Starting phenix.real_space_refine on Fri Sep 27 19:47:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtb_34248/09_2024/8gtb_34248.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtb_34248/09_2024/8gtb_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtb_34248/09_2024/8gtb_34248.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtb_34248/09_2024/8gtb_34248.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtb_34248/09_2024/8gtb_34248.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtb_34248/09_2024/8gtb_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-5461/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: 5.06, per 1000 atoms: 0.30 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: 4.09 Conformation dependent library (CDL) restraints added in 2.5 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: 1.77 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 8 through 11 removed outlier: 3.706A pdb=" N ASP B 16 " --> pdb=" O ASN B 11 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 16 through 17 current: chain 'B' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 44 through 59 current: chain 'B' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN B 116 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR B 101 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR B 114 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLU B 103 " --> pdb=" O MET B 112 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET B 112 " --> pdb=" O GLU B 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 112 through 119 current: chain 'A' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 16 through 17 current: chain 'A' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 44 through 59 current: chain 'A' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN A 116 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR A 101 " --> pdb=" O THR A 114 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR A 114 " --> pdb=" O THR A 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU A 103 " --> pdb=" O MET A 112 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET A 112 " --> pdb=" O GLU A 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 112 through 119 current: chain 'C' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 16 through 17 current: chain 'C' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 44 through 59 current: chain 'C' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN C 116 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR C 101 " --> pdb=" O THR C 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR C 114 " --> pdb=" O THR C 101 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLU C 103 " --> pdb=" O MET C 112 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET C 112 " --> pdb=" O GLU C 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 112 through 119 current: chain 'D' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 16 through 17 current: chain 'D' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 44 through 59 current: chain 'D' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN D 116 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR D 101 " --> pdb=" O THR D 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR D 114 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLU D 103 " --> pdb=" O MET D 112 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET D 112 " --> pdb=" O GLU D 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 112 through 119 current: chain 'E' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 16 through 17 current: chain 'E' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 44 through 59 current: chain 'E' and resid 91 through 104 removed outlier: 6.940A pdb=" N ASN E 116 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR E 101 " --> pdb=" O THR E 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR E 114 " --> pdb=" O THR E 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU E 103 " --> pdb=" O MET E 112 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET E 112 " --> pdb=" O GLU E 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 112 through 119 current: chain 'F' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 16 through 17 current: chain 'F' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 44 through 59 current: chain 'F' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN F 116 " --> pdb=" O LEU F 99 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR F 101 " --> pdb=" O THR F 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR F 114 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU F 103 " --> pdb=" O MET F 112 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N MET F 112 " --> pdb=" O GLU F 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 8 through 11 removed outlier: 3.706A pdb=" N ASP I 16 " --> pdb=" O ASN I 11 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 16 through 17 current: chain 'I' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 44 through 59 current: chain 'I' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN I 116 " --> pdb=" O LEU I 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR I 101 " --> pdb=" O THR I 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR I 114 " --> pdb=" O THR I 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU I 103 " --> pdb=" O MET I 112 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N MET I 112 " --> pdb=" O GLU I 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 112 through 119 current: chain 'G' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 16 through 17 current: chain 'G' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 44 through 59 current: chain 'G' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN G 116 " --> pdb=" O LEU G 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR G 101 " --> pdb=" O THR G 114 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR G 114 " --> pdb=" O THR G 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU G 103 " --> pdb=" O MET G 112 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET G 112 " --> pdb=" O GLU G 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 112 through 119 current: chain 'K' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 16 through 17 current: chain 'K' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 44 through 59 current: chain 'K' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN K 116 " --> pdb=" O LEU K 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR K 101 " --> pdb=" O THR K 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR K 114 " --> pdb=" O THR K 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU K 103 " --> pdb=" O MET K 112 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N MET K 112 " --> pdb=" O GLU K 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 112 through 119 current: chain 'M' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 16 through 17 current: chain 'M' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 44 through 59 current: chain 'M' and resid 91 through 106 removed outlier: 6.940A pdb=" N ASN M 116 " --> pdb=" O LEU M 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR M 101 " --> pdb=" O THR M 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR M 114 " --> pdb=" O THR M 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU M 103 " --> pdb=" O MET M 112 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET M 112 " --> pdb=" O GLU M 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 112 through 119 current: chain 'O' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 16 through 17 current: chain 'O' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 44 through 59 current: chain 'O' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN O 116 " --> pdb=" O LEU O 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR O 101 " --> pdb=" O THR O 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR O 114 " --> pdb=" O THR O 101 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLU O 103 " --> pdb=" O MET O 112 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET O 112 " --> pdb=" O GLU O 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 112 through 119 current: chain 'Q' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 16 through 17 current: chain 'Q' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 44 through 59 current: chain 'Q' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN Q 116 " --> pdb=" O LEU Q 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR Q 101 " --> pdb=" O THR Q 114 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR Q 114 " --> pdb=" O THR Q 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU Q 103 " --> pdb=" O MET Q 112 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N MET Q 112 " --> pdb=" O GLU Q 103 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 8 through 11 removed outlier: 3.707A pdb=" N ASP J 16 " --> pdb=" O ASN J 11 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 16 through 17 current: chain 'J' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 44 through 59 current: chain 'J' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN J 116 " --> pdb=" O LEU J 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR J 101 " --> pdb=" O THR J 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR J 114 " --> pdb=" O THR J 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU J 103 " --> pdb=" O MET J 112 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N MET J 112 " --> pdb=" O GLU J 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 112 through 119 current: chain 'H' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 16 through 17 current: chain 'H' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 44 through 59 current: chain 'H' and resid 91 through 104 removed outlier: 6.940A pdb=" N ASN H 116 " --> pdb=" O LEU H 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR H 101 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR H 114 " --> pdb=" O THR H 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU H 103 " --> pdb=" O MET H 112 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N MET H 112 " --> pdb=" O GLU H 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 112 through 119 current: chain 'L' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 16 through 17 current: chain 'L' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 44 through 59 current: chain 'L' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN L 116 " --> pdb=" O LEU L 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR L 101 " --> pdb=" O THR L 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR L 114 " --> pdb=" O THR L 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU L 103 " --> pdb=" O MET L 112 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET L 112 " --> pdb=" O GLU L 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 112 through 119 current: chain 'N' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 16 through 17 current: chain 'N' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 44 through 59 current: chain 'N' and resid 91 through 106 removed outlier: 6.941A pdb=" N ASN N 116 " --> pdb=" O LEU N 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR N 101 " --> pdb=" O THR N 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR N 114 " --> pdb=" O THR N 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU N 103 " --> pdb=" O MET N 112 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET N 112 " --> pdb=" O GLU N 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 112 through 119 current: chain 'P' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 16 through 17 current: chain 'P' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 44 through 59 current: chain 'P' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN P 116 " --> pdb=" O LEU P 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR P 101 " --> pdb=" O THR P 114 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR P 114 " --> pdb=" O THR P 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU P 103 " --> pdb=" O MET P 112 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N MET P 112 " --> pdb=" O GLU P 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 112 through 119 current: chain 'R' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 16 through 17 current: chain 'R' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 44 through 59 current: chain 'R' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN R 116 " --> pdb=" O LEU R 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR R 101 " --> pdb=" O THR R 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR R 114 " --> pdb=" O THR R 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU R 103 " --> pdb=" O MET R 112 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET R 112 " --> pdb=" O GLU R 103 " (cutoff:3.500A) 57 hydrogen bonds defined for protein. 171 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.70 Time building geometry restraints manager: 4.82 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 31.900 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.160 ------------------------------------------------------------------------------- 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= 0.478 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 420 time to evaluate : 1.711 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: 0.3325 time to fit residues: 201.6968 Evaluate side-chains 205 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 2.9990 chunk 177 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 60 optimal weight: 0.0170 chunk 119 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 111 optimal weight: 0.3980 chunk 136 optimal weight: 0.3980 chunk 212 optimal weight: 0.9990 overall best weight: 0.5620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN A 125 GLN D 125 GLN E 125 GLN F 20 HIS ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 GLN I 125 GLN G 125 GLN K 125 GLN O 125 GLN Q 125 GLN H 125 GLN L 125 GLN P 125 GLN R 125 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3525 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17442 Z= 0.188 Angle : 0.671 11.508 23688 Z= 0.324 Chirality : 0.043 0.182 2628 Planarity : 0.004 0.042 3150 Dihedral : 4.169 20.454 2466 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.81 % Allowed : 12.60 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.15), residues: 2304 helix: None (None), residues: 0 sheet: -1.17 (0.13), residues: 1242 loop : -1.12 (0.16), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 36 HIS 0.005 0.001 HIS F 20 PHE 0.046 0.002 PHE N 56 TYR 0.017 0.002 TYR D 59 ARG 0.005 0.001 ARG N 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 297 time to evaluate : 1.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.5843 (pmm) cc_final: 0.5513 (mtp) REVERT: F 1 MET cc_start: 0.1802 (pmm) cc_final: 0.1290 (ptm) REVERT: G 93 VAL cc_start: 0.4326 (t) cc_final: 0.4121 (t) REVERT: K 1 MET cc_start: 0.3991 (ttm) cc_final: 0.3114 (tmm) REVERT: K 38 MET cc_start: 0.0895 (mtp) cc_final: 0.0140 (ttm) REVERT: K 112 MET cc_start: 0.5956 (pmm) cc_final: 0.5571 (pmm) REVERT: J 1 MET cc_start: 0.4952 (pmm) cc_final: 0.4305 (ptm) REVERT: H 11 ASN cc_start: 0.6787 (t0) cc_final: 0.6576 (t0) REVERT: H 93 VAL cc_start: 0.4568 (t) cc_final: 0.4347 (t) REVERT: N 1 MET cc_start: 0.4874 (tmm) cc_final: 0.4499 (tpp) REVERT: P 38 MET cc_start: 0.4144 (mtp) cc_final: 0.2987 (tmm) REVERT: R 38 MET cc_start: 0.5931 (mtp) cc_final: 0.3032 (tmm) outliers start: 51 outliers final: 27 residues processed: 325 average time/residue: 0.2823 time to fit residues: 139.1250 Evaluate side-chains 237 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 210 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain D residue 5 LYS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain Q residue 14 THR Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 67 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 176 optimal weight: 7.9990 chunk 144 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 212 optimal weight: 6.9990 chunk 229 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 170 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 20 HIS C 22 GLN ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 22 GLN O 22 GLN Q 55 ASN ** Q 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 22 GLN N 22 GLN P 11 ASN R 55 ASN ** R 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 2.0677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.105 17442 Z= 0.594 Angle : 1.254 13.968 23688 Z= 0.649 Chirality : 0.060 0.364 2628 Planarity : 0.009 0.089 3150 Dihedral : 8.367 36.038 2466 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.68 % Favored : 93.23 % Rotamer: Outliers : 5.83 % Allowed : 17.49 % Favored : 76.68 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -3.59 (0.15), residues: 2304 helix: None (None), residues: 0 sheet: -2.29 (0.15), residues: 1068 loop : -2.43 (0.13), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP E 24 HIS 0.014 0.003 HIS M 20 PHE 0.053 0.004 PHE F 46 TYR 0.065 0.004 TYR D 59 ARG 0.015 0.002 ARG Q 51 *********************** 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 791 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 685 time to evaluate : 1.960 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: B 3 LYS cc_start: 0.7502 (mmmt) cc_final: 0.6926 (mmtm) REVERT: B 44 ARG cc_start: 0.7414 (mpt-90) cc_final: 0.7196 (mmm-85) REVERT: B 78 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7054 (mt-10) REVERT: A 31 ASP cc_start: 0.8145 (m-30) cc_final: 0.7921 (m-30) REVERT: C 32 GLU cc_start: 0.7821 (pm20) cc_final: 0.7527 (pm20) REVERT: C 68 ASP cc_start: 0.7763 (m-30) cc_final: 0.7552 (p0) REVERT: C 73 ASP cc_start: 0.7155 (p0) cc_final: 0.6870 (p0) REVERT: C 78 GLU cc_start: 0.7675 (pt0) cc_final: 0.7461 (mt-10) REVERT: C 119 THR cc_start: 0.9301 (OUTLIER) cc_final: 0.8909 (p) REVERT: D 38 MET cc_start: 0.6351 (OUTLIER) cc_final: 0.4266 (ptt) REVERT: D 43 GLU cc_start: 0.8196 (pp20) cc_final: 0.7859 (pt0) REVERT: E 27 ASP cc_start: 0.6339 (t70) cc_final: 0.5517 (t0) REVERT: E 112 MET cc_start: 0.8486 (mmm) cc_final: 0.8229 (mmm) REVERT: F 11 ASN cc_start: 0.7199 (t0) cc_final: 0.6817 (t0) REVERT: F 16 ASP cc_start: 0.6833 (p0) cc_final: 0.6570 (p0) REVERT: F 27 ASP cc_start: 0.7150 (t70) cc_final: 0.6182 (t70) REVERT: I 27 ASP cc_start: 0.7756 (t70) cc_final: 0.6919 (t70) REVERT: G 31 ASP cc_start: 0.7700 (m-30) cc_final: 0.7011 (m-30) REVERT: G 84 GLU cc_start: 0.7789 (tt0) cc_final: 0.7545 (tt0) REVERT: G 106 SER cc_start: 0.7471 (OUTLIER) cc_final: 0.6915 (t) REVERT: G 107 LYS cc_start: 0.6490 (pttm) cc_final: 0.4625 (tptt) REVERT: G 113 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.7063 (pt) REVERT: K 40 ASP cc_start: 0.7305 (OUTLIER) cc_final: 0.6988 (p0) REVERT: K 41 ASP cc_start: 0.8416 (t0) cc_final: 0.8161 (t0) REVERT: K 90 TYR cc_start: 0.7965 (p90) cc_final: 0.7635 (p90) REVERT: M 1 MET cc_start: 0.6403 (tmm) cc_final: 0.6191 (tmm) REVERT: M 43 GLU cc_start: 0.7835 (pp20) cc_final: 0.6987 (pt0) REVERT: M 68 ASP cc_start: 0.7200 (m-30) cc_final: 0.6917 (m-30) REVERT: M 93 VAL cc_start: 0.8170 (OUTLIER) cc_final: 0.7686 (m) REVERT: O 27 ASP cc_start: 0.5791 (p0) cc_final: 0.5358 (p0) REVERT: O 29 GLN cc_start: 0.8118 (mp10) cc_final: 0.7405 (mp10) REVERT: O 70 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7804 (mm-30) REVERT: Q 27 ASP cc_start: 0.6793 (t70) cc_final: 0.6505 (t70) REVERT: Q 28 THR cc_start: 0.7568 (OUTLIER) cc_final: 0.7294 (m) REVERT: Q 29 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.7508 (pm20) REVERT: Q 80 TYR cc_start: 0.5319 (m-80) cc_final: 0.5011 (m-10) REVERT: J 125 GLN cc_start: 0.7896 (tp-100) cc_final: 0.7654 (tm-30) REVERT: H 9 VAL cc_start: 0.7386 (t) cc_final: 0.7077 (t) REVERT: H 11 ASN cc_start: 0.7284 (t0) cc_final: 0.6967 (t0) REVERT: H 31 ASP cc_start: 0.7847 (m-30) cc_final: 0.7591 (m-30) REVERT: H 32 GLU cc_start: 0.8160 (pt0) cc_final: 0.7558 (pt0) REVERT: L 5 LYS cc_start: 0.7226 (mmtm) cc_final: 0.7004 (mtmm) REVERT: L 115 VAL cc_start: 0.8716 (OUTLIER) cc_final: 0.8293 (t) REVERT: N 29 GLN cc_start: 0.8236 (mt0) cc_final: 0.8023 (mt0) REVERT: P 29 GLN cc_start: 0.8014 (pm20) cc_final: 0.7643 (pm20) REVERT: R 27 ASP cc_start: 0.7450 (t70) cc_final: 0.6410 (t70) REVERT: R 29 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7543 (pm20) REVERT: R 58 VAL cc_start: 0.7249 (m) cc_final: 0.6580 (m) outliers start: 106 outliers final: 25 residues processed: 753 average time/residue: 0.2960 time to fit residues: 334.7534 Evaluate side-chains 470 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 435 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain K residue 16 ASP Chi-restraints excluded: chain K residue 40 ASP Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain Q residue 14 THR Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain Q residue 29 GLN Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 64 ASP Chi-restraints excluded: chain N residue 68 ASP Chi-restraints excluded: chain P residue 59 TYR Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain R residue 29 GLN Chi-restraints excluded: chain R residue 74 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 0.9980 chunk 160 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 142 optimal weight: 8.9990 chunk 213 optimal weight: 2.9990 chunk 226 optimal weight: 3.9990 chunk 111 optimal weight: 0.4980 chunk 202 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 22 GLN ** Q 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 55 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 2.0787 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= 0.233 Angle : 0.739 10.446 23688 Z= 0.366 Chirality : 0.046 0.154 2628 Planarity : 0.005 0.056 3150 Dihedral : 4.819 24.071 2466 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.62 % Allowed : 25.30 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.16), residues: 2304 helix: None (None), residues: 0 sheet: -1.79 (0.13), residues: 1350 loop : -1.77 (0.17), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Q 24 HIS 0.002 0.001 HIS I 20 PHE 0.019 0.002 PHE F 46 TYR 0.015 0.002 TYR A 90 ARG 0.008 0.001 ARG I 91 *********************** 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 567 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 483 time to evaluate : 2.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 GLN cc_start: 0.8573 (tp40) cc_final: 0.8043 (tp40) REVERT: B 32 GLU cc_start: 0.7555 (pt0) cc_final: 0.7041 (tt0) REVERT: B 84 GLU cc_start: 0.8120 (tt0) cc_final: 0.7894 (tt0) REVERT: B 112 MET cc_start: 0.7947 (mmm) cc_final: 0.7587 (mmm) REVERT: B 125 GLN cc_start: 0.8215 (mm-40) cc_final: 0.7896 (tm-30) REVERT: A 31 ASP cc_start: 0.8424 (m-30) cc_final: 0.8140 (m-30) REVERT: A 68 ASP cc_start: 0.8419 (m-30) cc_final: 0.8094 (p0) REVERT: C 1 MET cc_start: 0.6540 (tmm) cc_final: 0.5804 (tpp) REVERT: C 68 ASP cc_start: 0.8110 (m-30) cc_final: 0.7770 (p0) REVERT: C 125 GLN cc_start: 0.8466 (mp10) cc_final: 0.8241 (mp10) REVERT: D 43 GLU cc_start: 0.8340 (pp20) cc_final: 0.8025 (pt0) REVERT: D 57 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8324 (tm-30) REVERT: E 27 ASP cc_start: 0.6795 (t70) cc_final: 0.6558 (t70) REVERT: F 11 ASN cc_start: 0.7820 (t0) cc_final: 0.7298 (t0) REVERT: F 70 GLU cc_start: 0.8799 (mp0) cc_final: 0.8528 (mp0) REVERT: I 1 MET cc_start: 0.8314 (ptp) cc_final: 0.7968 (mtm) REVERT: I 70 GLU cc_start: 0.8418 (mp0) cc_final: 0.8149 (mp0) REVERT: G 31 ASP cc_start: 0.8034 (m-30) cc_final: 0.7653 (m-30) REVERT: G 69 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7308 (pp) REVERT: G 84 GLU cc_start: 0.8247 (tt0) cc_final: 0.7890 (tt0) REVERT: G 125 GLN cc_start: 0.8210 (mm110) cc_final: 0.7790 (mm-40) REVERT: K 31 ASP cc_start: 0.7838 (m-30) cc_final: 0.7463 (m-30) REVERT: K 84 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7777 (mt-10) REVERT: K 90 TYR cc_start: 0.8799 (p90) cc_final: 0.8369 (p90) REVERT: M 1 MET cc_start: 0.6886 (tmm) cc_final: 0.6165 (ttt) REVERT: M 31 ASP cc_start: 0.8000 (m-30) cc_final: 0.7753 (m-30) REVERT: M 43 GLU cc_start: 0.8043 (pp20) cc_final: 0.7123 (pt0) REVERT: O 29 GLN cc_start: 0.8337 (mp10) cc_final: 0.7229 (mp10) REVERT: O 70 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7775 (mm-30) REVERT: Q 1 MET cc_start: 0.9066 (ptm) cc_final: 0.8376 (ptm) REVERT: Q 11 ASN cc_start: 0.7352 (t0) cc_final: 0.7125 (t0) REVERT: Q 27 ASP cc_start: 0.7070 (t70) cc_final: 0.6852 (t70) REVERT: Q 29 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7590 (pm20) REVERT: Q 70 GLU cc_start: 0.8094 (mp0) cc_final: 0.7846 (mp0) REVERT: Q 93 VAL cc_start: 0.8894 (t) cc_final: 0.8235 (m) REVERT: J 125 GLN cc_start: 0.8429 (tp-100) cc_final: 0.8188 (tm-30) REVERT: H 44 ARG cc_start: 0.7716 (mpt-90) cc_final: 0.6809 (ptt180) REVERT: H 125 GLN cc_start: 0.7991 (mm-40) cc_final: 0.7764 (mm-40) REVERT: L 27 ASP cc_start: 0.8797 (p0) cc_final: 0.7949 (p0) REVERT: P 29 GLN cc_start: 0.8324 (pm20) cc_final: 0.7319 (pm20) REVERT: P 43 GLU cc_start: 0.7964 (pp20) cc_final: 0.7668 (pt0) REVERT: R 27 ASP cc_start: 0.7497 (t70) cc_final: 0.7054 (t70) REVERT: R 29 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7535 (pm20) REVERT: R 118 ARG cc_start: 0.8228 (ttt-90) cc_final: 0.7999 (ttt-90) REVERT: R 125 GLN cc_start: 0.8289 (tm-30) cc_final: 0.7977 (tm-30) outliers start: 84 outliers final: 42 residues processed: 536 average time/residue: 0.3013 time to fit residues: 238.8592 Evaluate side-chains 422 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 377 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain E residue 20 HIS Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain F residue 20 HIS Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain O residue 53 SER Chi-restraints excluded: chain O residue 55 ASN Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain Q residue 29 GLN Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain P residue 115 VAL Chi-restraints excluded: chain R residue 29 GLN Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 128 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 168 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 193 optimal weight: 0.9990 chunk 156 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 chunk 203 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 20 HIS ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 11 ASN O 125 GLN ** Q 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 125 GLN N 22 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 2.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17442 Z= 0.334 Angle : 0.757 9.727 23688 Z= 0.376 Chirality : 0.046 0.159 2628 Planarity : 0.005 0.047 3150 Dihedral : 5.128 23.800 2466 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 6.16 % Allowed : 26.57 % 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: -2.78 (0.16), residues: 2304 helix: None (None), residues: 0 sheet: -1.60 (0.14), residues: 1224 loop : -2.02 (0.15), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP O 24 HIS 0.004 0.001 HIS F 20 PHE 0.018 0.002 PHE R 46 TYR 0.019 0.002 TYR B 80 ARG 0.007 0.001 ARG F 118 *********************** 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 481 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 369 time to evaluate : 1.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 GLN cc_start: 0.8838 (tp40) cc_final: 0.8566 (tp40) REVERT: B 32 GLU cc_start: 0.7831 (pt0) cc_final: 0.7599 (tt0) REVERT: B 76 ASP cc_start: 0.8404 (t0) cc_final: 0.7846 (p0) REVERT: B 103 GLU cc_start: 0.8061 (pm20) cc_final: 0.7812 (pm20) REVERT: B 125 GLN cc_start: 0.8593 (mm-40) cc_final: 0.7916 (mm110) REVERT: A 44 ARG cc_start: 0.8624 (mmm-85) cc_final: 0.8376 (mmm-85) REVERT: A 68 ASP cc_start: 0.8597 (m-30) cc_final: 0.8145 (p0) REVERT: C 57 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7974 (tm-30) REVERT: C 125 GLN cc_start: 0.8368 (mp10) cc_final: 0.8096 (mp10) REVERT: D 29 GLN cc_start: 0.8033 (mp10) cc_final: 0.7819 (mp10) REVERT: E 27 ASP cc_start: 0.7703 (t70) cc_final: 0.7011 (t0) REVERT: E 29 GLN cc_start: 0.7965 (mp10) cc_final: 0.7657 (mp10) REVERT: F 32 GLU cc_start: 0.8328 (pt0) cc_final: 0.8099 (pt0) REVERT: F 44 ARG cc_start: 0.8267 (mpp80) cc_final: 0.8060 (mtp85) REVERT: F 103 GLU cc_start: 0.7696 (mp0) cc_final: 0.7456 (mp0) REVERT: F 112 MET cc_start: 0.8473 (mmm) cc_final: 0.8210 (mmm) REVERT: I 73 ASP cc_start: 0.8920 (OUTLIER) cc_final: 0.8600 (p0) REVERT: G 32 GLU cc_start: 0.8356 (pt0) cc_final: 0.8034 (pt0) REVERT: G 44 ARG cc_start: 0.8160 (mpp80) cc_final: 0.7897 (mmm-85) REVERT: G 103 GLU cc_start: 0.7407 (mt-10) cc_final: 0.6951 (mp0) REVERT: K 84 GLU cc_start: 0.8285 (mt-10) cc_final: 0.8060 (mt-10) REVERT: M 43 GLU cc_start: 0.8416 (pp20) cc_final: 0.7972 (pt0) REVERT: O 1 MET cc_start: 0.8688 (ttp) cc_final: 0.8212 (ptm) REVERT: O 16 ASP cc_start: 0.6873 (t0) cc_final: 0.6180 (m-30) REVERT: O 29 GLN cc_start: 0.8537 (mp10) cc_final: 0.8129 (mp10) REVERT: Q 27 ASP cc_start: 0.7953 (t70) cc_final: 0.7496 (t70) REVERT: Q 29 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.7578 (pm20) REVERT: Q 123 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8940 (mp) REVERT: J 125 GLN cc_start: 0.8668 (tp-100) cc_final: 0.8140 (tm-30) REVERT: H 44 ARG cc_start: 0.7905 (mpt-90) cc_final: 0.7176 (ptt180) REVERT: L 27 ASP cc_start: 0.8553 (p0) cc_final: 0.7697 (p0) REVERT: P 29 GLN cc_start: 0.8302 (pm20) cc_final: 0.7851 (pm20) REVERT: P 51 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7847 (ptp-110) REVERT: P 126 LYS cc_start: 0.8844 (ttmm) cc_final: 0.8242 (mtpp) REVERT: R 27 ASP cc_start: 0.7930 (t70) cc_final: 0.7304 (t70) REVERT: R 29 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.7252 (pm20) REVERT: R 70 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7368 (pm20) outliers start: 112 outliers final: 68 residues processed: 447 average time/residue: 0.2939 time to fit residues: 195.8786 Evaluate side-chains 400 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 326 time to evaluate : 1.997 ------------------------------------------------------------------------------- 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 101 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain F residue 20 HIS Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 58 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 G residue 8 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 23 SER Chi-restraints excluded: chain M residue 91 ARG Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 11 ASN Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 29 GLN Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 74 LEU Chi-restraints excluded: chain Q residue 123 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 32 GLU Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 29 GLN Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 91 ARG Chi-restraints excluded: chain P residue 51 ARG Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 115 VAL Chi-restraints excluded: chain R residue 29 GLN Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 128 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 2.9990 chunk 203 optimal weight: 0.0030 chunk 44 optimal weight: 2.9990 chunk 132 optimal weight: 0.0980 chunk 55 optimal weight: 0.0470 chunk 226 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 118 optimal weight: 0.0040 overall best weight: 0.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN D 11 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 HIS ** Q 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 125 GLN L 125 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 2.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17442 Z= 0.143 Angle : 0.595 9.222 23688 Z= 0.289 Chirality : 0.042 0.165 2628 Planarity : 0.004 0.040 3150 Dihedral : 3.956 17.761 2466 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.70 % Allowed : 29.15 % Favored : 68.15 % 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: -1.91 (0.16), residues: 2304 helix: None (None), residues: 0 sheet: -1.08 (0.14), residues: 1350 loop : -1.35 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 36 HIS 0.002 0.001 HIS Q 20 PHE 0.023 0.002 PHE F 46 TYR 0.010 0.001 TYR J 90 ARG 0.005 0.001 ARG O 44 *********************** 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 397 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 348 time to evaluate : 1.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 76 ASP cc_start: 0.8348 (t0) cc_final: 0.7716 (p0) REVERT: B 103 GLU cc_start: 0.7950 (pm20) cc_final: 0.7662 (pm20) REVERT: B 125 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8033 (tm-30) REVERT: A 44 ARG cc_start: 0.8647 (mmm-85) cc_final: 0.8372 (mmm-85) REVERT: A 68 ASP cc_start: 0.8390 (m-30) cc_final: 0.8146 (p0) REVERT: C 11 ASN cc_start: 0.8830 (m-40) cc_final: 0.8575 (t0) REVERT: C 125 GLN cc_start: 0.8367 (mp10) cc_final: 0.8063 (mp10) REVERT: D 11 ASN cc_start: 0.8787 (m-40) cc_final: 0.8549 (t0) REVERT: D 57 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8325 (tm-30) REVERT: E 91 ARG cc_start: 0.8439 (mpt90) cc_final: 0.8238 (mpt180) REVERT: E 126 LYS cc_start: 0.8565 (ttmm) cc_final: 0.8329 (ttmt) REVERT: F 29 GLN cc_start: 0.8274 (pm20) cc_final: 0.8042 (pm20) REVERT: F 44 ARG cc_start: 0.8384 (mpp80) cc_final: 0.8076 (mtp85) REVERT: F 103 GLU cc_start: 0.7686 (mp0) cc_final: 0.7386 (mp0) REVERT: F 112 MET cc_start: 0.8459 (mmm) cc_final: 0.8245 (mmm) REVERT: I 70 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8191 (mp0) REVERT: G 29 GLN cc_start: 0.8508 (pt0) cc_final: 0.8233 (pt0) REVERT: G 32 GLU cc_start: 0.8357 (pt0) cc_final: 0.8052 (pt0) REVERT: G 44 ARG cc_start: 0.8204 (mpp80) cc_final: 0.7894 (mmm-85) REVERT: G 69 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8154 (pp) REVERT: G 76 ASP cc_start: 0.8585 (t0) cc_final: 0.8380 (t0) REVERT: G 103 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7053 (mp0) REVERT: K 84 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7967 (mt-10) REVERT: K 103 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7065 (tm-30) REVERT: M 24 TRP cc_start: 0.8371 (p90) cc_final: 0.8145 (p-90) REVERT: M 43 GLU cc_start: 0.8219 (pp20) cc_final: 0.7823 (pt0) REVERT: M 91 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8323 (ptp90) REVERT: O 1 MET cc_start: 0.8635 (ttp) cc_final: 0.8043 (ptm) REVERT: O 29 GLN cc_start: 0.8380 (mp10) cc_final: 0.7982 (mp10) REVERT: Q 1 MET cc_start: 0.9262 (ptm) cc_final: 0.8769 (ptm) REVERT: Q 27 ASP cc_start: 0.7709 (t70) cc_final: 0.7450 (t70) REVERT: Q 29 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7580 (pm20) REVERT: Q 123 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8888 (mp) REVERT: Q 126 LYS cc_start: 0.8290 (tptp) cc_final: 0.8073 (ttmt) REVERT: J 125 GLN cc_start: 0.8621 (tp-100) cc_final: 0.8203 (tm-30) REVERT: H 22 GLN cc_start: 0.8747 (tp40) cc_final: 0.8467 (mm-40) REVERT: H 44 ARG cc_start: 0.8001 (mpt-90) cc_final: 0.7328 (ptt180) REVERT: H 51 ARG cc_start: 0.8700 (ptp-170) cc_final: 0.8429 (ptp-170) REVERT: H 103 GLU cc_start: 0.7616 (mp0) cc_final: 0.6939 (mp0) REVERT: H 125 GLN cc_start: 0.8473 (mm-40) cc_final: 0.8116 (mm110) REVERT: L 27 ASP cc_start: 0.8399 (p0) cc_final: 0.7481 (p0) REVERT: P 29 GLN cc_start: 0.8092 (pm20) cc_final: 0.7380 (pm20) REVERT: P 126 LYS cc_start: 0.8540 (ttmm) cc_final: 0.8340 (mtpp) REVERT: R 3 LYS cc_start: 0.8298 (mmmt) cc_final: 0.7889 (mmmt) REVERT: R 29 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7864 (pm20) outliers start: 49 outliers final: 30 residues processed: 372 average time/residue: 0.3085 time to fit residues: 167.7871 Evaluate side-chains 360 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 324 time to evaluate : 2.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 GLN Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain E residue 20 HIS Chi-restraints excluded: chain F residue 20 HIS Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain M residue 91 ARG Chi-restraints excluded: chain O residue 97 LEU 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 Q residue 123 LEU Chi-restraints excluded: chain Q residue 128 THR Chi-restraints excluded: chain J residue 29 GLN Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain H residue 29 GLN Chi-restraints excluded: chain L residue 32 GLU Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 29 GLN Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 91 ARG Chi-restraints excluded: chain P residue 128 THR Chi-restraints excluded: chain R residue 29 GLN 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 218 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 128 optimal weight: 4.9990 chunk 165 optimal weight: 8.9990 chunk 190 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 225 optimal weight: 6.9990 chunk 141 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 139 optimal weight: 0.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 GLN ** Q 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 2.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 17442 Z= 0.389 Angle : 0.707 9.301 23688 Z= 0.346 Chirality : 0.045 0.182 2628 Planarity : 0.005 0.040 3150 Dihedral : 4.962 18.497 2466 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.35 % Allowed : 28.93 % Favored : 66.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.16), residues: 2304 helix: None (None), residues: 0 sheet: -1.31 (0.14), residues: 1260 loop : -1.68 (0.16), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP O 24 HIS 0.005 0.001 HIS Q 20 PHE 0.011 0.002 PHE P 56 TYR 0.019 0.002 TYR I 90 ARG 0.008 0.001 ARG O 118 *********************** 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 400 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 321 time to evaluate : 1.997 Fit side-chains revert: symmetry clash REVERT: B 103 GLU cc_start: 0.8079 (pm20) cc_final: 0.7814 (pm20) REVERT: B 125 GLN cc_start: 0.8608 (mm-40) cc_final: 0.8074 (mm110) REVERT: A 27 ASP cc_start: 0.8826 (p0) cc_final: 0.8467 (p0) REVERT: C 11 ASN cc_start: 0.8800 (m-40) cc_final: 0.8183 (t0) REVERT: C 43 GLU cc_start: 0.8055 (pm20) cc_final: 0.7828 (pt0) REVERT: C 125 GLN cc_start: 0.8475 (mp10) cc_final: 0.8167 (mp10) REVERT: D 11 ASN cc_start: 0.8792 (m-40) cc_final: 0.8552 (t0) REVERT: D 57 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8290 (tm-30) REVERT: D 103 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7493 (tm-30) REVERT: E 91 ARG cc_start: 0.8664 (mpt90) cc_final: 0.8419 (mpt180) REVERT: E 126 LYS cc_start: 0.8820 (ttmm) cc_final: 0.8588 (ttmt) REVERT: F 29 GLN cc_start: 0.8396 (pm20) cc_final: 0.8099 (pm20) REVERT: F 103 GLU cc_start: 0.7874 (mp0) cc_final: 0.7619 (mp0) REVERT: F 112 MET cc_start: 0.8514 (mmm) cc_final: 0.8226 (mmm) REVERT: I 29 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.7821 (mp10) REVERT: G 32 GLU cc_start: 0.8372 (pt0) cc_final: 0.8097 (pt0) REVERT: G 43 GLU cc_start: 0.7986 (pm20) cc_final: 0.7650 (pt0) REVERT: G 44 ARG cc_start: 0.8174 (mpp80) cc_final: 0.7830 (mmm-85) REVERT: G 76 ASP cc_start: 0.8577 (t0) cc_final: 0.8367 (t0) REVERT: G 103 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7228 (mp0) REVERT: K 43 GLU cc_start: 0.8424 (tt0) cc_final: 0.8064 (tt0) REVERT: K 126 LYS cc_start: 0.8854 (mtpp) cc_final: 0.8542 (mtpp) REVERT: M 43 GLU cc_start: 0.8431 (pp20) cc_final: 0.8178 (pt0) REVERT: O 1 MET cc_start: 0.8626 (ttp) cc_final: 0.8350 (ptm) REVERT: O 29 GLN cc_start: 0.8408 (mp10) cc_final: 0.8077 (mp10) REVERT: O 112 MET cc_start: 0.8764 (mmm) cc_final: 0.8564 (mmt) REVERT: Q 1 MET cc_start: 0.9185 (ptm) cc_final: 0.8752 (ptm) REVERT: Q 27 ASP cc_start: 0.8043 (t70) cc_final: 0.7784 (t70) REVERT: Q 29 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7713 (pm20) REVERT: J 125 GLN cc_start: 0.8623 (tp-100) cc_final: 0.8213 (tm-30) REVERT: H 32 GLU cc_start: 0.8294 (pp20) cc_final: 0.7817 (pp20) REVERT: H 44 ARG cc_start: 0.7880 (mpt-90) cc_final: 0.7209 (ptt180) REVERT: H 103 GLU cc_start: 0.8075 (mp0) cc_final: 0.7712 (mp0) REVERT: L 27 ASP cc_start: 0.8858 (p0) cc_final: 0.7952 (p0) REVERT: L 125 GLN cc_start: 0.8414 (mm-40) cc_final: 0.7969 (mm110) REVERT: P 29 GLN cc_start: 0.8177 (pm20) cc_final: 0.7599 (pm20) REVERT: P 51 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.7702 (ptp-170) REVERT: P 126 LYS cc_start: 0.8786 (ttmm) cc_final: 0.8507 (mtpp) REVERT: R 29 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8295 (pm20) outliers start: 79 outliers final: 62 residues processed: 366 average time/residue: 0.3443 time to fit residues: 181.6413 Evaluate side-chains 374 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 308 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 20 HIS Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 29 GLN Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 91 ARG Chi-restraints excluded: chain Q residue 20 HIS Chi-restraints excluded: chain Q residue 29 GLN Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 101 THR Chi-restraints excluded: chain Q residue 128 THR Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain H residue 29 GLN Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 32 GLU Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 29 GLN Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 91 ARG Chi-restraints excluded: chain P residue 51 ARG Chi-restraints excluded: chain P residue 115 VAL Chi-restraints excluded: chain P residue 128 THR Chi-restraints excluded: chain R residue 27 ASP Chi-restraints excluded: chain R residue 29 GLN Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 114 THR 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 90 optimal weight: 4.9990 chunk 134 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 153 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 177 optimal weight: 6.9990 chunk 205 optimal weight: 0.4980 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 2.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17442 Z= 0.307 Angle : 0.649 10.194 23688 Z= 0.320 Chirality : 0.043 0.157 2628 Planarity : 0.004 0.044 3150 Dihedral : 4.564 18.387 2466 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.73 % Allowed : 28.22 % Favored : 67.05 % 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: -1.95 (0.16), residues: 2304 helix: None (None), residues: 0 sheet: -1.20 (0.13), residues: 1386 loop : -1.16 (0.18), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 24 HIS 0.003 0.001 HIS Q 20 PHE 0.013 0.002 PHE C 56 TYR 0.013 0.002 TYR O 80 ARG 0.005 0.001 ARG L 91 *********************** 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 416 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 330 time to evaluate : 2.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 51 ARG cc_start: 0.8264 (mtm-85) cc_final: 0.8058 (mtm-85) REVERT: B 76 ASP cc_start: 0.8337 (t0) cc_final: 0.7891 (m-30) REVERT: B 103 GLU cc_start: 0.8116 (pm20) cc_final: 0.7849 (pm20) REVERT: B 125 GLN cc_start: 0.8680 (mm-40) cc_final: 0.8184 (mm110) REVERT: A 27 ASP cc_start: 0.8806 (p0) cc_final: 0.8446 (p0) REVERT: A 76 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7697 (p0) REVERT: A 125 GLN cc_start: 0.8396 (mm-40) cc_final: 0.8143 (mm-40) REVERT: C 11 ASN cc_start: 0.8927 (m-40) cc_final: 0.8355 (t0) REVERT: D 11 ASN cc_start: 0.8809 (m-40) cc_final: 0.8599 (t0) REVERT: D 57 GLU cc_start: 0.8333 (tm-30) cc_final: 0.8073 (tm-30) REVERT: D 103 GLU cc_start: 0.7521 (tm-30) cc_final: 0.7275 (tm-30) REVERT: E 17 SER cc_start: 0.8437 (OUTLIER) cc_final: 0.8027 (t) REVERT: F 29 GLN cc_start: 0.8476 (pm20) cc_final: 0.8146 (pm20) REVERT: F 103 GLU cc_start: 0.7968 (mp0) cc_final: 0.7738 (mp0) REVERT: F 112 MET cc_start: 0.8510 (mmm) cc_final: 0.8236 (mmm) REVERT: G 32 GLU cc_start: 0.8375 (pt0) cc_final: 0.8156 (pt0) REVERT: G 43 GLU cc_start: 0.7998 (pm20) cc_final: 0.7734 (pt0) REVERT: G 44 ARG cc_start: 0.8237 (mpp80) cc_final: 0.7868 (mmm-85) REVERT: G 103 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7369 (mp0) REVERT: K 43 GLU cc_start: 0.8311 (tt0) cc_final: 0.7989 (tt0) REVERT: M 21 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8820 (mm) REVERT: M 91 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8461 (ptp-170) REVERT: O 29 GLN cc_start: 0.8200 (mp10) cc_final: 0.7795 (mp10) REVERT: O 112 MET cc_start: 0.8711 (mmm) cc_final: 0.8411 (mmt) REVERT: Q 1 MET cc_start: 0.9179 (ptm) cc_final: 0.8794 (ptm) REVERT: Q 27 ASP cc_start: 0.8048 (t70) cc_final: 0.7802 (t70) REVERT: Q 29 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7834 (pm20) REVERT: J 125 GLN cc_start: 0.8644 (tp-100) cc_final: 0.8173 (tm-30) REVERT: H 22 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8701 (mm-40) REVERT: H 32 GLU cc_start: 0.8276 (pp20) cc_final: 0.7748 (pp20) REVERT: H 44 ARG cc_start: 0.7889 (mpt-90) cc_final: 0.7267 (ptt180) REVERT: H 84 GLU cc_start: 0.8164 (tt0) cc_final: 0.7964 (tt0) REVERT: L 27 ASP cc_start: 0.8790 (p0) cc_final: 0.7858 (p0) REVERT: L 103 GLU cc_start: 0.8147 (pt0) cc_final: 0.7715 (pm20) REVERT: L 125 GLN cc_start: 0.8427 (mm-40) cc_final: 0.7982 (mm110) REVERT: P 29 GLN cc_start: 0.8122 (pm20) cc_final: 0.7604 (pm20) REVERT: P 80 TYR cc_start: 0.8831 (m-80) cc_final: 0.8602 (m-80) REVERT: P 126 LYS cc_start: 0.8710 (ttmm) cc_final: 0.8444 (mtpp) REVERT: R 1 MET cc_start: 0.8697 (ptp) cc_final: 0.8410 (ptp) REVERT: R 29 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8214 (pm20) outliers start: 86 outliers final: 69 residues processed: 383 average time/residue: 0.3306 time to fit residues: 182.1760 Evaluate side-chains 394 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 318 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 3 LYS Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain F residue 20 HIS Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 114 THR 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 G residue 53 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 29 GLN Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 91 ARG Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain Q residue 20 HIS 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 29 GLN Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 126 LYS Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain H residue 22 GLN Chi-restraints excluded: chain H residue 29 GLN Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 32 GLU Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 29 GLN Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 91 ARG Chi-restraints excluded: chain P residue 115 VAL Chi-restraints excluded: chain R residue 27 ASP Chi-restraints excluded: chain R residue 29 GLN Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 114 THR 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 216 optimal weight: 9.9990 chunk 197 optimal weight: 5.9990 chunk 210 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 189 optimal weight: 7.9990 chunk 198 optimal weight: 6.9990 chunk 209 optimal weight: 8.9990 chunk 138 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 11 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 2.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 17442 Z= 0.565 Angle : 0.777 10.555 23688 Z= 0.387 Chirality : 0.046 0.154 2628 Planarity : 0.005 0.044 3150 Dihedral : 5.455 22.484 2466 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 5.50 % Allowed : 28.16 % Favored : 66.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.16), residues: 2304 helix: None (None), residues: 0 sheet: -1.65 (0.15), residues: 1098 loop : -1.55 (0.15), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP M 24 HIS 0.005 0.002 HIS Q 20 PHE 0.012 0.002 PHE P 56 TYR 0.024 0.003 TYR O 80 ARG 0.006 0.001 ARG O 118 *********************** 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 405 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 305 time to evaluate : 1.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 103 GLU cc_start: 0.8177 (pm20) cc_final: 0.7972 (pm20) REVERT: B 125 GLN cc_start: 0.8675 (mm-40) cc_final: 0.8164 (mm110) REVERT: A 27 ASP cc_start: 0.8894 (OUTLIER) cc_final: 0.8561 (p0) REVERT: C 11 ASN cc_start: 0.8854 (m-40) cc_final: 0.8368 (t0) REVERT: C 91 ARG cc_start: 0.8678 (mmt-90) cc_final: 0.8077 (mtt90) REVERT: C 125 GLN cc_start: 0.8461 (mp10) cc_final: 0.8237 (mp10) REVERT: D 57 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8082 (tm-30) REVERT: F 29 GLN cc_start: 0.8503 (pm20) cc_final: 0.8140 (pm20) REVERT: F 103 GLU cc_start: 0.8198 (mp0) cc_final: 0.7953 (mp0) REVERT: I 27 ASP cc_start: 0.8303 (t70) cc_final: 0.7850 (t0) REVERT: I 29 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8172 (pm20) REVERT: G 27 ASP cc_start: 0.8380 (t0) cc_final: 0.8023 (t0) REVERT: G 32 GLU cc_start: 0.8385 (pt0) cc_final: 0.8150 (pt0) REVERT: G 44 ARG cc_start: 0.8252 (mpp80) cc_final: 0.7889 (mmm-85) REVERT: G 103 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7414 (mp0) REVERT: K 27 ASP cc_start: 0.8861 (p0) cc_final: 0.8466 (p0) REVERT: K 43 GLU cc_start: 0.8464 (tt0) cc_final: 0.8088 (tt0) REVERT: O 112 MET cc_start: 0.8674 (mmm) cc_final: 0.8388 (mmt) REVERT: O 126 LYS cc_start: 0.8809 (ttmm) cc_final: 0.8385 (mtpp) REVERT: Q 27 ASP cc_start: 0.8360 (t70) cc_final: 0.8043 (t70) REVERT: Q 29 GLN cc_start: 0.8440 (mp10) cc_final: 0.7781 (pm20) REVERT: J 78 GLU cc_start: 0.8509 (pt0) cc_final: 0.8288 (pt0) REVERT: J 125 GLN cc_start: 0.8575 (tp-100) cc_final: 0.8080 (tm-30) REVERT: H 22 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8837 (mm-40) REVERT: H 32 GLU cc_start: 0.8327 (pp20) cc_final: 0.7809 (pp20) REVERT: H 44 ARG cc_start: 0.7863 (mpt-90) cc_final: 0.7294 (ptt180) REVERT: H 103 GLU cc_start: 0.8221 (mp0) cc_final: 0.7881 (mp0) REVERT: H 125 GLN cc_start: 0.8377 (mm-40) cc_final: 0.8026 (mm110) REVERT: L 27 ASP cc_start: 0.8976 (p0) cc_final: 0.8070 (p0) REVERT: L 103 GLU cc_start: 0.8177 (pt0) cc_final: 0.7661 (pm20) REVERT: L 125 GLN cc_start: 0.8510 (mm-40) cc_final: 0.8034 (mm110) REVERT: P 29 GLN cc_start: 0.8207 (pm20) cc_final: 0.7674 (pm20) REVERT: P 126 LYS cc_start: 0.8806 (ttmm) cc_final: 0.8395 (mtpp) REVERT: R 1 MET cc_start: 0.8782 (ptp) cc_final: 0.8521 (ptp) REVERT: R 29 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8561 (pm20) outliers start: 100 outliers final: 84 residues processed: 372 average time/residue: 0.3377 time to fit residues: 180.0609 Evaluate side-chains 383 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 295 time to evaluate : 2.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain F residue 20 HIS Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 29 GLN Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 114 THR 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 G residue 53 SER Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain K residue 32 GLU Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain K residue 104 SER Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain M residue 29 GLN Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 91 ARG Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain Q residue 20 HIS Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 74 LEU Chi-restraints excluded: chain Q residue 101 THR Chi-restraints excluded: chain Q residue 128 THR Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain H residue 22 GLN Chi-restraints excluded: chain H residue 29 GLN Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 32 GLU Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 29 GLN Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 91 ARG Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 115 VAL Chi-restraints excluded: chain R residue 29 GLN Chi-restraints excluded: chain R residue 57 GLU Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 114 THR 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 222 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 233 optimal weight: 6.9990 chunk 214 optimal weight: 0.9980 chunk 185 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 147 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 11 ASN ** Q 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 2.4029 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= 0.261 Angle : 0.641 10.751 23688 Z= 0.316 Chirality : 0.042 0.156 2628 Planarity : 0.004 0.047 3150 Dihedral : 4.644 18.526 2466 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.18 % Allowed : 28.77 % Favored : 67.05 % 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: -2.08 (0.16), residues: 2304 helix: None (None), residues: 0 sheet: -1.34 (0.13), residues: 1386 loop : -1.16 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 24 HIS 0.002 0.001 HIS E 20 PHE 0.014 0.002 PHE C 56 TYR 0.014 0.001 TYR O 80 ARG 0.007 0.001 ARG O 44 ********************** 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 386 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 310 time to evaluate : 2.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 ASP cc_start: 0.8229 (t0) cc_final: 0.7808 (m-30) REVERT: B 103 GLU cc_start: 0.8104 (pm20) cc_final: 0.7851 (pm20) REVERT: B 125 GLN cc_start: 0.8670 (mm-40) cc_final: 0.8163 (mm110) REVERT: A 27 ASP cc_start: 0.8840 (p0) cc_final: 0.8524 (p0) REVERT: A 125 GLN cc_start: 0.8448 (mm-40) cc_final: 0.8204 (mm-40) REVERT: C 11 ASN cc_start: 0.8922 (m-40) cc_final: 0.8350 (t0) REVERT: C 125 GLN cc_start: 0.8400 (mp10) cc_final: 0.8168 (mp10) REVERT: F 26 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8197 (tt) REVERT: F 29 GLN cc_start: 0.8521 (pm20) cc_final: 0.8155 (pm20) REVERT: F 91 ARG cc_start: 0.8787 (mmt-90) cc_final: 0.8438 (mmt-90) REVERT: F 103 GLU cc_start: 0.8128 (mp0) cc_final: 0.7883 (mp0) REVERT: F 126 LYS cc_start: 0.8726 (ttpt) cc_final: 0.8438 (mtpp) REVERT: I 1 MET cc_start: 0.9047 (ptm) cc_final: 0.8814 (ptm) REVERT: I 27 ASP cc_start: 0.8185 (t70) cc_final: 0.7866 (t0) REVERT: I 29 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8103 (pm20) REVERT: G 32 GLU cc_start: 0.8378 (pt0) cc_final: 0.8170 (pt0) REVERT: G 44 ARG cc_start: 0.8228 (mpp80) cc_final: 0.7863 (mmm-85) REVERT: K 27 ASP cc_start: 0.8717 (p0) cc_final: 0.8236 (p0) REVERT: K 43 GLU cc_start: 0.8381 (tt0) cc_final: 0.8047 (tt0) REVERT: M 91 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8419 (ptp-170) REVERT: O 112 MET cc_start: 0.8624 (mmm) cc_final: 0.8401 (mmt) REVERT: Q 27 ASP cc_start: 0.8034 (t70) cc_final: 0.7819 (t70) REVERT: Q 29 GLN cc_start: 0.8317 (mp10) cc_final: 0.7900 (pm20) REVERT: H 32 GLU cc_start: 0.8261 (pp20) cc_final: 0.7650 (pp20) REVERT: H 44 ARG cc_start: 0.7901 (mpt-90) cc_final: 0.7328 (ptt180) REVERT: H 125 GLN cc_start: 0.8379 (mm-40) cc_final: 0.8036 (mm110) REVERT: L 27 ASP cc_start: 0.8843 (p0) cc_final: 0.7932 (p0) REVERT: L 103 GLU cc_start: 0.8122 (pt0) cc_final: 0.7743 (pm20) REVERT: P 29 GLN cc_start: 0.8095 (pm20) cc_final: 0.7421 (pm20) REVERT: P 51 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7525 (ptp-170) REVERT: R 1 MET cc_start: 0.8768 (ptp) cc_final: 0.8507 (ptp) outliers start: 76 outliers final: 67 residues processed: 359 average time/residue: 0.3444 time to fit residues: 176.6455 Evaluate side-chains 372 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 301 time to evaluate : 2.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 3 LYS Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain F residue 20 HIS Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 29 GLN Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 114 THR 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 G residue 53 SER Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain K residue 32 GLU Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain M residue 29 GLN Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 91 ARG Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 20 HIS Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 74 LEU Chi-restraints excluded: chain Q residue 128 THR Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain H residue 29 GLN Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 32 GLU Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 29 GLN Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 91 ARG Chi-restraints excluded: chain P residue 51 ARG Chi-restraints excluded: chain P residue 115 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 114 THR 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 197 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 185 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 163 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.072138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.059079 restraints weight = 36884.482| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 3.37 r_work: 0.2710 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 2.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17442 Z= 0.326 Angle : 0.659 10.621 23688 Z= 0.324 Chirality : 0.043 0.161 2628 Planarity : 0.004 0.046 3150 Dihedral : 4.715 17.759 2466 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.68 % Allowed : 27.83 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.16), residues: 2304 helix: None (None), residues: 0 sheet: -1.33 (0.13), residues: 1386 loop : -1.13 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP M 24 HIS 0.003 0.001 HIS Q 20 PHE 0.013 0.002 PHE C 56 TYR 0.015 0.002 TYR O 80 ARG 0.007 0.001 ARG O 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4238.95 seconds wall clock time: 76 minutes 1.55 seconds (4561.55 seconds total)