Starting phenix.real_space_refine on Sun Jun 15 05:19:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gtb_34248/06_2025/8gtb_34248.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gtb_34248/06_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_34248/06_2025/8gtb_34248.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gtb_34248/06_2025/8gtb_34248.map" model { file = "/net/cci-nas-00/data/ceres_data/8gtb_34248/06_2025/8gtb_34248.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gtb_34248/06_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 5.31, per 1000 atoms: 0.31 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: 4.67 Conformation dependent library (CDL) restraints added in 2.7 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: 1.97 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: 4.03 Time building geometry restraints manager: 5.53 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: 0.19 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: 3.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.630 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 35.580 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.690 ------------------------------------------------------------------------------- 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 : 1.856 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: 0.3316 time to fit residues: 199.1252 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 : 1.733 ------------------------------------------------------------------------------- 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: 0.0070 chunk 136 optimal weight: 0.3980 chunk 212 optimal weight: 0.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.102332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.090588 restraints weight = 31827.242| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.60 r_work: 0.3313 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3234 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17442 Z= 0.141 Angle : 0.658 11.164 23688 Z= 0.318 Chirality : 0.043 0.186 2628 Planarity : 0.004 0.038 3150 Dihedral : 4.159 21.527 2466 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.26 % Allowed : 13.15 % 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: -1.76 (0.15), residues: 2304 helix: None (None), residues: 0 sheet: -1.09 (0.13), residues: 1242 loop : -1.09 (0.16), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 36 HIS 0.004 0.001 HIS D 20 PHE 0.043 0.002 PHE N 56 TYR 0.017 0.002 TYR D 59 ARG 0.007 0.001 ARG M 91 Details of bonding type rmsd hydrogen bonds : bond 0.02470 ( 57) hydrogen bonds : angle 6.38756 ( 171) covalent geometry : bond 0.00262 (17442) covalent geometry : angle 0.65764 (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 326 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 285 time to evaluate : 1.931 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: B 1 MET cc_start: 0.5778 (pmm) cc_final: 0.5446 (mtp) REVERT: K 1 MET cc_start: 0.3499 (ttm) cc_final: 0.2926 (tmm) REVERT: K 38 MET cc_start: -0.0131 (mtp) cc_final: -0.0468 (ttm) REVERT: K 78 GLU cc_start: 0.4835 (pt0) cc_final: 0.4202 (pt0) REVERT: J 1 MET cc_start: 0.4488 (pmm) cc_final: 0.3899 (ptm) REVERT: P 38 MET cc_start: 0.3839 (mtp) cc_final: 0.2881 (tmm) REVERT: R 38 MET cc_start: 0.5558 (mtp) cc_final: 0.3066 (tmm) outliers start: 41 outliers final: 19 residues processed: 308 average time/residue: 0.2969 time to fit residues: 136.5143 Evaluate side-chains 225 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 206 time to evaluate : 1.918 ------------------------------------------------------------------------------- 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 D residue 5 LYS Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain M residue 98 ILE 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 H residue 38 MET Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain N residue 98 ILE 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: 8.9990 chunk 207 optimal weight: 7.9990 chunk 146 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 208 optimal weight: 0.0270 chunk 213 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 201 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 GLN Q 125 GLN H 11 ASN L 22 GLN N 22 GLN P 11 ASN R 11 ASN R 125 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.112710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.100013 restraints weight = 33407.510| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.44 r_work: 0.3464 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5759 moved from start: 1.0759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.137 17442 Z= 0.237 Angle : 0.900 17.650 23688 Z= 0.451 Chirality : 0.049 0.419 2628 Planarity : 0.007 0.129 3150 Dihedral : 5.297 24.829 2466 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 5.34 % Allowed : 14.63 % Favored : 80.03 % Cbeta Deviations : 0.05 % 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: -1.63 (0.16), residues: 2304 helix: None (None), residues: 0 sheet: -0.92 (0.14), residues: 1260 loop : -1.12 (0.17), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP N 36 HIS 0.005 0.002 HIS L 20 PHE 0.039 0.003 PHE N 56 TYR 0.035 0.003 TYR D 59 ARG 0.017 0.001 ARG L 51 Details of bonding type rmsd hydrogen bonds : bond 0.03760 ( 57) hydrogen bonds : angle 6.81681 ( 171) covalent geometry : bond 0.00529 (17442) covalent geometry : angle 0.90031 (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 617 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 520 time to evaluate : 2.865 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: B 11 ASN cc_start: 0.6846 (t0) cc_final: 0.6599 (t0) REVERT: A 112 MET cc_start: 0.5408 (mtp) cc_final: 0.5194 (mmm) REVERT: C 9 VAL cc_start: 0.2772 (OUTLIER) cc_final: 0.2538 (m) REVERT: C 60 LEU cc_start: 0.6401 (tt) cc_final: 0.6156 (tp) REVERT: D 115 VAL cc_start: 0.6963 (t) cc_final: 0.6743 (m) REVERT: I 1 MET cc_start: 0.6145 (pmm) cc_final: 0.5129 (ptp) REVERT: G 106 SER cc_start: 0.4470 (OUTLIER) cc_final: 0.4024 (t) REVERT: G 112 MET cc_start: 0.5612 (mtt) cc_final: 0.5336 (mtt) REVERT: M 18 ILE cc_start: 0.6169 (mm) cc_final: 0.5571 (mm) REVERT: M 74 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6948 (pp) REVERT: O 27 ASP cc_start: 0.6973 (p0) cc_final: 0.6561 (p0) REVERT: O 28 THR cc_start: 0.7491 (m) cc_final: 0.6603 (p) REVERT: Q 112 MET cc_start: 0.0090 (OUTLIER) cc_final: -0.0241 (ttp) REVERT: J 11 ASN cc_start: 0.7161 (t0) cc_final: 0.6920 (t0) REVERT: J 24 TRP cc_start: 0.5714 (p-90) cc_final: 0.5191 (p90) REVERT: J 112 MET cc_start: 0.5195 (OUTLIER) cc_final: 0.4720 (mmm) REVERT: J 125 GLN cc_start: 0.7856 (tp-100) cc_final: 0.7307 (tm-30) REVERT: H 47 THR cc_start: 0.6387 (p) cc_final: 0.5992 (p) REVERT: H 76 ASP cc_start: 0.8543 (t0) cc_final: 0.7208 (p0) REVERT: H 84 GLU cc_start: 0.8014 (tt0) cc_final: 0.7684 (tt0) REVERT: R 29 GLN cc_start: 0.6040 (OUTLIER) cc_final: 0.5688 (pm20) outliers start: 97 outliers final: 28 residues processed: 567 average time/residue: 0.3439 time to fit residues: 292.9165 Evaluate side-chains 382 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 348 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain O residue 40 ASP 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 112 MET Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 68 ASP Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain P residue 80 TYR Chi-restraints excluded: chain R residue 29 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 13 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 213 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 109 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 21 optimal weight: 0.2980 chunk 75 optimal weight: 0.0030 chunk 221 optimal weight: 0.0010 chunk 110 optimal weight: 3.9990 overall best weight: 1.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN C 20 HIS C 22 GLN E 11 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 HIS ** H 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 22 GLN R 11 ASN ** R 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.101470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.088414 restraints weight = 36148.191| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 3.44 r_work: 0.3317 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 1.7945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 17442 Z= 0.249 Angle : 0.981 16.254 23688 Z= 0.484 Chirality : 0.051 0.217 2628 Planarity : 0.008 0.128 3150 Dihedral : 6.018 34.789 2466 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 6.38 % Allowed : 19.91 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.15), residues: 2304 helix: None (None), residues: 0 sheet: -1.13 (0.15), residues: 1044 loop : -1.71 (0.14), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP K 117 HIS 0.011 0.002 HIS F 20 PHE 0.028 0.003 PHE G 46 TYR 0.036 0.003 TYR M 59 ARG 0.011 0.001 ARG E 118 Details of bonding type rmsd hydrogen bonds : bond 0.03367 ( 57) hydrogen bonds : angle 6.93557 ( 171) covalent geometry : bond 0.00530 (17442) covalent geometry : angle 0.98107 (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 711 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 595 time to evaluate : 1.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 VAL cc_start: 0.8974 (t) cc_final: 0.8637 (m) REVERT: A 26 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7928 (tt) REVERT: A 32 GLU cc_start: 0.7672 (pt0) cc_final: 0.7451 (pt0) REVERT: A 38 MET cc_start: 0.8062 (ptp) cc_final: 0.7844 (ptp) REVERT: A 90 TYR cc_start: 0.8625 (p90) cc_final: 0.8226 (p90) REVERT: A 112 MET cc_start: 0.8405 (mtp) cc_final: 0.8027 (mtt) REVERT: C 1 MET cc_start: 0.6086 (tmm) cc_final: 0.5765 (tmm) REVERT: C 68 ASP cc_start: 0.8011 (m-30) cc_final: 0.7187 (p0) REVERT: C 112 MET cc_start: 0.8986 (mmt) cc_final: 0.8782 (mmm) REVERT: C 125 GLN cc_start: 0.8126 (pm20) cc_final: 0.7714 (mp10) REVERT: D 43 GLU cc_start: 0.8087 (pp20) cc_final: 0.7026 (pp20) REVERT: D 76 ASP cc_start: 0.8214 (m-30) cc_final: 0.7776 (m-30) REVERT: E 13 SER cc_start: 0.7795 (m) cc_final: 0.7266 (t) REVERT: E 49 VAL cc_start: 0.7548 (p) cc_final: 0.7143 (p) REVERT: E 70 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7854 (mt-10) REVERT: E 75 VAL cc_start: 0.5936 (OUTLIER) cc_final: 0.5696 (p) REVERT: E 116 ASN cc_start: 0.8932 (m110) cc_final: 0.8704 (m110) REVERT: F 1 MET cc_start: 0.7656 (ppp) cc_final: 0.6580 (ptt) REVERT: F 68 ASP cc_start: 0.6668 (m-30) cc_final: 0.5720 (p0) REVERT: F 70 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8774 (mp0) REVERT: F 126 LYS cc_start: 0.8653 (tttp) cc_final: 0.8401 (ttpt) REVERT: I 1 MET cc_start: 0.7934 (pmm) cc_final: 0.7671 (ptp) REVERT: I 73 ASP cc_start: 0.8910 (OUTLIER) cc_final: 0.8332 (p0) REVERT: G 76 ASP cc_start: 0.8595 (t0) cc_final: 0.8334 (t0) REVERT: G 84 GLU cc_start: 0.8334 (tt0) cc_final: 0.7946 (tt0) REVERT: K 99 LEU cc_start: 0.8940 (tp) cc_final: 0.8738 (tp) REVERT: M 78 GLU cc_start: 0.7340 (pt0) cc_final: 0.7030 (pp20) REVERT: M 99 LEU cc_start: 0.8081 (tp) cc_final: 0.7566 (tp) REVERT: M 110 ILE cc_start: 0.7520 (mm) cc_final: 0.7136 (mm) REVERT: O 70 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7407 (mm-30) REVERT: O 84 GLU cc_start: 0.5949 (pp20) cc_final: 0.5532 (pp20) REVERT: Q 29 GLN cc_start: 0.7378 (mp10) cc_final: 0.7116 (pm20) REVERT: Q 118 ARG cc_start: 0.7723 (tpt-90) cc_final: 0.7490 (tmt-80) REVERT: J 11 ASN cc_start: 0.7484 (t0) cc_final: 0.7271 (t0) REVERT: J 70 GLU cc_start: 0.8991 (pm20) cc_final: 0.8789 (mp0) REVERT: J 93 VAL cc_start: 0.8140 (t) cc_final: 0.7693 (m) REVERT: J 125 GLN cc_start: 0.8568 (tp-100) cc_final: 0.8331 (tm-30) REVERT: H 31 ASP cc_start: 0.8244 (m-30) cc_final: 0.7786 (m-30) REVERT: H 84 GLU cc_start: 0.8221 (tt0) cc_final: 0.8014 (tt0) REVERT: L 40 ASP cc_start: 0.6178 (OUTLIER) cc_final: 0.5953 (p0) REVERT: L 84 GLU cc_start: 0.8340 (mt-10) cc_final: 0.8095 (mt-10) REVERT: L 90 TYR cc_start: 0.8621 (p90) cc_final: 0.8415 (p90) REVERT: L 123 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.7759 (mm) REVERT: L 125 GLN cc_start: 0.7924 (mm-40) cc_final: 0.7481 (mm110) REVERT: N 31 ASP cc_start: 0.7850 (m-30) cc_final: 0.7519 (m-30) REVERT: N 32 GLU cc_start: 0.8465 (pm20) cc_final: 0.8205 (pt0) REVERT: N 76 ASP cc_start: 0.8046 (t0) cc_final: 0.7764 (m-30) REVERT: N 78 GLU cc_start: 0.8352 (pt0) cc_final: 0.8148 (mt-10) REVERT: P 27 ASP cc_start: 0.7745 (t70) cc_final: 0.6770 (t0) REVERT: P 29 GLN cc_start: 0.8399 (pm20) cc_final: 0.7808 (pm20) REVERT: R 43 GLU cc_start: 0.8324 (pp20) cc_final: 0.8060 (pt0) outliers start: 116 outliers final: 51 residues processed: 670 average time/residue: 0.2864 time to fit residues: 285.2351 Evaluate side-chains 480 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 423 time to evaluate : 2.044 ------------------------------------------------------------------------------- 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 B residue 130 SER Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 56 PHE Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 11 ASN Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 60 LEU Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain M residue 55 ASN Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 68 ASP Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain J residue 49 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 H residue 49 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 40 ASP Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain R residue 26 LEU Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 129 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 134 optimal weight: 3.9990 chunk 92 optimal weight: 0.0060 chunk 207 optimal weight: 0.9980 chunk 100 optimal weight: 8.9990 chunk 197 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 209 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 chunk 169 optimal weight: 4.9990 chunk 188 optimal weight: 5.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 20 HIS D 20 HIS E 11 ASN E 22 GLN G 125 GLN K 20 HIS M 22 GLN ** Q 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 22 GLN R 22 GLN ** R 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.087301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.073770 restraints weight = 37187.158| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 3.48 r_work: 0.3049 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 1.9899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17442 Z= 0.169 Angle : 0.738 10.153 23688 Z= 0.356 Chirality : 0.045 0.188 2628 Planarity : 0.005 0.048 3150 Dihedral : 4.573 23.382 2466 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.84 % Allowed : 25.80 % Favored : 69.36 % 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: -1.52 (0.16), residues: 2304 helix: None (None), residues: 0 sheet: -0.66 (0.15), residues: 1188 loop : -1.31 (0.16), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP O 24 HIS 0.006 0.001 HIS C 20 PHE 0.017 0.002 PHE Q 46 TYR 0.018 0.002 TYR Q 80 ARG 0.008 0.001 ARG I 91 Details of bonding type rmsd hydrogen bonds : bond 0.02059 ( 57) hydrogen bonds : angle 6.35853 ( 171) covalent geometry : bond 0.00382 (17442) covalent geometry : angle 0.73833 (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 559 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 471 time to evaluate : 2.014 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: B 29 GLN cc_start: 0.8669 (pm20) cc_final: 0.8419 (pm20) REVERT: A 51 ARG cc_start: 0.9007 (ptt180) cc_final: 0.8776 (ptp90) REVERT: A 68 ASP cc_start: 0.8397 (m-30) cc_final: 0.7988 (p0) REVERT: A 112 MET cc_start: 0.8454 (mtp) cc_final: 0.8057 (mtt) REVERT: C 1 MET cc_start: 0.6319 (tmm) cc_final: 0.5657 (tmm) REVERT: C 51 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8392 (ptp90) REVERT: C 68 ASP cc_start: 0.8313 (m-30) cc_final: 0.7613 (p0) REVERT: D 43 GLU cc_start: 0.8326 (pp20) cc_final: 0.7696 (pt0) REVERT: D 44 ARG cc_start: 0.8808 (mmm-85) cc_final: 0.8599 (mmm-85) REVERT: D 59 TYR cc_start: 0.7400 (OUTLIER) cc_final: 0.6497 (t80) REVERT: E 13 SER cc_start: 0.8152 (m) cc_final: 0.7713 (p) REVERT: E 43 GLU cc_start: 0.8407 (pp20) cc_final: 0.7581 (pt0) REVERT: E 125 GLN cc_start: 0.8334 (pp30) cc_final: 0.7829 (pp30) REVERT: F 27 ASP cc_start: 0.7722 (t0) cc_final: 0.6413 (t70) REVERT: F 29 GLN cc_start: 0.8207 (mt0) cc_final: 0.7757 (mp10) REVERT: F 70 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8304 (pm20) REVERT: I 51 ARG cc_start: 0.8722 (mtm-85) cc_final: 0.8254 (ptp90) REVERT: I 70 GLU cc_start: 0.8755 (mp0) cc_final: 0.8372 (mp0) REVERT: I 73 ASP cc_start: 0.9027 (OUTLIER) cc_final: 0.8596 (p0) REVERT: G 31 ASP cc_start: 0.8670 (m-30) cc_final: 0.8275 (m-30) REVERT: G 76 ASP cc_start: 0.8796 (t0) cc_final: 0.8566 (t0) REVERT: G 80 TYR cc_start: 0.8278 (m-80) cc_final: 0.7970 (m-80) REVERT: G 84 GLU cc_start: 0.8537 (tt0) cc_final: 0.8110 (tt0) REVERT: K 31 ASP cc_start: 0.8103 (m-30) cc_final: 0.7839 (m-30) REVERT: K 76 ASP cc_start: 0.8429 (m-30) cc_final: 0.8156 (p0) REVERT: K 84 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7846 (mt-10) REVERT: K 90 TYR cc_start: 0.8097 (p90) cc_final: 0.7662 (p90) REVERT: M 43 GLU cc_start: 0.7952 (pp20) cc_final: 0.7222 (pt0) REVERT: M 78 GLU cc_start: 0.7964 (pt0) cc_final: 0.7723 (pt0) REVERT: O 29 GLN cc_start: 0.8097 (mp10) cc_final: 0.7600 (mp10) REVERT: O 57 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8386 (tm-30) REVERT: O 67 ASP cc_start: 0.7288 (OUTLIER) cc_final: 0.7000 (t0) REVERT: Q 29 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7565 (pm20) REVERT: Q 108 ASP cc_start: 0.8893 (t0) cc_final: 0.8397 (p0) REVERT: J 11 ASN cc_start: 0.7773 (t0) cc_final: 0.7487 (t0) REVERT: J 70 GLU cc_start: 0.8902 (pm20) cc_final: 0.8640 (mp0) REVERT: J 125 GLN cc_start: 0.8706 (tp-100) cc_final: 0.8090 (tp-100) REVERT: J 128 THR cc_start: 0.8810 (m) cc_final: 0.8456 (t) REVERT: H 29 GLN cc_start: 0.9083 (pt0) cc_final: 0.8837 (pt0) REVERT: H 31 ASP cc_start: 0.8634 (m-30) cc_final: 0.8406 (m-30) REVERT: H 76 ASP cc_start: 0.8515 (t0) cc_final: 0.7878 (p0) REVERT: H 84 GLU cc_start: 0.8410 (tt0) cc_final: 0.8203 (tt0) REVERT: H 130 SER cc_start: 0.8801 (m) cc_final: 0.8235 (p) REVERT: L 76 ASP cc_start: 0.8734 (m-30) cc_final: 0.8281 (p0) REVERT: L 125 GLN cc_start: 0.8341 (mm-40) cc_final: 0.8065 (mm110) REVERT: N 1 MET cc_start: 0.7698 (tmm) cc_final: 0.7327 (ttt) REVERT: N 112 MET cc_start: 0.9167 (mmm) cc_final: 0.8885 (mmm) REVERT: P 27 ASP cc_start: 0.7970 (t70) cc_final: 0.7756 (t0) REVERT: P 43 GLU cc_start: 0.8120 (pp20) cc_final: 0.7629 (pt0) REVERT: P 67 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7491 (t0) REVERT: R 69 LEU cc_start: 0.8859 (mt) cc_final: 0.8603 (mp) outliers start: 88 outliers final: 47 residues processed: 535 average time/residue: 0.2909 time to fit residues: 230.8362 Evaluate side-chains 445 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 391 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain K residue 60 LEU Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain K residue 104 SER Chi-restraints excluded: chain M residue 55 ASN Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain Q residue 29 GLN Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 123 LEU Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain J residue 123 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 L residue 103 GLU Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain P residue 93 VAL Chi-restraints excluded: chain R residue 20 HIS Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 128 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 173 optimal weight: 3.9990 chunk 203 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 138 optimal weight: 0.0970 chunk 218 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 79 optimal weight: 0.0270 chunk 196 optimal weight: 7.9990 chunk 141 optimal weight: 7.9990 chunk 167 optimal weight: 4.9990 overall best weight: 1.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 11 ASN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 GLN M 11 ASN M 22 GLN O 20 HIS ** Q 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 22 GLN R 11 ASN ** R 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.082841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.069428 restraints weight = 36299.090| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.44 r_work: 0.2953 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 2.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17442 Z= 0.144 Angle : 0.665 9.349 23688 Z= 0.321 Chirality : 0.043 0.166 2628 Planarity : 0.005 0.048 3150 Dihedral : 4.246 19.346 2466 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 5.01 % Allowed : 28.16 % Favored : 66.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.25 (0.17), residues: 2304 helix: None (None), residues: 0 sheet: -0.50 (0.15), residues: 1224 loop : -1.12 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP O 24 HIS 0.004 0.001 HIS C 20 PHE 0.019 0.002 PHE Q 46 TYR 0.024 0.002 TYR G 90 ARG 0.005 0.001 ARG O 44 Details of bonding type rmsd hydrogen bonds : bond 0.01843 ( 57) hydrogen bonds : angle 6.17742 ( 171) covalent geometry : bond 0.00329 (17442) covalent geometry : angle 0.66479 (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 484 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 393 time to evaluate : 2.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 GLN cc_start: 0.8945 (pm20) cc_final: 0.8293 (pm20) REVERT: A 29 GLN cc_start: 0.8828 (pt0) cc_final: 0.8579 (pt0) REVERT: A 43 GLU cc_start: 0.8043 (pm20) cc_final: 0.7619 (pt0) REVERT: A 57 GLU cc_start: 0.8304 (tt0) cc_final: 0.8061 (tt0) REVERT: A 68 ASP cc_start: 0.8607 (m-30) cc_final: 0.8213 (p0) REVERT: A 125 GLN cc_start: 0.8498 (mm-40) cc_final: 0.7912 (mm-40) REVERT: C 1 MET cc_start: 0.6643 (tmm) cc_final: 0.5655 (tpt) REVERT: C 57 GLU cc_start: 0.8217 (tm-30) cc_final: 0.8015 (tm-30) REVERT: C 125 GLN cc_start: 0.8331 (pm20) cc_final: 0.8081 (mp10) REVERT: D 43 GLU cc_start: 0.8525 (pp20) cc_final: 0.8183 (pt0) REVERT: E 43 GLU cc_start: 0.8312 (pp20) cc_final: 0.7863 (pt0) REVERT: E 125 GLN cc_start: 0.8350 (pp30) cc_final: 0.7835 (pp30) REVERT: E 126 LYS cc_start: 0.8299 (mtmm) cc_final: 0.7753 (mtpp) REVERT: F 1 MET cc_start: 0.8960 (ptp) cc_final: 0.8440 (ptp) REVERT: F 70 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8046 (pm20) REVERT: F 125 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8364 (tm-30) REVERT: I 31 ASP cc_start: 0.7684 (m-30) cc_final: 0.7322 (m-30) REVERT: I 51 ARG cc_start: 0.7741 (mtm-85) cc_final: 0.7285 (mtm-85) REVERT: I 73 ASP cc_start: 0.9082 (OUTLIER) cc_final: 0.8754 (p0) REVERT: I 123 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8809 (mp) REVERT: G 1 MET cc_start: 0.8841 (ttm) cc_final: 0.8586 (ttp) REVERT: G 32 GLU cc_start: 0.8157 (pt0) cc_final: 0.7885 (pt0) REVERT: G 76 ASP cc_start: 0.8792 (t0) cc_final: 0.8524 (t0) REVERT: G 78 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7757 (tm-30) REVERT: G 80 TYR cc_start: 0.8353 (m-80) cc_final: 0.8062 (m-80) REVERT: G 84 GLU cc_start: 0.8610 (tt0) cc_final: 0.8220 (tt0) REVERT: K 84 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8261 (mt-10) REVERT: K 90 TYR cc_start: 0.8550 (p90) cc_final: 0.8049 (p90) REVERT: M 1 MET cc_start: 0.7042 (tmm) cc_final: 0.5979 (ttt) REVERT: M 29 GLN cc_start: 0.8365 (mp10) cc_final: 0.8100 (mp10) REVERT: M 43 GLU cc_start: 0.8040 (pp20) cc_final: 0.7651 (pt0) REVERT: M 78 GLU cc_start: 0.8084 (pt0) cc_final: 0.7822 (pt0) REVERT: O 27 ASP cc_start: 0.7536 (p0) cc_final: 0.7287 (p0) REVERT: O 29 GLN cc_start: 0.8276 (mp10) cc_final: 0.7884 (mp10) REVERT: O 57 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8472 (tm-30) REVERT: O 67 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7812 (t0) REVERT: O 91 ARG cc_start: 0.8793 (mmt180) cc_final: 0.8584 (mmt180) REVERT: O 119 THR cc_start: 0.9390 (OUTLIER) cc_final: 0.9182 (t) REVERT: Q 29 GLN cc_start: 0.8295 (mp10) cc_final: 0.8070 (pm20) REVERT: Q 108 ASP cc_start: 0.8968 (t0) cc_final: 0.8649 (p0) REVERT: J 70 GLU cc_start: 0.8963 (pm20) cc_final: 0.8733 (mp0) REVERT: J 125 GLN cc_start: 0.8672 (tp-100) cc_final: 0.8193 (mm110) REVERT: J 128 THR cc_start: 0.9053 (m) cc_final: 0.8705 (t) REVERT: H 76 ASP cc_start: 0.8476 (t0) cc_final: 0.8148 (m-30) REVERT: H 130 SER cc_start: 0.8949 (m) cc_final: 0.8424 (p) REVERT: N 27 ASP cc_start: 0.8767 (m-30) cc_final: 0.8369 (m-30) REVERT: N 76 ASP cc_start: 0.8807 (m-30) cc_final: 0.8153 (p0) REVERT: N 125 GLN cc_start: 0.8337 (mp10) cc_final: 0.8135 (pm20) REVERT: P 43 GLU cc_start: 0.8284 (pp20) cc_final: 0.7926 (pt0) REVERT: R 46 PHE cc_start: 0.6475 (OUTLIER) cc_final: 0.6163 (t80) REVERT: R 118 ARG cc_start: 0.9019 (ptm-80) cc_final: 0.8809 (ptm-80) outliers start: 91 outliers final: 53 residues processed: 459 average time/residue: 0.3047 time to fit residues: 206.3589 Evaluate side-chains 405 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 346 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 20 HIS Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 123 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain K residue 20 HIS Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 60 LEU Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 112 MET Chi-restraints excluded: chain J residue 49 VAL 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 21 LEU Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain N residue 2 LEU Chi-restraints excluded: chain N residue 55 ASN Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain R residue 20 HIS Chi-restraints excluded: chain R residue 46 PHE Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 123 LEU 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: 7.9990 chunk 165 optimal weight: 0.3980 chunk 208 optimal weight: 8.9990 chunk 164 optimal weight: 0.0070 chunk 133 optimal weight: 8.9990 chunk 207 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 overall best weight: 1.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 29 GLN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 125 GLN P 22 GLN R 11 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.081490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.068041 restraints weight = 35888.066| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.43 r_work: 0.2923 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 2.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17442 Z= 0.118 Angle : 0.626 8.505 23688 Z= 0.301 Chirality : 0.042 0.145 2628 Planarity : 0.004 0.044 3150 Dihedral : 3.890 18.477 2466 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.63 % Allowed : 29.48 % 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: -0.89 (0.17), residues: 2304 helix: None (None), residues: 0 sheet: -0.19 (0.14), residues: 1260 loop : -1.00 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 24 HIS 0.002 0.001 HIS K 20 PHE 0.027 0.002 PHE F 46 TYR 0.026 0.001 TYR L 90 ARG 0.006 0.001 ARG E 44 Details of bonding type rmsd hydrogen bonds : bond 0.01650 ( 57) hydrogen bonds : angle 5.93866 ( 171) covalent geometry : bond 0.00272 (17442) covalent geometry : angle 0.62581 (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 445 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 379 time to evaluate : 3.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 GLN cc_start: 0.8892 (pm20) cc_final: 0.8390 (pm20) REVERT: A 68 ASP cc_start: 0.8788 (m-30) cc_final: 0.8198 (p0) REVERT: A 103 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7330 (mt-10) REVERT: A 104 SER cc_start: 0.8851 (p) cc_final: 0.8534 (p) REVERT: A 125 GLN cc_start: 0.8507 (mm-40) cc_final: 0.7950 (mm-40) REVERT: C 1 MET cc_start: 0.6770 (tmm) cc_final: 0.6188 (tpp) REVERT: C 44 ARG cc_start: 0.8424 (mpp80) cc_final: 0.8015 (mmm-85) REVERT: C 57 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7876 (tm-30) REVERT: D 43 GLU cc_start: 0.8529 (pp20) cc_final: 0.8211 (pt0) REVERT: D 59 TYR cc_start: 0.7583 (OUTLIER) cc_final: 0.6674 (t80) REVERT: E 43 GLU cc_start: 0.8317 (pp20) cc_final: 0.7974 (pt0) REVERT: F 1 MET cc_start: 0.9021 (ptp) cc_final: 0.8515 (ptp) REVERT: F 67 ASP cc_start: 0.8284 (t0) cc_final: 0.7798 (t0) REVERT: F 70 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7583 (pm20) REVERT: I 1 MET cc_start: 0.8959 (ptt) cc_final: 0.8664 (ptp) REVERT: I 31 ASP cc_start: 0.8130 (m-30) cc_final: 0.7808 (m-30) REVERT: I 51 ARG cc_start: 0.8200 (mtm-85) cc_final: 0.7784 (mtm-85) REVERT: I 73 ASP cc_start: 0.9029 (OUTLIER) cc_final: 0.8634 (p0) REVERT: G 1 MET cc_start: 0.8894 (ttm) cc_final: 0.8627 (ttp) REVERT: G 31 ASP cc_start: 0.8785 (m-30) cc_final: 0.8548 (m-30) REVERT: G 44 ARG cc_start: 0.8499 (mmt90) cc_final: 0.8021 (mmm-85) REVERT: G 76 ASP cc_start: 0.8784 (t0) cc_final: 0.8557 (t0) REVERT: G 78 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7658 (tm-30) REVERT: G 80 TYR cc_start: 0.8423 (m-80) cc_final: 0.8164 (m-80) REVERT: G 84 GLU cc_start: 0.8589 (tt0) cc_final: 0.8220 (tt0) REVERT: K 80 TYR cc_start: 0.8383 (m-80) cc_final: 0.8163 (m-80) REVERT: K 84 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8305 (mt-10) REVERT: K 101 THR cc_start: 0.8419 (OUTLIER) cc_final: 0.8184 (p) REVERT: M 1 MET cc_start: 0.7125 (tmm) cc_final: 0.6311 (ttt) REVERT: M 29 GLN cc_start: 0.8337 (mp10) cc_final: 0.8070 (mp10) REVERT: M 43 GLU cc_start: 0.8036 (pp20) cc_final: 0.7776 (pt0) REVERT: O 27 ASP cc_start: 0.7240 (p0) cc_final: 0.7014 (p0) REVERT: O 29 GLN cc_start: 0.7927 (mp10) cc_final: 0.7363 (mp10) REVERT: O 68 ASP cc_start: 0.8721 (m-30) cc_final: 0.8454 (m-30) REVERT: O 108 ASP cc_start: 0.8729 (t0) cc_final: 0.8349 (t0) REVERT: O 126 LYS cc_start: 0.8349 (mtmm) cc_final: 0.7980 (mtpp) REVERT: Q 1 MET cc_start: 0.9271 (ptt) cc_final: 0.8994 (ptm) REVERT: Q 29 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8077 (pm20) REVERT: Q 108 ASP cc_start: 0.9021 (t0) cc_final: 0.8679 (p0) REVERT: J 1 MET cc_start: 0.8664 (ttm) cc_final: 0.8437 (ttp) REVERT: J 125 GLN cc_start: 0.8667 (tp-100) cc_final: 0.8197 (mm-40) REVERT: H 84 GLU cc_start: 0.8496 (tt0) cc_final: 0.8097 (tt0) REVERT: H 125 GLN cc_start: 0.8559 (mm-40) cc_final: 0.8137 (mm-40) REVERT: N 27 ASP cc_start: 0.8531 (m-30) cc_final: 0.7974 (t0) REVERT: N 101 THR cc_start: 0.8071 (OUTLIER) cc_final: 0.7847 (p) REVERT: N 125 GLN cc_start: 0.8331 (mp10) cc_final: 0.8104 (pm20) REVERT: P 27 ASP cc_start: 0.7889 (t70) cc_final: 0.7205 (t0) REVERT: P 43 GLU cc_start: 0.8300 (pp20) cc_final: 0.7964 (pt0) REVERT: R 1 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8381 (ppp) REVERT: R 29 GLN cc_start: 0.8641 (pm20) cc_final: 0.8162 (pm20) REVERT: R 125 GLN cc_start: 0.8493 (tm-30) cc_final: 0.8101 (tm-30) outliers start: 66 outliers final: 36 residues processed: 425 average time/residue: 0.3426 time to fit residues: 217.0635 Evaluate side-chains 384 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 341 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 29 GLN 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 D residue 104 SER Chi-restraints excluded: chain E residue 20 HIS Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain K residue 20 HIS Chi-restraints excluded: chain K residue 60 LEU Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain Q residue 29 GLN Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 20 HIS Chi-restraints excluded: chain R residue 49 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: 8.9990 chunk 123 optimal weight: 0.0070 chunk 100 optimal weight: 0.3980 chunk 40 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 48 optimal weight: 0.1980 chunk 139 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 106 optimal weight: 0.0060 chunk 169 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 overall best weight: 0.9216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 GLN ** O 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.080662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.067346 restraints weight = 35856.484| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 3.41 r_work: 0.2907 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 2.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17442 Z= 0.106 Angle : 0.618 8.496 23688 Z= 0.295 Chirality : 0.041 0.140 2628 Planarity : 0.004 0.040 3150 Dihedral : 3.732 17.468 2466 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.92 % Allowed : 29.81 % Favored : 67.27 % 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: -0.64 (0.17), residues: 2304 helix: None (None), residues: 0 sheet: 0.00 (0.15), residues: 1260 loop : -0.87 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 24 HIS 0.002 0.000 HIS C 20 PHE 0.016 0.001 PHE N 56 TYR 0.024 0.001 TYR K 90 ARG 0.008 0.001 ARG N 91 Details of bonding type rmsd hydrogen bonds : bond 0.01487 ( 57) hydrogen bonds : angle 5.89987 ( 171) covalent geometry : bond 0.00246 (17442) covalent geometry : angle 0.61792 (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 407 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 354 time to evaluate : 2.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 GLN cc_start: 0.8844 (pm20) cc_final: 0.8486 (pm20) REVERT: A 68 ASP cc_start: 0.8823 (m-30) cc_final: 0.8228 (p0) REVERT: C 1 MET cc_start: 0.6886 (tmm) cc_final: 0.6288 (tpt) REVERT: C 44 ARG cc_start: 0.8545 (mpp80) cc_final: 0.8069 (mmm-85) REVERT: C 57 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7958 (tm-30) REVERT: D 43 GLU cc_start: 0.8470 (pp20) cc_final: 0.8227 (pt0) REVERT: D 59 TYR cc_start: 0.7632 (OUTLIER) cc_final: 0.6904 (t80) REVERT: D 103 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7589 (tm-30) REVERT: E 13 SER cc_start: 0.8510 (m) cc_final: 0.8249 (p) REVERT: E 43 GLU cc_start: 0.8299 (pp20) cc_final: 0.7956 (pt0) REVERT: E 51 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7700 (ptp90) REVERT: F 1 MET cc_start: 0.9018 (ptp) cc_final: 0.8485 (ptp) REVERT: F 67 ASP cc_start: 0.8390 (t0) cc_final: 0.7916 (t0) REVERT: F 84 GLU cc_start: 0.8608 (tt0) cc_final: 0.8255 (tt0) REVERT: F 125 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8410 (tm-30) REVERT: I 1 MET cc_start: 0.9043 (ptt) cc_final: 0.8766 (ptp) REVERT: I 70 GLU cc_start: 0.8773 (mp0) cc_final: 0.8522 (mp0) REVERT: I 73 ASP cc_start: 0.8966 (OUTLIER) cc_final: 0.8573 (p0) REVERT: G 44 ARG cc_start: 0.8502 (mmt90) cc_final: 0.8104 (mmm-85) REVERT: G 76 ASP cc_start: 0.8821 (t0) cc_final: 0.8588 (t0) REVERT: G 78 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7753 (tm-30) REVERT: G 84 GLU cc_start: 0.8672 (tt0) cc_final: 0.8306 (tt0) REVERT: K 84 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8296 (mt-10) REVERT: M 1 MET cc_start: 0.7209 (tmm) cc_final: 0.6685 (ttt) REVERT: M 43 GLU cc_start: 0.8074 (pp20) cc_final: 0.7830 (pt0) REVERT: O 27 ASP cc_start: 0.7415 (p0) cc_final: 0.7191 (p0) REVERT: O 29 GLN cc_start: 0.8064 (mp10) cc_final: 0.7447 (mp10) REVERT: O 126 LYS cc_start: 0.8139 (mtmm) cc_final: 0.7931 (mtpp) REVERT: Q 1 MET cc_start: 0.9265 (ptt) cc_final: 0.8932 (ptm) REVERT: Q 29 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8219 (pm20) REVERT: Q 91 ARG cc_start: 0.8758 (mpt90) cc_final: 0.8549 (mmt-90) REVERT: Q 108 ASP cc_start: 0.9021 (t0) cc_final: 0.8680 (p0) REVERT: J 1 MET cc_start: 0.8747 (ttm) cc_final: 0.8507 (ttp) REVERT: J 13 SER cc_start: 0.7815 (m) cc_final: 0.7493 (p) REVERT: J 125 GLN cc_start: 0.8697 (tp-100) cc_final: 0.8270 (mm110) REVERT: H 103 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7369 (mp0) REVERT: H 125 GLN cc_start: 0.8597 (mm-40) cc_final: 0.8217 (mm110) REVERT: N 27 ASP cc_start: 0.8479 (m-30) cc_final: 0.7909 (t0) REVERT: N 103 GLU cc_start: 0.8321 (tm-30) cc_final: 0.7802 (tm-30) REVERT: N 125 GLN cc_start: 0.8352 (mp10) cc_final: 0.8106 (pm20) REVERT: P 43 GLU cc_start: 0.8242 (pp20) cc_final: 0.8009 (pt0) REVERT: R 29 GLN cc_start: 0.8673 (pm20) cc_final: 0.8079 (pm20) outliers start: 53 outliers final: 36 residues processed: 386 average time/residue: 0.3049 time to fit residues: 172.2742 Evaluate side-chains 372 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 332 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain D residue 23 SER 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 49 VAL Chi-restraints excluded: chain E residue 51 ARG Chi-restraints excluded: chain I residue 27 ASP Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain K residue 20 HIS Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain Q residue 29 GLN Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain J residue 49 VAL 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 L residue 21 LEU Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain N residue 2 LEU Chi-restraints excluded: chain N residue 29 GLN Chi-restraints excluded: chain R residue 20 HIS 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: 6.9990 chunk 233 optimal weight: 2.9990 chunk 197 optimal weight: 0.8980 chunk 160 optimal weight: 3.9990 chunk 175 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 168 optimal weight: 3.9990 chunk 221 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.075927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.062922 restraints weight = 37790.998| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 3.38 r_work: 0.2820 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 2.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17442 Z= 0.138 Angle : 0.646 9.348 23688 Z= 0.310 Chirality : 0.042 0.137 2628 Planarity : 0.004 0.040 3150 Dihedral : 4.175 21.358 2466 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.52 % Allowed : 29.04 % Favored : 67.44 % 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: -0.58 (0.17), residues: 2304 helix: None (None), residues: 0 sheet: 0.04 (0.15), residues: 1260 loop : -0.84 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP O 24 HIS 0.002 0.001 HIS D 20 PHE 0.017 0.002 PHE O 46 TYR 0.023 0.002 TYR L 90 ARG 0.007 0.001 ARG M 118 Details of bonding type rmsd hydrogen bonds : bond 0.01855 ( 57) hydrogen bonds : angle 6.01076 ( 171) covalent geometry : bond 0.00321 (17442) covalent geometry : angle 0.64597 (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 415 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 351 time to evaluate : 3.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 13 SER cc_start: 0.8496 (m) cc_final: 0.8114 (p) REVERT: B 29 GLN cc_start: 0.8861 (pm20) cc_final: 0.8559 (pm20) REVERT: B 125 GLN cc_start: 0.8682 (tp-100) cc_final: 0.7747 (tm-30) REVERT: A 68 ASP cc_start: 0.8782 (m-30) cc_final: 0.8314 (p0) REVERT: C 1 MET cc_start: 0.7435 (tmm) cc_final: 0.7189 (tpt) REVERT: C 11 ASN cc_start: 0.8594 (m-40) cc_final: 0.7996 (t0) REVERT: C 44 ARG cc_start: 0.8698 (mpp80) cc_final: 0.8093 (mmm-85) REVERT: C 57 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8121 (tm-30) REVERT: D 56 PHE cc_start: 0.9059 (p90) cc_final: 0.8755 (p90) REVERT: D 59 TYR cc_start: 0.7890 (OUTLIER) cc_final: 0.7176 (t80) REVERT: E 43 GLU cc_start: 0.8428 (pp20) cc_final: 0.8185 (pt0) REVERT: F 1 MET cc_start: 0.9128 (ptp) cc_final: 0.8623 (ptp) REVERT: I 1 MET cc_start: 0.8960 (ptt) cc_final: 0.8417 (ptp) REVERT: I 13 SER cc_start: 0.8169 (m) cc_final: 0.7945 (p) REVERT: I 73 ASP cc_start: 0.9007 (OUTLIER) cc_final: 0.8356 (p0) REVERT: G 44 ARG cc_start: 0.8616 (mmt90) cc_final: 0.8217 (mmm-85) REVERT: K 26 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7886 (tt) REVERT: M 1 MET cc_start: 0.7607 (tmm) cc_final: 0.7377 (ttt) REVERT: M 57 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8254 (tm-30) REVERT: O 27 ASP cc_start: 0.7751 (p0) cc_final: 0.7551 (p0) REVERT: O 29 GLN cc_start: 0.8289 (mp10) cc_final: 0.7667 (mp10) REVERT: O 126 LYS cc_start: 0.8454 (mtmm) cc_final: 0.8163 (mtpp) REVERT: Q 1 MET cc_start: 0.9268 (ptt) cc_final: 0.8892 (ptm) REVERT: Q 29 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8457 (pm20) REVERT: Q 32 GLU cc_start: 0.8238 (pt0) cc_final: 0.8021 (pt0) REVERT: J 125 GLN cc_start: 0.8717 (tp-100) cc_final: 0.8403 (mm110) REVERT: H 32 GLU cc_start: 0.8564 (pp20) cc_final: 0.8009 (pp20) REVERT: H 103 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7535 (mp0) REVERT: H 112 MET cc_start: 0.8773 (mmt) cc_final: 0.8467 (mmm) REVERT: H 125 GLN cc_start: 0.8608 (mm-40) cc_final: 0.8353 (mm110) REVERT: L 43 GLU cc_start: 0.7923 (pm20) cc_final: 0.7706 (pm20) REVERT: N 27 ASP cc_start: 0.8554 (m-30) cc_final: 0.8193 (t0) REVERT: N 125 GLN cc_start: 0.8419 (mp10) cc_final: 0.8115 (pm20) REVERT: P 43 GLU cc_start: 0.8337 (pp20) cc_final: 0.8128 (pt0) outliers start: 64 outliers final: 45 residues processed: 389 average time/residue: 0.3766 time to fit residues: 216.9772 Evaluate side-chains 377 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 328 time to evaluate : 2.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 23 SER 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 20 HIS Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain I residue 27 ASP Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain K residue 20 HIS Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 60 LEU Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain Q residue 29 GLN Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 70 GLU Chi-restraints excluded: chain J residue 75 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 H residue 57 GLU Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain N residue 2 LEU Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain R residue 20 HIS Chi-restraints excluded: chain R residue 58 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 213 optimal weight: 6.9990 chunk 205 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 48 optimal weight: 0.0070 chunk 26 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 206 optimal weight: 1.9990 chunk 212 optimal weight: 10.0000 chunk 190 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 228 optimal weight: 5.9990 overall best weight: 2.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 116 ASN L 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.073804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.060982 restraints weight = 38037.454| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 3.34 r_work: 0.2772 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 2.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17442 Z= 0.181 Angle : 0.692 10.107 23688 Z= 0.333 Chirality : 0.043 0.165 2628 Planarity : 0.004 0.040 3150 Dihedral : 4.471 21.436 2466 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.14 % Allowed : 29.76 % Favored : 67.11 % 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: -0.72 (0.17), residues: 2304 helix: None (None), residues: 0 sheet: -0.18 (0.15), residues: 1278 loop : -0.73 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 24 HIS 0.003 0.001 HIS D 20 PHE 0.014 0.002 PHE N 56 TYR 0.024 0.002 TYR K 90 ARG 0.008 0.001 ARG M 118 Details of bonding type rmsd hydrogen bonds : bond 0.01757 ( 57) hydrogen bonds : angle 6.23132 ( 171) covalent geometry : bond 0.00419 (17442) covalent geometry : angle 0.69203 (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 382 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 325 time to evaluate : 2.150 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 29 GLN cc_start: 0.8930 (pm20) cc_final: 0.8529 (pm20) REVERT: A 68 ASP cc_start: 0.8896 (m-30) cc_final: 0.8334 (p0) REVERT: C 11 ASN cc_start: 0.8789 (m-40) cc_final: 0.8030 (t0) REVERT: C 44 ARG cc_start: 0.8696 (mpp80) cc_final: 0.8062 (mmm-85) REVERT: C 57 GLU cc_start: 0.8484 (tm-30) cc_final: 0.8259 (tm-30) REVERT: D 23 SER cc_start: 0.9424 (OUTLIER) cc_final: 0.9168 (p) REVERT: D 59 TYR cc_start: 0.8043 (OUTLIER) cc_final: 0.6732 (t80) REVERT: E 43 GLU cc_start: 0.8522 (pp20) cc_final: 0.8306 (pt0) REVERT: F 1 MET cc_start: 0.9048 (ptp) cc_final: 0.8494 (ptp) REVERT: F 91 ARG cc_start: 0.9037 (mmt-90) cc_final: 0.8474 (mmt-90) REVERT: I 1 MET cc_start: 0.8968 (ptt) cc_final: 0.8448 (ptp) REVERT: I 51 ARG cc_start: 0.8566 (mtm-85) cc_final: 0.8182 (mtm-85) REVERT: I 73 ASP cc_start: 0.9048 (OUTLIER) cc_final: 0.8331 (p0) REVERT: G 44 ARG cc_start: 0.8552 (mmt90) cc_final: 0.8115 (mmm-85) REVERT: K 26 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8068 (tt) REVERT: M 57 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8223 (tm-30) REVERT: O 29 GLN cc_start: 0.8354 (mp10) cc_final: 0.7617 (mp10) REVERT: Q 1 MET cc_start: 0.9230 (ptt) cc_final: 0.8832 (ptm) REVERT: Q 29 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8485 (pm20) REVERT: Q 32 GLU cc_start: 0.8319 (pt0) cc_final: 0.8083 (pt0) REVERT: J 125 GLN cc_start: 0.8640 (tp-100) cc_final: 0.8416 (mm-40) REVERT: H 32 GLU cc_start: 0.8554 (pp20) cc_final: 0.8024 (pp20) REVERT: H 43 GLU cc_start: 0.8351 (pt0) cc_final: 0.8110 (pt0) REVERT: H 103 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7753 (mp0) REVERT: H 112 MET cc_start: 0.8787 (mmt) cc_final: 0.8444 (mmm) REVERT: H 125 GLN cc_start: 0.8605 (mm-40) cc_final: 0.8326 (mm110) REVERT: L 70 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7584 (mp0) REVERT: N 27 ASP cc_start: 0.8549 (m-30) cc_final: 0.8244 (t0) REVERT: N 125 GLN cc_start: 0.8381 (mp10) cc_final: 0.8178 (pm20) outliers start: 57 outliers final: 47 residues processed: 360 average time/residue: 0.4148 time to fit residues: 217.0572 Evaluate side-chains 367 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 315 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 23 SER 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 20 HIS Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain I residue 27 ASP Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain K residue 20 HIS Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 32 GLU Chi-restraints excluded: chain K residue 60 LEU Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain Q residue 29 GLN Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 128 THR Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 70 GLU Chi-restraints excluded: chain J residue 75 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 H residue 57 GLU Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain N residue 2 LEU Chi-restraints excluded: chain N residue 32 GLU Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain R residue 20 HIS Chi-restraints excluded: chain R residue 58 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: 2.9990 chunk 162 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 145 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 75 optimal weight: 9.9990 chunk 110 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 11 ASN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 GLN L 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.074984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.062212 restraints weight = 37736.854| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.33 r_work: 0.2806 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 2.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17442 Z= 0.126 Angle : 0.645 8.879 23688 Z= 0.310 Chirality : 0.042 0.137 2628 Planarity : 0.004 0.038 3150 Dihedral : 4.098 20.685 2466 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.97 % Allowed : 30.47 % 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: -0.53 (0.17), residues: 2304 helix: None (None), residues: 0 sheet: 0.03 (0.15), residues: 1260 loop : -0.73 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 24 HIS 0.001 0.000 HIS D 20 PHE 0.016 0.002 PHE N 56 TYR 0.023 0.001 TYR K 90 ARG 0.007 0.001 ARG N 91 Details of bonding type rmsd hydrogen bonds : bond 0.01521 ( 57) hydrogen bonds : angle 5.96458 ( 171) covalent geometry : bond 0.00298 (17442) covalent geometry : angle 0.64543 (23688) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8712.32 seconds wall clock time: 156 minutes 30.18 seconds (9390.18 seconds total)