20) cc_final: 0.6626 (mt-10) REVERT: E 44 ARG cc_start: 0.8575 (tpp80) cc_final: 0.8339 (mtp85) REVERT: E 49 VAL cc_start: 0.8028 (p) cc_final: 0.7739 (p) REVERT: E 70 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7751 (mt-10) REVERT: F 118 ARG cc_start: 0.8713 (tmt-80) cc_final: 0.8509 (tmt-80) REVERT: F 119 THR cc_start: 0.8909 (m) cc_final: 0.8664 (t) REVERT: F 125 GLN cc_start: 0.8304 (tm-30) cc_final: 0.7852 (tm-30) REVERT: I 1 MET cc_start: 0.7563 (pmm) cc_final: 0.7063 (ptp) REVERT: I 11 ASN cc_start: 0.7292 (t0) cc_final: 0.7079 (t0) REVERT: I 120 SER cc_start: 0.8487 (OUTLIER) cc_final: 0.8234 (p) REVERT: G 78 GLU cc_start: 0.8086 (tt0) cc_final: 0.7875 (tt0) REVERT: G 84 GLU cc_start: 0.8153 (tt0) cc_final: 0.7731 (tt0) REVERT: G 125 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7676 (mm-40) REVERT: M 1 MET cc_start: 0.5576 (tmm) cc_final: 0.5265 (tpp) REVERT: M 31 ASP cc_start: 0.6912 (m-30) cc_final: 0.6537 (m-30) REVERT: M 32 GLU cc_start: 0.8104 (pm20) cc_final: 0.7648 (pt0) REVERT: M 38 MET cc_start: 0.6036 (mmp) cc_final: 0.5129 (mtt) REVERT: O 29 GLN cc_start: 0.8384 (mp10) cc_final: 0.8131 (mp10) REVERT: Q 14 THR cc_start: 0.7466 (OUTLIER) cc_final: 0.7168 (p) REVERT: Q 70 GLU cc_start: 0.8435 (mp0) cc_final: 0.8102 (mp0) REVERT: J 40 ASP cc_start: 0.5037 (m-30) cc_final: 0.4824 (m-30) REVERT: J 73 ASP cc_start: 0.9186 (OUTLIER) cc_final: 0.8965 (t0) REVERT: J 125 GLN cc_start: 0.8762 (tp-100) cc_final: 0.8131 (tm-30) REVERT: J 126 LYS cc_start: 0.8633 (tptp) cc_final: 0.8027 (ttpt) REVERT: H 48 THR cc_start: 0.8062 (p) cc_final: 0.7840 (p) REVERT: H 78 GLU cc_start: 0.8397 (tt0) cc_final: 0.8194 (tt0) REVERT: H 130 SER cc_start: 0.8736 (m) cc_final: 0.8230 (p) REVERT: L 65 PRO cc_start: 0.8046 (Cg_exo) cc_final: 0.7381 (Cg_endo) REVERT: L 68 ASP cc_start: 0.8267 (m-30) cc_final: 0.7665 (p0) REVERT: L 90 TYR cc_start: 0.8340 (p90) cc_final: 0.8023 (p90) REVERT: N 29 GLN cc_start: 0.8376 (mp10) cc_final: 0.8170 (mp10) REVERT: N 32 GLU cc_start: 0.8076 (pm20) cc_final: 0.7844 (pt0) REVERT: N 76 ASP cc_start: 0.7969 (t0) cc_final: 0.7668 (m-30) REVERT: N 84 GLU cc_start: 0.7337 (mp0) cc_final: 0.6726 (mt-10) REVERT: N 125 GLN cc_start: 0.7810 (pm20) cc_final: 0.7513 (mp10) REVERT: P 99 LEU cc_start: 0.8537 (tp) cc_final: 0.8332 (tp) REVERT: P 126 LYS cc_start: 0.8185 (mtmm) cc_final: 0.7734 (mtmm) REVERT: R 49 VAL cc_start: 0.8245 (p) cc_final: 0.7759 (p) REVERT: R 70 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8260 (pm20) outliers start: 79 outliers final: 41 residues processed: 601 average time/residue: 0.2662 time to fit residues: 241.2619 Evaluate side-chains 440 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 394 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 24 TRP Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 120 SER Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 55 ASN Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain Q residue 14 THR Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain R residue 70 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 173 optimal weight: 7.9990 chunk 203 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 138 optimal weight: 10.0000 chunk 218 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 196 optimal weight: 0.6980 chunk 141 optimal weight: 0.9990 chunk 167 optimal weight: 3.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.095232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.081105 restraints weight = 35568.782| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 3.53 r_work: 0.3180 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 1.8757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17442 Z= 0.145 Angle : 0.724 10.668 23688 Z= 0.343 Chirality : 0.045 0.162 2628 Planarity : 0.005 0.051 3150 Dihedral : 4.310 20.960 2466 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.91 % Allowed : 27.01 % Favored : 69.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.17), residues: 2304 helix: None (None), residues: 0 sheet: -0.12 (0.14), residues: 1260 loop : -0.93 (0.17), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 24 HIS 0.003 0.001 HIS R 20 PHE 0.041 0.002 PHE Q 46 TYR 0.014 0.002 TYR E 59 ARG 0.010 0.001 ARG I 118 Details of bonding type rmsd hydrogen bonds : bond 0.01938 ( 57) hydrogen bonds : angle 5.87153 ( 171) covalent geometry : bond 0.00330 (17442) covalent geometry : angle 0.72403 (23688) *********************** 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 511 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 440 time to evaluate : 1.769 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: B 11 ASN cc_start: 0.7217 (t0) cc_final: 0.6937 (t0) REVERT: B 31 ASP cc_start: 0.8727 (m-30) cc_final: 0.8433 (m-30) REVERT: B 40 ASP cc_start: 0.7824 (m-30) cc_final: 0.7273 (m-30) REVERT: B 49 VAL cc_start: 0.9045 (t) cc_final: 0.8379 (m) REVERT: A 43 GLU cc_start: 0.7885 (pm20) cc_final: 0.7193 (pt0) REVERT: A 68 ASP cc_start: 0.8522 (m-30) cc_final: 0.8107 (p0) REVERT: A 112 MET cc_start: 0.8684 (mtt) cc_final: 0.8375 (mtt) REVERT: C 1 MET cc_start: 0.5236 (tmm) cc_final: 0.4896 (tpp) REVERT: C 78 GLU cc_start: 0.8405 (pt0) cc_final: 0.8195 (pt0) REVERT: C 90 TYR cc_start: 0.8517 (p90) cc_final: 0.8072 (p90) REVERT: D 43 GLU cc_start: 0.7975 (pp20) cc_final: 0.7169 (pt0) REVERT: D 44 ARG cc_start: 0.8706 (mtp85) cc_final: 0.8493 (mmm-85) REVERT: D 57 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8562 (tm-30) REVERT: D 76 ASP cc_start: 0.8074 (m-30) cc_final: 0.7686 (t0) REVERT: E 32 GLU cc_start: 0.7445 (pt0) cc_final: 0.7187 (pt0) REVERT: E 70 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8093 (mt-10) REVERT: F 29 GLN cc_start: 0.7631 (mt0) cc_final: 0.7420 (pm20) REVERT: F 40 ASP cc_start: 0.8327 (t0) cc_final: 0.8067 (t0) REVERT: F 125 GLN cc_start: 0.8408 (tm-30) cc_final: 0.7819 (tm-30) REVERT: I 70 GLU cc_start: 0.8703 (mp0) cc_final: 0.8424 (mp0) REVERT: I 73 ASP cc_start: 0.8911 (OUTLIER) cc_final: 0.8480 (p0) REVERT: I 108 ASP cc_start: 0.8704 (t0) cc_final: 0.8312 (p0) REVERT: I 120 SER cc_start: 0.8787 (OUTLIER) cc_final: 0.8549 (p) REVERT: G 76 ASP cc_start: 0.8572 (t0) cc_final: 0.7284 (p0) REVERT: G 78 GLU cc_start: 0.7960 (tt0) cc_final: 0.7689 (tt0) REVERT: G 84 GLU cc_start: 0.8575 (tt0) cc_final: 0.8237 (tt0) REVERT: K 123 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8117 (mp) REVERT: M 9 VAL cc_start: 0.9125 (m) cc_final: 0.8870 (m) REVERT: M 31 ASP cc_start: 0.7731 (m-30) cc_final: 0.7351 (m-30) REVERT: M 38 MET cc_start: 0.6868 (mmp) cc_final: 0.5998 (mtt) REVERT: M 43 GLU cc_start: 0.7627 (pp20) cc_final: 0.7028 (pt0) REVERT: M 78 GLU cc_start: 0.7809 (pt0) cc_final: 0.7524 (pt0) REVERT: O 29 GLN cc_start: 0.8022 (mp10) cc_final: 0.7739 (mp10) REVERT: O 38 MET cc_start: 0.4272 (tmm) cc_final: 0.4062 (tmm) REVERT: O 84 GLU cc_start: 0.6371 (pp20) cc_final: 0.6119 (pp20) REVERT: Q 27 ASP cc_start: 0.6779 (t70) cc_final: 0.6399 (t70) REVERT: Q 53 SER cc_start: 0.7870 (t) cc_final: 0.7271 (m) REVERT: Q 108 ASP cc_start: 0.8965 (t0) cc_final: 0.8410 (p0) REVERT: J 93 VAL cc_start: 0.8391 (t) cc_final: 0.7981 (m) REVERT: J 125 GLN cc_start: 0.8624 (tp-100) cc_final: 0.8066 (tm-30) REVERT: J 126 LYS cc_start: 0.8728 (tptp) cc_final: 0.8215 (ttpt) REVERT: H 76 ASP cc_start: 0.8663 (t0) cc_final: 0.7581 (p0) REVERT: H 130 SER cc_start: 0.8906 (m) cc_final: 0.8421 (p) REVERT: L 76 ASP cc_start: 0.8724 (m-30) cc_final: 0.8227 (p0) REVERT: N 1 MET cc_start: 0.7344 (tmm) cc_final: 0.6707 (ttt) REVERT: N 31 ASP cc_start: 0.8075 (m-30) cc_final: 0.7765 (m-30) REVERT: N 84 GLU cc_start: 0.7837 (mp0) cc_final: 0.7463 (mt-10) REVERT: N 92 SER cc_start: 0.8726 (t) cc_final: 0.8376 (p) REVERT: N 119 THR cc_start: 0.8782 (p) cc_final: 0.8473 (p) REVERT: R 27 ASP cc_start: 0.7074 (t70) cc_final: 0.6674 (t0) outliers start: 71 outliers final: 32 residues processed: 483 average time/residue: 0.2697 time to fit residues: 195.3327 Evaluate side-chains 402 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 367 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain C residue 20 HIS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 120 SER Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 55 ASN Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain P residue 80 TYR 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 161 optimal weight: 4.9990 chunk 165 optimal weight: 6.9990 chunk 208 optimal weight: 8.9990 chunk 164 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 110 optimal weight: 0.0770 chunk 153 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 HIS E 20 HIS F 22 GLN O 11 ASN ** Q 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 22 GLN P 22 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.079764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.066376 restraints weight = 36545.972| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.41 r_work: 0.2893 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 2.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17442 Z= 0.233 Angle : 0.868 14.525 23688 Z= 0.421 Chirality : 0.049 0.163 2628 Planarity : 0.006 0.050 3150 Dihedral : 5.721 26.915 2466 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.18 % Allowed : 27.89 % Favored : 67.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.16), residues: 2304 helix: None (None), residues: 0 sheet: -0.58 (0.14), residues: 1278 loop : -1.08 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 24 HIS 0.003 0.001 HIS C 20 PHE 0.029 0.003 PHE Q 46 TYR 0.029 0.003 TYR G 90 ARG 0.009 0.001 ARG M 118 Details of bonding type rmsd hydrogen bonds : bond 0.02802 ( 57) hydrogen bonds : angle 7.15272 ( 171) covalent geometry : bond 0.00531 (17442) covalent geometry : angle 0.86845 (23688) *********************** 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 507 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 431 time to evaluate : 1.923 Fit side-chains revert: symmetry clash REVERT: B 11 ASN cc_start: 0.7720 (t0) cc_final: 0.7169 (t0) REVERT: B 31 ASP cc_start: 0.8309 (m-30) cc_final: 0.7999 (m-30) REVERT: B 125 GLN cc_start: 0.8654 (tp-100) cc_final: 0.7708 (tm-30) REVERT: A 68 ASP cc_start: 0.8896 (m-30) cc_final: 0.8294 (p0) REVERT: A 112 MET cc_start: 0.8860 (mtt) cc_final: 0.8377 (mtt) REVERT: A 125 GLN cc_start: 0.8353 (mm-40) cc_final: 0.7678 (mm-40) REVERT: C 1 MET cc_start: 0.6643 (tmm) cc_final: 0.6307 (tpp) REVERT: C 78 GLU cc_start: 0.8810 (pt0) cc_final: 0.8190 (pt0) REVERT: D 59 TYR cc_start: 0.7610 (OUTLIER) cc_final: 0.6809 (t80) REVERT: D 76 ASP cc_start: 0.8567 (m-30) cc_final: 0.8348 (m-30) REVERT: E 10 LYS cc_start: 0.8640 (mttt) cc_final: 0.8245 (mtpp) REVERT: F 29 GLN cc_start: 0.8800 (mt0) cc_final: 0.8534 (mt0) REVERT: F 108 ASP cc_start: 0.8857 (t0) cc_final: 0.8641 (t0) REVERT: F 123 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8793 (mp) REVERT: F 125 GLN cc_start: 0.8518 (tm-30) cc_final: 0.8068 (tm-30) REVERT: I 73 ASP cc_start: 0.9182 (OUTLIER) cc_final: 0.8607 (p0) REVERT: I 112 MET cc_start: 0.8472 (mmm) cc_final: 0.8171 (mmm) REVERT: G 78 GLU cc_start: 0.8254 (tt0) cc_final: 0.8013 (tt0) REVERT: G 125 GLN cc_start: 0.8384 (mm-40) cc_final: 0.7995 (mm110) REVERT: M 1 MET cc_start: 0.7001 (tmm) cc_final: 0.6472 (ttt) REVERT: M 57 GLU cc_start: 0.8503 (tm-30) cc_final: 0.7897 (tm-30) REVERT: M 76 ASP cc_start: 0.8250 (t70) cc_final: 0.8048 (m-30) REVERT: O 16 ASP cc_start: 0.7071 (t0) cc_final: 0.6464 (p0) REVERT: O 29 GLN cc_start: 0.8474 (mp10) cc_final: 0.8021 (mp10) REVERT: O 76 ASP cc_start: 0.8410 (m-30) cc_final: 0.7830 (m-30) REVERT: Q 1 MET cc_start: 0.9287 (ptt) cc_final: 0.8931 (ptm) REVERT: Q 27 ASP cc_start: 0.8102 (t70) cc_final: 0.7828 (t70) REVERT: J 112 MET cc_start: 0.8521 (mmm) cc_final: 0.8201 (mmm) REVERT: J 125 GLN cc_start: 0.8714 (tp-100) cc_final: 0.8289 (tm-30) REVERT: H 38 MET cc_start: 0.2742 (OUTLIER) cc_final: 0.2282 (ptp) REVERT: H 57 GLU cc_start: 0.8552 (pt0) cc_final: 0.8255 (pt0) REVERT: H 112 MET cc_start: 0.8888 (mtp) cc_final: 0.8437 (mmm) REVERT: L 125 GLN cc_start: 0.8532 (mm-40) cc_final: 0.8273 (mm110) REVERT: L 126 LYS cc_start: 0.9178 (mtmm) cc_final: 0.8958 (mtpp) REVERT: N 27 ASP cc_start: 0.8773 (m-30) cc_final: 0.8455 (m-30) REVERT: N 57 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8553 (tm-30) REVERT: N 70 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7678 (mt-10) REVERT: P 27 ASP cc_start: 0.8539 (p0) cc_final: 0.7735 (p0) REVERT: P 43 GLU cc_start: 0.8466 (pp20) cc_final: 0.8047 (pt0) REVERT: P 78 GLU cc_start: 0.8707 (pt0) cc_final: 0.8414 (pt0) REVERT: R 1 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8042 (ppp) outliers start: 76 outliers final: 36 residues processed: 491 average time/residue: 0.2990 time to fit residues: 214.2471 Evaluate side-chains 389 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 348 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 104 SER 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 100 SER Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain O residue 11 ASN Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain J residue 114 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain N residue 55 ASN Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 18 ILE Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 58 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 88 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 169 optimal weight: 0.3980 chunk 161 optimal weight: 6.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 22 GLN Q 22 GLN ** Q 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 125 GLN ** R 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.075651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.062569 restraints weight = 37797.928| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 3.39 r_work: 0.2807 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 2.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17442 Z= 0.187 Angle : 0.728 11.960 23688 Z= 0.349 Chirality : 0.044 0.147 2628 Planarity : 0.005 0.041 3150 Dihedral : 4.726 23.557 2466 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.36 % Allowed : 29.76 % Favored : 66.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.17), residues: 2304 helix: None (None), residues: 0 sheet: -0.44 (0.14), residues: 1260 loop : -1.10 (0.17), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 24 HIS 0.003 0.001 HIS E 20 PHE 0.023 0.002 PHE Q 46 TYR 0.020 0.002 TYR G 90 ARG 0.006 0.001 ARG E 44 Details of bonding type rmsd hydrogen bonds : bond 0.01502 ( 57) hydrogen bonds : angle 6.29202 ( 171) covalent geometry : bond 0.00429 (17442) covalent geometry : angle 0.72824 (23688) *********************** 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 428 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 367 time to evaluate : 1.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 ASN cc_start: 0.8120 (t0) cc_final: 0.7635 (t0) REVERT: B 27 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7781 (t0) REVERT: B 78 GLU cc_start: 0.8568 (tt0) cc_final: 0.8220 (tt0) REVERT: B 125 GLN cc_start: 0.8725 (tp-100) cc_final: 0.7757 (tm-30) REVERT: A 57 GLU cc_start: 0.8620 (tt0) cc_final: 0.8352 (tt0) REVERT: A 68 ASP cc_start: 0.8775 (m-30) cc_final: 0.8412 (p0) REVERT: A 112 MET cc_start: 0.8824 (mtt) cc_final: 0.8449 (mtt) REVERT: C 1 MET cc_start: 0.6962 (tmm) cc_final: 0.6326 (tpp) REVERT: C 44 ARG cc_start: 0.8651 (mpp80) cc_final: 0.8114 (mmm-85) REVERT: C 78 GLU cc_start: 0.8812 (pt0) cc_final: 0.8176 (pt0) REVERT: D 11 ASN cc_start: 0.8625 (m-40) cc_final: 0.8304 (t0) REVERT: D 59 TYR cc_start: 0.7859 (OUTLIER) cc_final: 0.6999 (t80) REVERT: D 103 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7900 (tm-30) REVERT: E 29 GLN cc_start: 0.8754 (mp10) cc_final: 0.8457 (mp10) REVERT: E 125 GLN cc_start: 0.8237 (pp30) cc_final: 0.7722 (pp30) REVERT: F 112 MET cc_start: 0.8512 (mmt) cc_final: 0.8190 (mmt) REVERT: F 123 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8929 (mp) REVERT: F 125 GLN cc_start: 0.8394 (tm-30) cc_final: 0.7940 (tm-30) REVERT: I 1 MET cc_start: 0.8934 (ptp) cc_final: 0.8656 (ptp) REVERT: I 73 ASP cc_start: 0.9103 (OUTLIER) cc_final: 0.8541 (p0) REVERT: G 32 GLU cc_start: 0.8510 (pt0) cc_final: 0.8308 (pt0) REVERT: G 44 ARG cc_start: 0.8592 (mmm-85) cc_final: 0.8070 (mmm-85) REVERT: K 125 GLN cc_start: 0.8617 (mm-40) cc_final: 0.8170 (mm110) REVERT: M 1 MET cc_start: 0.7272 (tmm) cc_final: 0.6840 (ttt) REVERT: M 57 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8205 (tm-30) REVERT: M 101 THR cc_start: 0.8558 (OUTLIER) cc_final: 0.8337 (p) REVERT: O 29 GLN cc_start: 0.8563 (mp10) cc_final: 0.7986 (mp10) REVERT: O 76 ASP cc_start: 0.8549 (m-30) cc_final: 0.8106 (m-30) REVERT: Q 1 MET cc_start: 0.9365 (ptt) cc_final: 0.9071 (ptm) REVERT: Q 27 ASP cc_start: 0.8162 (t70) cc_final: 0.7532 (t0) REVERT: Q 29 GLN cc_start: 0.8404 (mp10) cc_final: 0.8000 (mp10) REVERT: J 125 GLN cc_start: 0.8707 (tp-100) cc_final: 0.8212 (tm-30) REVERT: J 126 LYS cc_start: 0.9155 (ttpp) cc_final: 0.8411 (ttpt) REVERT: H 57 GLU cc_start: 0.8525 (pt0) cc_final: 0.8225 (pt0) REVERT: L 125 GLN cc_start: 0.8600 (mm-40) cc_final: 0.8360 (mm110) REVERT: N 27 ASP cc_start: 0.8468 (m-30) cc_final: 0.8158 (m-30) REVERT: N 57 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8463 (tt0) REVERT: P 27 ASP cc_start: 0.8448 (p0) cc_final: 0.7545 (p0) REVERT: P 29 GLN cc_start: 0.8663 (pm20) cc_final: 0.7599 (pm20) REVERT: P 78 GLU cc_start: 0.8600 (pt0) cc_final: 0.8288 (pt0) REVERT: P 103 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7582 (tm-30) REVERT: R 1 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8060 (ppp) outliers start: 61 outliers final: 33 residues processed: 409 average time/residue: 0.2939 time to fit residues: 177.1549 Evaluate side-chains 376 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 337 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 28 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 D residue 49 VAL Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain Q residue 14 THR Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 128 THR Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain J residue 114 THR 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 L residue 28 THR Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain N residue 55 ASN Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 27 ASP Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 58 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 9 optimal weight: 4.9990 chunk 233 optimal weight: 5.9990 chunk 197 optimal weight: 7.9990 chunk 160 optimal weight: 0.7980 chunk 175 optimal weight: 0.1980 chunk 45 optimal weight: 0.0050 chunk 60 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 chunk 221 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 11 ASN ** Q 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 125 GLN ** R 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.078910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.065759 restraints weight = 37448.144| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.42 r_work: 0.2876 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 2.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17442 Z= 0.098 Angle : 0.655 11.788 23688 Z= 0.308 Chirality : 0.042 0.142 2628 Planarity : 0.004 0.037 3150 Dihedral : 3.889 21.003 2466 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.87 % Allowed : 31.46 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.17), residues: 2304 helix: None (None), residues: 0 sheet: -0.09 (0.14), residues: 1260 loop : -0.88 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 24 HIS 0.001 0.000 HIS L 20 PHE 0.020 0.001 PHE Q 46 TYR 0.018 0.001 TYR L 90 ARG 0.007 0.001 ARG E 44 Details of bonding type rmsd hydrogen bonds : bond 0.01412 ( 57) hydrogen bonds : angle 5.84034 ( 171) covalent geometry : bond 0.00230 (17442) covalent geometry : angle 0.65503 (23688) *********************** 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 404 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 370 time to evaluate : 1.785 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.8792 (ptm) cc_final: 0.8476 (ptm) REVERT: B 11 ASN cc_start: 0.8120 (t0) cc_final: 0.7657 (t0) REVERT: B 78 GLU cc_start: 0.8355 (tt0) cc_final: 0.8087 (tt0) REVERT: A 11 ASN cc_start: 0.8437 (m-40) cc_final: 0.7719 (t0) REVERT: A 57 GLU cc_start: 0.8578 (tt0) cc_final: 0.8234 (tt0) REVERT: A 68 ASP cc_start: 0.8822 (m-30) cc_final: 0.8401 (p0) REVERT: A 112 MET cc_start: 0.8762 (mtt) cc_final: 0.8459 (mtt) REVERT: A 125 GLN cc_start: 0.8393 (mm-40) cc_final: 0.7888 (mm110) REVERT: C 1 MET cc_start: 0.6852 (tmm) cc_final: 0.6308 (tpp) REVERT: C 11 ASN cc_start: 0.8610 (m-40) cc_final: 0.7928 (t0) REVERT: C 29 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8412 (mt0) REVERT: C 44 ARG cc_start: 0.8708 (mpp80) cc_final: 0.8109 (mmm-85) REVERT: C 78 GLU cc_start: 0.8553 (pt0) cc_final: 0.8003 (pt0) REVERT: E 27 ASP cc_start: 0.7745 (t70) cc_final: 0.7349 (t0) REVERT: F 29 GLN cc_start: 0.8698 (mt0) cc_final: 0.8486 (mt0) REVERT: F 84 GLU cc_start: 0.8482 (tt0) cc_final: 0.8207 (tt0) REVERT: I 1 MET cc_start: 0.8905 (ptp) cc_final: 0.8627 (ptp) REVERT: I 73 ASP cc_start: 0.8997 (t70) cc_final: 0.8563 (p0) REVERT: G 32 GLU cc_start: 0.8482 (pt0) cc_final: 0.7710 (pt0) REVERT: G 44 ARG cc_start: 0.8628 (mmm-85) cc_final: 0.8119 (mmm-85) REVERT: G 76 ASP cc_start: 0.8761 (t0) cc_final: 0.7805 (p0) REVERT: G 125 GLN cc_start: 0.8538 (mm-40) cc_final: 0.8022 (mm-40) REVERT: K 11 ASN cc_start: 0.8447 (m-40) cc_final: 0.7899 (t0) REVERT: K 125 GLN cc_start: 0.8631 (mm-40) cc_final: 0.8247 (mm110) REVERT: M 57 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8349 (tm-30) REVERT: M 84 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7928 (mm-30) REVERT: O 29 GLN cc_start: 0.8381 (mp10) cc_final: 0.7771 (mp10) REVERT: Q 1 MET cc_start: 0.9353 (ptt) cc_final: 0.9024 (ptm) REVERT: J 125 GLN cc_start: 0.8749 (tp-100) cc_final: 0.8042 (tm-30) REVERT: J 126 LYS cc_start: 0.9087 (ttpp) cc_final: 0.8861 (ttpt) REVERT: H 57 GLU cc_start: 0.8432 (pt0) cc_final: 0.8161 (pt0) REVERT: H 112 MET cc_start: 0.8907 (mtp) cc_final: 0.8404 (mmm) REVERT: H 125 GLN cc_start: 0.8535 (mm-40) cc_final: 0.8098 (mm-40) REVERT: L 125 GLN cc_start: 0.8603 (mm-40) cc_final: 0.8341 (mm110) REVERT: L 126 LYS cc_start: 0.9271 (mtmm) cc_final: 0.8944 (mtpp) REVERT: N 27 ASP cc_start: 0.8348 (m-30) cc_final: 0.7890 (t0) REVERT: P 27 ASP cc_start: 0.8274 (p0) cc_final: 0.8045 (p0) REVERT: P 29 GLN cc_start: 0.8570 (pm20) cc_final: 0.8134 (pm20) REVERT: P 43 GLU cc_start: 0.8156 (pt0) cc_final: 0.7949 (pt0) REVERT: P 78 GLU cc_start: 0.8554 (pt0) cc_final: 0.8274 (pt0) REVERT: R 1 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.7758 (ppp) outliers start: 34 outliers final: 19 residues processed: 393 average time/residue: 0.3054 time to fit residues: 173.2753 Evaluate side-chains 359 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 338 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain C residue 20 HIS Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain F residue 10 LYS Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain O residue 23 SER Chi-restraints excluded: chain Q residue 128 THR Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 27 ASP 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 213 optimal weight: 3.9990 chunk 205 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 26 optimal weight: 0.1980 chunk 42 optimal weight: 10.0000 chunk 206 optimal weight: 0.9990 chunk 212 optimal weight: 0.7980 chunk 190 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 228 optimal weight: 0.0010 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 116 ASN ** R 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.076945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.063896 restraints weight = 37416.522| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 3.38 r_work: 0.2833 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 2.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17442 Z= 0.122 Angle : 0.660 11.775 23688 Z= 0.312 Chirality : 0.042 0.168 2628 Planarity : 0.004 0.038 3150 Dihedral : 3.969 22.945 2466 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.65 % Allowed : 31.79 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.17), residues: 2304 helix: None (None), residues: 0 sheet: 0.06 (0.15), residues: 1242 loop : -0.80 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 24 HIS 0.002 0.001 HIS F 20 PHE 0.020 0.002 PHE Q 46 TYR 0.019 0.001 TYR L 90 ARG 0.007 0.001 ARG I 118 Details of bonding type rmsd hydrogen bonds : bond 0.01423 ( 57) hydrogen bonds : angle 5.85765 ( 171) covalent geometry : bond 0.00287 (17442) covalent geometry : angle 0.66029 (23688) ********************** 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 366 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 336 time to evaluate : 1.922 Fit side-chains revert: symmetry clash REVERT: B 11 ASN cc_start: 0.8221 (t0) cc_final: 0.7666 (t0) REVERT: B 78 GLU cc_start: 0.8327 (tt0) cc_final: 0.8039 (tt0) REVERT: A 11 ASN cc_start: 0.8448 (m-40) cc_final: 0.7561 (t0) REVERT: A 68 ASP cc_start: 0.8799 (m-30) cc_final: 0.8399 (p0) REVERT: A 112 MET cc_start: 0.8815 (mtt) cc_final: 0.8473 (mtt) REVERT: A 125 GLN cc_start: 0.8318 (mm-40) cc_final: 0.7837 (mm110) REVERT: C 1 MET cc_start: 0.7004 (tmm) cc_final: 0.6610 (tpp) REVERT: C 11 ASN cc_start: 0.8610 (m-40) cc_final: 0.8020 (t0) REVERT: C 29 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8468 (mt0) REVERT: C 44 ARG cc_start: 0.8727 (mpp80) cc_final: 0.8135 (mmm-85) REVERT: C 78 GLU cc_start: 0.8566 (pt0) cc_final: 0.8046 (pt0) REVERT: E 3 LYS cc_start: 0.9087 (mmtm) cc_final: 0.8611 (mmtm) REVERT: F 29 GLN cc_start: 0.8751 (mt0) cc_final: 0.8521 (mt0) REVERT: F 84 GLU cc_start: 0.8528 (tt0) cc_final: 0.8226 (tt0) REVERT: F 91 ARG cc_start: 0.8944 (mpt180) cc_final: 0.8372 (mmt-90) REVERT: F 125 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7986 (tm-30) REVERT: I 73 ASP cc_start: 0.8989 (t70) cc_final: 0.8432 (p0) REVERT: G 44 ARG cc_start: 0.8562 (mmm-85) cc_final: 0.8126 (mmm-85) REVERT: G 76 ASP cc_start: 0.8727 (t0) cc_final: 0.7758 (p0) REVERT: G 91 ARG cc_start: 0.8719 (mpt90) cc_final: 0.8457 (mmt-90) REVERT: G 125 GLN cc_start: 0.8536 (mm-40) cc_final: 0.8067 (mm110) REVERT: K 11 ASN cc_start: 0.8506 (m-40) cc_final: 0.7810 (t0) REVERT: K 43 GLU cc_start: 0.8118 (pm20) cc_final: 0.7814 (pm20) REVERT: K 125 GLN cc_start: 0.8691 (mm-40) cc_final: 0.8348 (mm110) REVERT: M 57 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8332 (tm-30) REVERT: O 16 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7638 (p0) REVERT: O 29 GLN cc_start: 0.8452 (mp10) cc_final: 0.7848 (mp10) REVERT: Q 1 MET cc_start: 0.9350 (ptt) cc_final: 0.9030 (ptm) REVERT: Q 29 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8376 (mp10) REVERT: J 125 GLN cc_start: 0.8745 (tp-100) cc_final: 0.8022 (tm-30) REVERT: J 126 LYS cc_start: 0.9098 (ttpp) cc_final: 0.8864 (ttpt) REVERT: H 57 GLU cc_start: 0.8489 (pt0) cc_final: 0.8212 (pt0) REVERT: H 112 MET cc_start: 0.9023 (mtp) cc_final: 0.8486 (mmm) REVERT: L 125 GLN cc_start: 0.8633 (mm-40) cc_final: 0.8345 (mm110) REVERT: N 27 ASP cc_start: 0.8372 (m-30) cc_final: 0.7971 (t0) REVERT: P 27 ASP cc_start: 0.8536 (p0) cc_final: 0.8312 (p0) REVERT: P 29 GLN cc_start: 0.8550 (pm20) cc_final: 0.8108 (pm20) REVERT: P 78 GLU cc_start: 0.8598 (pt0) cc_final: 0.8306 (pt0) REVERT: R 1 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.7802 (ppp) outliers start: 30 outliers final: 22 residues processed: 355 average time/residue: 0.3119 time to fit residues: 161.4455 Evaluate side-chains 356 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 330 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain F residue 20 HIS Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain M residue 29 GLN Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain O residue 16 ASP Chi-restraints excluded: chain Q residue 29 GLN Chi-restraints excluded: chain Q residue 128 THR Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 27 ASP Chi-restraints excluded: chain R residue 49 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 201 optimal weight: 0.9990 chunk 162 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 20 optimal weight: 0.3980 chunk 75 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.077320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.064287 restraints weight = 37264.395| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 3.36 r_work: 0.2844 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 2.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17442 Z= 0.111 Angle : 0.645 11.472 23688 Z= 0.305 Chirality : 0.042 0.158 2628 Planarity : 0.004 0.035 3150 Dihedral : 3.814 20.107 2466 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.87 % Allowed : 31.52 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.17), residues: 2304 helix: None (None), residues: 0 sheet: 0.18 (0.15), residues: 1242 loop : -0.73 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 24 HIS 0.001 0.000 HIS J 20 PHE 0.017 0.001 PHE D 56 TYR 0.019 0.001 TYR L 90 ARG 0.005 0.001 ARG Q 51 Details of bonding type rmsd hydrogen bonds : bond 0.01408 ( 57) hydrogen bonds : angle 5.70584 ( 171) covalent geometry : bond 0.00265 (17442) covalent geometry : angle 0.64461 (23688) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6942.93 seconds wall clock time: 121 minutes 22.50 seconds (7282.50 seconds total)