Starting phenix.real_space_refine on Wed Sep 17 21:44:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l0e_62698/09_2025/9l0e_62698.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l0e_62698/09_2025/9l0e_62698.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9l0e_62698/09_2025/9l0e_62698.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l0e_62698/09_2025/9l0e_62698.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9l0e_62698/09_2025/9l0e_62698.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l0e_62698/09_2025/9l0e_62698.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.005 sd= 0.721 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 60 5.16 5 C 7704 2.51 5 N 2124 2.21 5 O 2208 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12096 Number of models: 1 Model: "" Number of chains: 12 Chain: "N" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1045 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "Q" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1045 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "T" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1045 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "V" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1045 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "Y" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1045 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "b" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1045 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "A" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 971 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 9, 'TRANS': 113} Chain: "B" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 971 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 9, 'TRANS': 113} Chain: "C" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 971 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 9, 'TRANS': 113} Chain: "D" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 971 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 9, 'TRANS': 113} Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 971 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 9, 'TRANS': 113} Chain: "G" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 971 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 9, 'TRANS': 113} Time building chain proxies: 3.62, per 1000 atoms: 0.30 Number of scatterers: 12096 At special positions: 0 Unit cell: (112.88, 103.36, 95.2, 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 60 16.00 O 2208 8.00 N 2124 7.00 C 7704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 604.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2772 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 19 sheets defined 18.3% alpha, 34.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'N' and resid 1 through 18 Processing helix chain 'N' and resid 77 through 88 Processing helix chain 'Q' and resid 2 through 18 Processing helix chain 'Q' and resid 77 through 88 Processing helix chain 'T' and resid 2 through 17 Processing helix chain 'T' and resid 77 through 88 Processing helix chain 'V' and resid 2 through 18 Processing helix chain 'V' and resid 77 through 88 Processing helix chain 'Y' and resid 2 through 18 Processing helix chain 'Y' and resid 77 through 88 Processing helix chain 'b' and resid 2 through 18 Processing helix chain 'b' and resid 77 through 88 Processing helix chain 'A' and resid 2 through 18 Processing helix chain 'B' and resid 2 through 18 Processing helix chain 'C' and resid 2 through 18 Processing helix chain 'D' and resid 2 through 18 Processing helix chain 'E' and resid 2 through 18 Processing helix chain 'G' and resid 2 through 18 Processing sheet with id=AA1, first strand: chain 'N' and resid 22 through 23 removed outlier: 3.505A pdb=" N PHE N 41 " --> pdb=" O TYR N 23 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE N 61 " --> pdb=" O GLY N 46 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR N 48 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N SER N 59 " --> pdb=" O THR N 48 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA N 62 " --> pdb=" O VAL N 125 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Q' and resid 22 through 23 removed outlier: 6.294A pdb=" N ILE Q 61 " --> pdb=" O GLY Q 46 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N THR Q 48 " --> pdb=" O SER Q 59 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N SER Q 59 " --> pdb=" O THR Q 48 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR Q 100 " --> pdb=" O ARG Q 126 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY Q 99 " --> pdb=" O LEU Q 96 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Q' and resid 22 through 23 removed outlier: 6.294A pdb=" N ILE Q 61 " --> pdb=" O GLY Q 46 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N THR Q 48 " --> pdb=" O SER Q 59 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N SER Q 59 " --> pdb=" O THR Q 48 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG Q 122 " --> pdb=" O ILE Q 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'T' and resid 22 through 23 removed outlier: 6.308A pdb=" N ILE T 61 " --> pdb=" O GLY T 46 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N THR T 48 " --> pdb=" O SER T 59 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N SER T 59 " --> pdb=" O THR T 48 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA T 62 " --> pdb=" O VAL T 125 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG T 122 " --> pdb=" O ILE T 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'V' and resid 22 through 23 removed outlier: 6.288A pdb=" N ILE V 61 " --> pdb=" O GLY V 46 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR V 48 " --> pdb=" O SER V 59 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N SER V 59 " --> pdb=" O THR V 48 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS V 58 " --> pdb=" O THR V 129 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA V 62 " --> pdb=" O VAL V 125 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG V 122 " --> pdb=" O ILE V 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Y' and resid 22 through 23 removed outlier: 6.359A pdb=" N ILE Y 61 " --> pdb=" O GLY Y 46 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N THR Y 48 " --> pdb=" O SER Y 59 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N SER Y 59 " --> pdb=" O THR Y 48 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA Y 62 " --> pdb=" O VAL Y 125 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG Y 122 " --> pdb=" O ILE Y 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 22 through 23 removed outlier: 6.513A pdb=" N TYR b 23 " --> pdb=" O PHE b 41 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N TYR b 43 " --> pdb=" O TYR b 23 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE b 61 " --> pdb=" O GLY b 46 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR b 48 " --> pdb=" O SER b 59 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N SER b 59 " --> pdb=" O THR b 48 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS b 58 " --> pdb=" O THR b 129 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA b 62 " --> pdb=" O VAL b 125 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL b 68 " --> pdb=" O ILE b 119 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG b 122 " --> pdb=" O ILE b 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 45 through 50 removed outlier: 4.056A pdb=" N MET A 24 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N VAL A 97 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ARG A 117 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP A 99 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG A 101 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG A 118 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N SER A 70 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 73 " --> pdb=" O ARG A 56 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ARG A 56 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILE A 75 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N THR A 54 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 33 through 34 removed outlier: 4.136A pdb=" N GLY A 33 " --> pdb=" O ILE A 41 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 45 through 50 removed outlier: 4.105A pdb=" N MET B 24 " --> pdb=" O ILE B 50 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N VAL B 97 " --> pdb=" O ARG B 117 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ARG B 117 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP B 99 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG B 101 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE B 72 " --> pdb=" O LEU B 116 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG B 118 " --> pdb=" O SER B 70 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N SER B 70 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU B 73 " --> pdb=" O ARG B 56 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ARG B 56 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE B 75 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N THR B 54 " --> pdb=" O ILE B 75 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 33 through 34 removed outlier: 4.373A pdb=" N GLY B 33 " --> pdb=" O ILE B 41 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 45 through 50 removed outlier: 4.069A pdb=" N MET C 24 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN C 25 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N VAL C 97 " --> pdb=" O ARG C 117 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ARG C 117 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP C 99 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG C 101 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG C 118 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N SER C 70 " --> pdb=" O ARG C 118 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU C 73 " --> pdb=" O ARG C 56 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ARG C 56 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE C 75 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N THR C 54 " --> pdb=" O ILE C 75 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 33 through 34 removed outlier: 4.105A pdb=" N GLY C 33 " --> pdb=" O ILE C 41 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 45 through 50 removed outlier: 4.057A pdb=" N MET D 24 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N VAL D 97 " --> pdb=" O ARG D 117 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ARG D 117 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP D 99 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG D 101 " --> pdb=" O ARG D 113 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG D 118 " --> pdb=" O SER D 70 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N SER D 70 " --> pdb=" O ARG D 118 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU D 73 " --> pdb=" O ARG D 56 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ARG D 56 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE D 75 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N THR D 54 " --> pdb=" O ILE D 75 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 33 through 34 removed outlier: 4.151A pdb=" N GLY D 33 " --> pdb=" O ILE D 41 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 45 through 50 removed outlier: 4.084A pdb=" N MET E 24 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N VAL E 97 " --> pdb=" O ARG E 117 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ARG E 117 " --> pdb=" O VAL E 97 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP E 99 " --> pdb=" O VAL E 115 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG E 101 " --> pdb=" O ARG E 113 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE E 72 " --> pdb=" O LEU E 116 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG E 118 " --> pdb=" O SER E 70 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N SER E 70 " --> pdb=" O ARG E 118 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU E 73 " --> pdb=" O ARG E 56 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ARG E 56 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE E 75 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N THR E 54 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 33 through 34 removed outlier: 4.146A pdb=" N GLY E 33 " --> pdb=" O ILE E 41 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 45 through 50 removed outlier: 4.069A pdb=" N MET G 24 " --> pdb=" O ILE G 50 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN G 25 " --> pdb=" O GLU G 89 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N VAL G 97 " --> pdb=" O ARG G 117 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ARG G 117 " --> pdb=" O VAL G 97 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP G 99 " --> pdb=" O VAL G 115 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG G 101 " --> pdb=" O ARG G 113 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG G 118 " --> pdb=" O SER G 70 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N SER G 70 " --> pdb=" O ARG G 118 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU G 73 " --> pdb=" O ARG G 56 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ARG G 56 " --> pdb=" O LEU G 73 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE G 75 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N THR G 54 " --> pdb=" O ILE G 75 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 33 through 34 removed outlier: 4.136A pdb=" N GLY G 33 " --> pdb=" O ILE G 41 " (cutoff:3.500A) 497 hydrogen bonds defined for protein. 1398 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: 1.83 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4052 1.34 - 1.46: 2783 1.46 - 1.58: 5435 1.58 - 1.70: 0 1.70 - 1.82: 114 Bond restraints: 12384 Sorted by residual: bond pdb=" C THR Q 30 " pdb=" N PRO Q 31 " ideal model delta sigma weight residual 1.329 1.349 -0.020 1.18e-02 7.18e+03 2.95e+00 bond pdb=" CA ASN G 2 " pdb=" C ASN G 2 " ideal model delta sigma weight residual 1.526 1.507 0.020 1.21e-02 6.83e+03 2.68e+00 bond pdb=" CA ASN C 2 " pdb=" C ASN C 2 " ideal model delta sigma weight residual 1.526 1.507 0.019 1.21e-02 6.83e+03 2.50e+00 bond pdb=" CA ASN G 58 " pdb=" CB ASN G 58 " ideal model delta sigma weight residual 1.533 1.561 -0.027 1.72e-02 3.38e+03 2.49e+00 bond pdb=" CA ASN C 58 " pdb=" CB ASN C 58 " ideal model delta sigma weight residual 1.533 1.560 -0.027 1.72e-02 3.38e+03 2.46e+00 ... (remaining 12379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 16288 1.96 - 3.92: 410 3.92 - 5.88: 32 5.88 - 7.83: 3 7.83 - 9.79: 1 Bond angle restraints: 16734 Sorted by residual: angle pdb=" N ALA b 12 " pdb=" CA ALA b 12 " pdb=" C ALA b 12 " ideal model delta sigma weight residual 111.14 116.43 -5.29 1.08e+00 8.57e-01 2.40e+01 angle pdb=" N HIS b 22 " pdb=" CA HIS b 22 " pdb=" C HIS b 22 " ideal model delta sigma weight residual 108.45 113.60 -5.15 1.26e+00 6.30e-01 1.67e+01 angle pdb=" O PRO b 71 " pdb=" C PRO b 71 " pdb=" N PRO b 72 " ideal model delta sigma weight residual 121.15 123.06 -1.91 4.70e-01 4.53e+00 1.66e+01 angle pdb=" N VAL b 76 " pdb=" CA VAL b 76 " pdb=" C VAL b 76 " ideal model delta sigma weight residual 106.53 111.71 -5.18 1.41e+00 5.03e-01 1.35e+01 angle pdb=" N HIS V 22 " pdb=" CA HIS V 22 " pdb=" C HIS V 22 " ideal model delta sigma weight residual 109.07 114.31 -5.24 1.52e+00 4.33e-01 1.19e+01 ... (remaining 16729 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 6406 17.29 - 34.59: 785 34.59 - 51.88: 203 51.88 - 69.18: 32 69.18 - 86.47: 14 Dihedral angle restraints: 7440 sinusoidal: 3096 harmonic: 4344 Sorted by residual: dihedral pdb=" CA VAL T 76 " pdb=" C VAL T 76 " pdb=" N ASP T 77 " pdb=" CA ASP T 77 " ideal model delta harmonic sigma weight residual 180.00 158.52 21.48 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA VAL N 76 " pdb=" C VAL N 76 " pdb=" N ASP N 77 " pdb=" CA ASP N 77 " ideal model delta harmonic sigma weight residual 180.00 159.60 20.40 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA VAL V 76 " pdb=" C VAL V 76 " pdb=" N ASP V 77 " pdb=" CA ASP V 77 " ideal model delta harmonic sigma weight residual 180.00 160.02 19.98 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 7437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1105 0.030 - 0.060: 333 0.060 - 0.089: 129 0.089 - 0.119: 139 0.119 - 0.149: 46 Chirality restraints: 1752 Sorted by residual: chirality pdb=" CA ILE T 106 " pdb=" N ILE T 106 " pdb=" C ILE T 106 " pdb=" CB ILE T 106 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.53e-01 chirality pdb=" CA ILE C 41 " pdb=" N ILE C 41 " pdb=" C ILE C 41 " pdb=" CB ILE C 41 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.39e-01 chirality pdb=" CA ILE E 41 " pdb=" N ILE E 41 " pdb=" C ILE E 41 " pdb=" CB ILE E 41 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.31e-01 ... (remaining 1749 not shown) Planarity restraints: 2214 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR T 30 " 0.035 5.00e-02 4.00e+02 5.30e-02 4.50e+00 pdb=" N PRO T 31 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO T 31 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO T 31 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR V 30 " 0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO V 31 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO V 31 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO V 31 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE V 119 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO V 120 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO V 120 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO V 120 " -0.018 5.00e-02 4.00e+02 ... (remaining 2211 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1272 2.75 - 3.29: 10868 3.29 - 3.82: 18688 3.82 - 4.36: 21247 4.36 - 4.90: 39671 Nonbonded interactions: 91746 Sorted by model distance: nonbonded pdb=" OG SER T 59 " pdb=" OD1 ASP T 128 " model vdw 2.212 3.040 nonbonded pdb=" O PRO b 72 " pdb=" OH TYR B 87 " model vdw 2.262 3.040 nonbonded pdb=" NZ LYS V 58 " pdb=" OH TYR V 60 " model vdw 2.269 3.120 nonbonded pdb=" O PRO N 72 " pdb=" OH TYR E 87 " model vdw 2.291 3.040 nonbonded pdb=" N GLU C 36 " pdb=" OE1 GLU C 36 " model vdw 2.329 3.120 ... (remaining 91741 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 'G' } ncs_group { reference = chain 'N' selection = chain 'Q' selection = chain 'T' selection = chain 'V' selection = chain 'Y' selection = chain 'b' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.690 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.270 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 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 : 0.003 0.047 12384 Z= 0.191 Angle : 0.694 9.792 16734 Z= 0.432 Chirality : 0.047 0.149 1752 Planarity : 0.004 0.053 2214 Dihedral : 15.974 86.470 4668 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.70 % Allowed : 23.71 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.21), residues: 1488 helix: 1.31 (0.31), residues: 276 sheet: 0.71 (0.25), residues: 456 loop : -1.98 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 122 TYR 0.016 0.001 TYR Q 23 PHE 0.009 0.001 PHE b 41 TRP 0.009 0.001 TRP Y 117 HIS 0.004 0.001 HIS b 108 Details of bonding type rmsd covalent geometry : bond 0.00322 (12384) covalent geometry : angle 0.69392 (16734) hydrogen bonds : bond 0.23030 ( 472) hydrogen bonds : angle 9.81288 ( 1398) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 513 time to evaluate : 0.438 Fit side-chains REVERT: N 56 LYS cc_start: 0.7917 (mttt) cc_final: 0.7323 (tmtt) REVERT: Q 55 ARG cc_start: 0.8232 (mmt-90) cc_final: 0.6853 (mpp80) REVERT: Q 58 LYS cc_start: 0.7833 (ptmm) cc_final: 0.7572 (ptmm) REVERT: Q 95 MET cc_start: 0.5874 (mmm) cc_final: 0.5145 (mmt) REVERT: Q 98 VAL cc_start: 0.8433 (t) cc_final: 0.8099 (m) REVERT: Q 114 GLU cc_start: 0.6842 (pt0) cc_final: 0.6565 (pt0) REVERT: T 20 PHE cc_start: 0.8033 (OUTLIER) cc_final: 0.7361 (t80) REVERT: T 56 LYS cc_start: 0.7723 (mtmm) cc_final: 0.7234 (tmtt) REVERT: T 96 LEU cc_start: 0.8579 (mt) cc_final: 0.8202 (mt) REVERT: Y 40 ARG cc_start: 0.8026 (ttm170) cc_final: 0.7754 (ttm170) REVERT: Y 61 ILE cc_start: 0.8770 (mt) cc_final: 0.8541 (mt) REVERT: Y 119 ILE cc_start: 0.9187 (mt) cc_final: 0.8977 (tt) REVERT: b 33 LYS cc_start: 0.8265 (mtmt) cc_final: 0.7957 (mtpp) REVERT: A 70 SER cc_start: 0.7793 (p) cc_final: 0.7562 (p) REVERT: B 5 GLN cc_start: 0.7454 (tm-30) cc_final: 0.7114 (tm-30) REVERT: B 73 LEU cc_start: 0.8560 (mt) cc_final: 0.7730 (mt) REVERT: C 46 GLN cc_start: 0.7603 (tt0) cc_final: 0.7240 (tt0) REVERT: C 65 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7628 (mm-30) REVERT: D 58 ASN cc_start: 0.8002 (t0) cc_final: 0.7640 (t0) REVERT: E 5 GLN cc_start: 0.7473 (tm-30) cc_final: 0.7159 (tm-30) REVERT: G 46 GLN cc_start: 0.7666 (tt0) cc_final: 0.7274 (tt0) REVERT: G 65 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7661 (mm-30) outliers start: 9 outliers final: 1 residues processed: 517 average time/residue: 0.1196 time to fit residues: 86.9837 Evaluate side-chains 354 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 352 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 20 PHE Chi-restraints excluded: chain b residue 98 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 113 HIS ** 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 = 0.2665 r_free = 0.2665 target = 0.063212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.056502 restraints weight = 33035.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.058420 restraints weight = 14337.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.059668 restraints weight = 7862.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.060516 restraints weight = 4913.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.061122 restraints weight = 3342.174| |-----------------------------------------------------------------------------| r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12384 Z= 0.209 Angle : 0.651 7.480 16734 Z= 0.352 Chirality : 0.051 0.148 1752 Planarity : 0.005 0.046 2214 Dihedral : 4.775 53.957 1695 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 4.62 % Allowed : 20.50 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.21), residues: 1488 helix: 2.09 (0.31), residues: 276 sheet: 1.34 (0.31), residues: 294 loop : -1.79 (0.18), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 22 TYR 0.021 0.002 TYR b 17 PHE 0.017 0.002 PHE V 70 TRP 0.017 0.002 TRP Q 38 HIS 0.006 0.002 HIS b 108 Details of bonding type rmsd covalent geometry : bond 0.00485 (12384) covalent geometry : angle 0.65133 (16734) hydrogen bonds : bond 0.05109 ( 472) hydrogen bonds : angle 6.82884 ( 1398) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 378 time to evaluate : 0.527 Fit side-chains REVERT: N 54 ASP cc_start: 0.8166 (p0) cc_final: 0.7937 (p0) REVERT: N 56 LYS cc_start: 0.9026 (mttt) cc_final: 0.7727 (tmtt) REVERT: Q 20 PHE cc_start: 0.8748 (OUTLIER) cc_final: 0.8212 (m-80) REVERT: Q 23 TYR cc_start: 0.8555 (t80) cc_final: 0.8333 (t80) REVERT: Q 26 ASN cc_start: 0.8965 (t0) cc_final: 0.8613 (t0) REVERT: Q 55 ARG cc_start: 0.9187 (mmt-90) cc_final: 0.7104 (mpp80) REVERT: T 20 PHE cc_start: 0.9136 (OUTLIER) cc_final: 0.8256 (t80) REVERT: T 56 LYS cc_start: 0.8988 (mtmm) cc_final: 0.7989 (tmtt) REVERT: T 88 ASP cc_start: 0.8522 (m-30) cc_final: 0.8259 (m-30) REVERT: T 96 LEU cc_start: 0.9375 (mt) cc_final: 0.9147 (mt) REVERT: Y 40 ARG cc_start: 0.9323 (ttm170) cc_final: 0.9016 (ttm170) REVERT: Y 51 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8937 (pp) REVERT: Y 54 ASP cc_start: 0.8420 (p0) cc_final: 0.8200 (p0) REVERT: Y 58 LYS cc_start: 0.8832 (ptmm) cc_final: 0.8620 (ptmm) REVERT: b 33 LYS cc_start: 0.9305 (mtmt) cc_final: 0.9024 (mtpp) REVERT: b 103 GLU cc_start: 0.8394 (tt0) cc_final: 0.8176 (tt0) REVERT: A 7 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8542 (tm-30) REVERT: A 58 ASN cc_start: 0.9056 (t0) cc_final: 0.8654 (t0) REVERT: A 65 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8269 (mm-30) REVERT: A 93 ILE cc_start: 0.9397 (OUTLIER) cc_final: 0.8869 (mp) REVERT: B 58 ASN cc_start: 0.9050 (t0) cc_final: 0.8776 (t0) REVERT: C 58 ASN cc_start: 0.9384 (t0) cc_final: 0.9102 (t0) REVERT: C 65 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8631 (mm-30) REVERT: C 91 ASP cc_start: 0.8237 (t0) cc_final: 0.7979 (t0) REVERT: D 58 ASN cc_start: 0.9124 (t0) cc_final: 0.8420 (t0) REVERT: D 104 GLN cc_start: 0.8381 (tp-100) cc_final: 0.8136 (tp-100) REVERT: E 58 ASN cc_start: 0.9069 (t0) cc_final: 0.8823 (t0) REVERT: E 65 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8443 (mp0) REVERT: E 91 ASP cc_start: 0.8215 (t0) cc_final: 0.7950 (t0) REVERT: G 7 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8683 (tm-30) REVERT: G 58 ASN cc_start: 0.9380 (t0) cc_final: 0.9097 (t0) REVERT: G 65 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8710 (mm-30) REVERT: G 91 ASP cc_start: 0.8310 (t0) cc_final: 0.8057 (t0) outliers start: 59 outliers final: 38 residues processed: 418 average time/residue: 0.1126 time to fit residues: 67.8925 Evaluate side-chains 360 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 318 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain Q residue 20 PHE Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain T residue 20 PHE Chi-restraints excluded: chain T residue 48 THR Chi-restraints excluded: chain T residue 51 LEU Chi-restraints excluded: chain T residue 81 LEU Chi-restraints excluded: chain T residue 119 ILE Chi-restraints excluded: chain V residue 76 VAL Chi-restraints excluded: chain V residue 129 THR Chi-restraints excluded: chain Y residue 48 THR Chi-restraints excluded: chain Y residue 51 LEU Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain b residue 68 VAL Chi-restraints excluded: chain b residue 98 VAL Chi-restraints excluded: chain b residue 106 ILE Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain E residue 4 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 119 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 92 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 chunk 108 optimal weight: 0.4980 chunk 85 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 108 HIS A 104 GLN C 29 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.062240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.055656 restraints weight = 33347.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.057554 restraints weight = 14501.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.058796 restraints weight = 7970.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.059605 restraints weight = 4964.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.060217 restraints weight = 3388.190| |-----------------------------------------------------------------------------| r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12384 Z= 0.174 Angle : 0.585 7.204 16734 Z= 0.313 Chirality : 0.049 0.154 1752 Planarity : 0.004 0.044 2214 Dihedral : 4.748 54.103 1695 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 4.15 % Allowed : 21.13 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.21), residues: 1488 helix: 2.16 (0.31), residues: 276 sheet: 1.20 (0.31), residues: 294 loop : -1.70 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 56 TYR 0.017 0.001 TYR b 17 PHE 0.015 0.002 PHE V 70 TRP 0.008 0.001 TRP b 38 HIS 0.006 0.001 HIS T 113 Details of bonding type rmsd covalent geometry : bond 0.00396 (12384) covalent geometry : angle 0.58486 (16734) hydrogen bonds : bond 0.04788 ( 472) hydrogen bonds : angle 6.26112 ( 1398) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 338 time to evaluate : 0.516 Fit side-chains REVERT: N 54 ASP cc_start: 0.8341 (p0) cc_final: 0.8082 (p0) REVERT: N 56 LYS cc_start: 0.9004 (mttt) cc_final: 0.7857 (tmtt) REVERT: Q 23 TYR cc_start: 0.8793 (t80) cc_final: 0.8343 (t80) REVERT: Q 55 ARG cc_start: 0.9139 (mmt-90) cc_final: 0.7203 (mpt180) REVERT: Q 58 LYS cc_start: 0.9032 (ptmm) cc_final: 0.8819 (ptmm) REVERT: T 20 PHE cc_start: 0.9168 (OUTLIER) cc_final: 0.8275 (t80) REVERT: T 56 LYS cc_start: 0.9020 (mtmm) cc_final: 0.7881 (tmtt) REVERT: T 88 ASP cc_start: 0.8566 (m-30) cc_final: 0.8285 (m-30) REVERT: T 96 LEU cc_start: 0.9406 (mt) cc_final: 0.9183 (mt) REVERT: Y 10 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.8651 (mtm-85) REVERT: Y 40 ARG cc_start: 0.9377 (ttm170) cc_final: 0.9070 (ttp80) REVERT: Y 58 LYS cc_start: 0.8966 (ptmm) cc_final: 0.8665 (ptmm) REVERT: b 33 LYS cc_start: 0.9291 (mtmt) cc_final: 0.9012 (mtpp) REVERT: b 58 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8594 (ptmm) REVERT: A 7 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8510 (tm-30) REVERT: A 58 ASN cc_start: 0.9093 (t0) cc_final: 0.8491 (t0) REVERT: A 104 GLN cc_start: 0.8553 (tp-100) cc_final: 0.8166 (tp-100) REVERT: C 58 ASN cc_start: 0.9391 (t0) cc_final: 0.8981 (t0) REVERT: C 91 ASP cc_start: 0.8174 (t0) cc_final: 0.7887 (t0) REVERT: D 51 SER cc_start: 0.9255 (t) cc_final: 0.8953 (m) REVERT: D 58 ASN cc_start: 0.9214 (t0) cc_final: 0.8664 (t0) REVERT: D 104 GLN cc_start: 0.8323 (tp-100) cc_final: 0.7996 (tp-100) REVERT: G 58 ASN cc_start: 0.9372 (t0) cc_final: 0.8949 (t0) REVERT: G 91 ASP cc_start: 0.8153 (t0) cc_final: 0.7900 (t0) outliers start: 53 outliers final: 31 residues processed: 373 average time/residue: 0.1172 time to fit residues: 62.2281 Evaluate side-chains 347 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 313 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain T residue 20 PHE Chi-restraints excluded: chain T residue 48 THR Chi-restraints excluded: chain T residue 51 LEU Chi-restraints excluded: chain T residue 81 LEU Chi-restraints excluded: chain T residue 119 ILE Chi-restraints excluded: chain V residue 58 LYS Chi-restraints excluded: chain V residue 76 VAL Chi-restraints excluded: chain Y residue 10 ARG Chi-restraints excluded: chain Y residue 48 THR Chi-restraints excluded: chain b residue 47 ASP Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain b residue 58 LYS Chi-restraints excluded: chain b residue 68 VAL Chi-restraints excluded: chain b residue 98 VAL Chi-restraints excluded: chain b residue 107 VAL Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 119 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 79 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 136 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 65 GLN ** T 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 ASN C 104 GLN D 29 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.057784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2391 r_free = 0.2391 target = 0.051312 restraints weight = 33878.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2435 r_free = 0.2435 target = 0.053142 restraints weight = 14690.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2462 r_free = 0.2462 target = 0.054285 restraints weight = 8099.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2481 r_free = 0.2481 target = 0.055114 restraints weight = 5206.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2495 r_free = 0.2495 target = 0.055692 restraints weight = 3545.630| |-----------------------------------------------------------------------------| r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12384 Z= 0.223 Angle : 0.607 6.572 16734 Z= 0.329 Chirality : 0.051 0.154 1752 Planarity : 0.005 0.059 2214 Dihedral : 4.932 53.495 1695 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 5.71 % Allowed : 20.42 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.21), residues: 1488 helix: 1.95 (0.31), residues: 276 sheet: 1.19 (0.31), residues: 294 loop : -1.63 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 56 TYR 0.031 0.002 TYR b 17 PHE 0.014 0.002 PHE T 70 TRP 0.007 0.001 TRP Y 38 HIS 0.007 0.002 HIS T 113 Details of bonding type rmsd covalent geometry : bond 0.00523 (12384) covalent geometry : angle 0.60703 (16734) hydrogen bonds : bond 0.05009 ( 472) hydrogen bonds : angle 6.03619 ( 1398) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 328 time to evaluate : 0.522 Fit side-chains REVERT: N 56 LYS cc_start: 0.9080 (mttt) cc_final: 0.8094 (tmtt) REVERT: Q 26 ASN cc_start: 0.9147 (t0) cc_final: 0.8691 (t0) REVERT: Q 55 ARG cc_start: 0.9242 (mmt-90) cc_final: 0.7170 (mpt180) REVERT: Q 112 LYS cc_start: 0.9216 (mtmt) cc_final: 0.9014 (mtmt) REVERT: T 20 PHE cc_start: 0.9186 (OUTLIER) cc_final: 0.8296 (t80) REVERT: T 45 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8025 (mm-30) REVERT: T 56 LYS cc_start: 0.9045 (mtmm) cc_final: 0.8067 (tptt) REVERT: T 88 ASP cc_start: 0.8648 (m-30) cc_final: 0.8378 (m-30) REVERT: Y 58 LYS cc_start: 0.9031 (ptmm) cc_final: 0.8691 (ptmm) REVERT: b 33 LYS cc_start: 0.9298 (mtmt) cc_final: 0.8983 (mtpp) REVERT: b 55 ARG cc_start: 0.9035 (mmp-170) cc_final: 0.6285 (mpt180) REVERT: b 58 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8514 (ptmm) REVERT: A 51 SER cc_start: 0.9274 (t) cc_final: 0.9018 (m) REVERT: A 58 ASN cc_start: 0.9222 (t0) cc_final: 0.8760 (t0) REVERT: A 104 GLN cc_start: 0.8484 (tp-100) cc_final: 0.8154 (tp-100) REVERT: C 7 GLU cc_start: 0.8961 (tm-30) cc_final: 0.8634 (tm-30) REVERT: C 58 ASN cc_start: 0.9449 (t0) cc_final: 0.9147 (t0) REVERT: C 65 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8375 (mm-30) REVERT: C 91 ASP cc_start: 0.8242 (t0) cc_final: 0.7988 (t0) REVERT: D 51 SER cc_start: 0.9302 (t) cc_final: 0.9045 (m) REVERT: D 58 ASN cc_start: 0.9221 (t0) cc_final: 0.8758 (t0) REVERT: D 104 GLN cc_start: 0.8431 (tp-100) cc_final: 0.8156 (tp-100) REVERT: E 51 SER cc_start: 0.9418 (t) cc_final: 0.9191 (m) REVERT: E 93 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.9059 (mt) REVERT: G 1 MET cc_start: 0.8689 (mmm) cc_final: 0.7856 (tpp) REVERT: G 58 ASN cc_start: 0.9428 (t0) cc_final: 0.9098 (t0) REVERT: G 84 GLU cc_start: 0.8270 (mp0) cc_final: 0.7959 (mp0) REVERT: G 91 ASP cc_start: 0.8221 (t0) cc_final: 0.7963 (t0) outliers start: 73 outliers final: 45 residues processed: 373 average time/residue: 0.1157 time to fit residues: 61.7751 Evaluate side-chains 354 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 305 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain Q residue 20 PHE Chi-restraints excluded: chain Q residue 30 THR Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain T residue 20 PHE Chi-restraints excluded: chain T residue 45 GLU Chi-restraints excluded: chain T residue 48 THR Chi-restraints excluded: chain T residue 51 LEU Chi-restraints excluded: chain T residue 81 LEU Chi-restraints excluded: chain T residue 119 ILE Chi-restraints excluded: chain V residue 48 THR Chi-restraints excluded: chain V residue 76 VAL Chi-restraints excluded: chain V residue 129 THR Chi-restraints excluded: chain Y residue 48 THR Chi-restraints excluded: chain Y residue 110 ILE Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain b residue 58 LYS Chi-restraints excluded: chain b residue 68 VAL Chi-restraints excluded: chain b residue 74 SER Chi-restraints excluded: chain b residue 94 LYS Chi-restraints excluded: chain b residue 98 VAL Chi-restraints excluded: chain b residue 107 VAL Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 118 MET Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain E residue 4 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 119 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 11 optimal weight: 0.0040 chunk 44 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 65 GLN ** T 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 ASN A 29 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.059761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2446 r_free = 0.2446 target = 0.053338 restraints weight = 33250.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2488 r_free = 0.2488 target = 0.055161 restraints weight = 14451.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.056343 restraints weight = 7991.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.057164 restraints weight = 5078.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.057745 restraints weight = 3433.464| |-----------------------------------------------------------------------------| r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12384 Z= 0.163 Angle : 0.578 8.672 16734 Z= 0.307 Chirality : 0.049 0.156 1752 Planarity : 0.004 0.049 2214 Dihedral : 4.809 52.734 1695 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.77 % Allowed : 21.60 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.22), residues: 1488 helix: 2.04 (0.31), residues: 276 sheet: 1.13 (0.28), residues: 378 loop : -1.56 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 56 TYR 0.028 0.001 TYR b 17 PHE 0.014 0.001 PHE V 70 TRP 0.007 0.001 TRP Q 38 HIS 0.005 0.001 HIS T 113 Details of bonding type rmsd covalent geometry : bond 0.00379 (12384) covalent geometry : angle 0.57822 (16734) hydrogen bonds : bond 0.04408 ( 472) hydrogen bonds : angle 5.84036 ( 1398) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 321 time to evaluate : 0.542 Fit side-chains REVERT: N 33 LYS cc_start: 0.9135 (mtpp) cc_final: 0.8878 (mmmt) REVERT: N 56 LYS cc_start: 0.9093 (mttt) cc_final: 0.8110 (tmtt) REVERT: Q 26 ASN cc_start: 0.9060 (t0) cc_final: 0.8750 (t0) REVERT: T 20 PHE cc_start: 0.9199 (OUTLIER) cc_final: 0.8363 (t80) REVERT: T 45 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7912 (mm-30) REVERT: T 56 LYS cc_start: 0.9060 (mtmm) cc_final: 0.8039 (tptt) REVERT: T 88 ASP cc_start: 0.8592 (m-30) cc_final: 0.8324 (m-30) REVERT: T 106 ILE cc_start: 0.9512 (mm) cc_final: 0.9278 (mm) REVERT: V 58 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8821 (ptmm) REVERT: Y 10 ARG cc_start: 0.9181 (OUTLIER) cc_final: 0.8711 (mtm-85) REVERT: Y 58 LYS cc_start: 0.9022 (ptmm) cc_final: 0.8710 (ptmm) REVERT: Y 77 ASP cc_start: 0.8247 (m-30) cc_final: 0.7933 (m-30) REVERT: b 33 LYS cc_start: 0.9171 (mtmt) cc_final: 0.8619 (mtpp) REVERT: b 55 ARG cc_start: 0.9028 (mmp-170) cc_final: 0.6233 (mpt180) REVERT: b 58 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8514 (ptmm) REVERT: A 51 SER cc_start: 0.9278 (t) cc_final: 0.9054 (m) REVERT: A 58 ASN cc_start: 0.9219 (t0) cc_final: 0.8702 (t0) REVERT: A 104 GLN cc_start: 0.8446 (tp-100) cc_final: 0.8104 (tp-100) REVERT: C 1 MET cc_start: 0.8734 (mmm) cc_final: 0.7865 (tpp) REVERT: C 58 ASN cc_start: 0.9397 (t0) cc_final: 0.9065 (t0) REVERT: C 91 ASP cc_start: 0.8185 (t0) cc_final: 0.7920 (t0) REVERT: D 51 SER cc_start: 0.9302 (t) cc_final: 0.9076 (m) REVERT: D 58 ASN cc_start: 0.9215 (t0) cc_final: 0.8884 (t0) REVERT: D 104 GLN cc_start: 0.8444 (tp-100) cc_final: 0.8144 (tp-100) REVERT: G 1 MET cc_start: 0.8736 (mmm) cc_final: 0.7861 (tpp) REVERT: G 58 ASN cc_start: 0.9385 (t0) cc_final: 0.9047 (t0) REVERT: G 84 GLU cc_start: 0.8302 (mp0) cc_final: 0.7905 (mp0) REVERT: G 91 ASP cc_start: 0.8161 (t0) cc_final: 0.7886 (t0) outliers start: 61 outliers final: 42 residues processed: 361 average time/residue: 0.1145 time to fit residues: 59.4301 Evaluate side-chains 356 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 309 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain Q residue 20 PHE Chi-restraints excluded: chain Q residue 33 LYS Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain T residue 20 PHE Chi-restraints excluded: chain T residue 42 ASN Chi-restraints excluded: chain T residue 45 GLU Chi-restraints excluded: chain T residue 48 THR Chi-restraints excluded: chain T residue 51 LEU Chi-restraints excluded: chain T residue 81 LEU Chi-restraints excluded: chain T residue 119 ILE Chi-restraints excluded: chain V residue 58 LYS Chi-restraints excluded: chain V residue 76 VAL Chi-restraints excluded: chain Y residue 10 ARG Chi-restraints excluded: chain Y residue 48 THR Chi-restraints excluded: chain Y residue 51 LEU Chi-restraints excluded: chain Y residue 110 ILE Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain b residue 58 LYS Chi-restraints excluded: chain b residue 68 VAL Chi-restraints excluded: chain b residue 98 VAL Chi-restraints excluded: chain b residue 107 VAL Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 118 MET Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain E residue 4 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 119 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 104 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 23 optimal weight: 0.6980 chunk 130 optimal weight: 0.0370 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 65 GLN ** T 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 113 HIS ** Y 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 ASN C 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.060106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2449 r_free = 0.2449 target = 0.053638 restraints weight = 33429.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2492 r_free = 0.2492 target = 0.055527 restraints weight = 14524.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2520 r_free = 0.2520 target = 0.056759 restraints weight = 7948.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.057593 restraints weight = 4928.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.058151 restraints weight = 3311.096| |-----------------------------------------------------------------------------| r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12384 Z= 0.104 Angle : 0.540 8.488 16734 Z= 0.284 Chirality : 0.048 0.160 1752 Planarity : 0.004 0.048 2214 Dihedral : 4.580 53.111 1695 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.99 % Allowed : 22.61 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.22), residues: 1488 helix: 2.20 (0.31), residues: 276 sheet: 1.12 (0.28), residues: 384 loop : -1.51 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 56 TYR 0.029 0.001 TYR b 17 PHE 0.012 0.001 PHE Q 123 TRP 0.013 0.001 TRP Q 38 HIS 0.003 0.001 HIS b 2 Details of bonding type rmsd covalent geometry : bond 0.00237 (12384) covalent geometry : angle 0.54002 (16734) hydrogen bonds : bond 0.03625 ( 472) hydrogen bonds : angle 5.56500 ( 1398) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 324 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: N 56 LYS cc_start: 0.9089 (mttt) cc_final: 0.7996 (tptt) REVERT: Q 25 GLU cc_start: 0.8838 (mp0) cc_final: 0.8551 (mt-10) REVERT: Q 26 ASN cc_start: 0.8904 (t0) cc_final: 0.8619 (t0) REVERT: T 20 PHE cc_start: 0.9202 (OUTLIER) cc_final: 0.8356 (t80) REVERT: T 45 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8008 (mm-30) REVERT: T 56 LYS cc_start: 0.9043 (mtmm) cc_final: 0.7991 (tmtt) REVERT: T 106 ILE cc_start: 0.9459 (mm) cc_final: 0.9204 (mm) REVERT: V 45 GLU cc_start: 0.8414 (mp0) cc_final: 0.8182 (mp0) REVERT: V 129 THR cc_start: 0.8008 (OUTLIER) cc_final: 0.7775 (p) REVERT: Y 10 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.8786 (mtm-85) REVERT: Y 58 LYS cc_start: 0.8956 (ptmm) cc_final: 0.8696 (ptmm) REVERT: Y 77 ASP cc_start: 0.8170 (m-30) cc_final: 0.7874 (m-30) REVERT: b 33 LYS cc_start: 0.9183 (mtmt) cc_final: 0.8644 (mtpp) REVERT: b 58 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8601 (ptmm) REVERT: A 51 SER cc_start: 0.9250 (t) cc_final: 0.9035 (m) REVERT: A 58 ASN cc_start: 0.9208 (t0) cc_final: 0.8672 (t0) REVERT: A 104 GLN cc_start: 0.8452 (tp-100) cc_final: 0.8146 (tp-100) REVERT: B 46 GLN cc_start: 0.8538 (tt0) cc_final: 0.8077 (tt0) REVERT: C 1 MET cc_start: 0.8711 (mmm) cc_final: 0.7835 (tpp) REVERT: C 58 ASN cc_start: 0.9370 (t0) cc_final: 0.8986 (t0) REVERT: C 84 GLU cc_start: 0.8286 (mp0) cc_final: 0.7998 (mp0) REVERT: C 91 ASP cc_start: 0.8251 (t0) cc_final: 0.7984 (t0) REVERT: C 104 GLN cc_start: 0.7707 (mm-40) cc_final: 0.7083 (pm20) REVERT: D 51 SER cc_start: 0.9283 (t) cc_final: 0.9056 (m) REVERT: D 56 ARG cc_start: 0.8659 (tpp80) cc_final: 0.8435 (ttm170) REVERT: D 58 ASN cc_start: 0.9206 (t0) cc_final: 0.8830 (t0) REVERT: D 104 GLN cc_start: 0.8526 (tp-100) cc_final: 0.8141 (tp-100) REVERT: G 1 MET cc_start: 0.8728 (mmm) cc_final: 0.7873 (tpp) REVERT: G 58 ASN cc_start: 0.9374 (t0) cc_final: 0.9004 (t0) REVERT: G 91 ASP cc_start: 0.8166 (t0) cc_final: 0.7893 (t0) outliers start: 51 outliers final: 32 residues processed: 356 average time/residue: 0.1133 time to fit residues: 57.7972 Evaluate side-chains 345 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 309 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain Q residue 20 PHE Chi-restraints excluded: chain Q residue 30 THR Chi-restraints excluded: chain Q residue 33 LYS Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain T residue 20 PHE Chi-restraints excluded: chain T residue 48 THR Chi-restraints excluded: chain T residue 51 LEU Chi-restraints excluded: chain T residue 81 LEU Chi-restraints excluded: chain T residue 119 ILE Chi-restraints excluded: chain V residue 129 THR Chi-restraints excluded: chain Y residue 10 ARG Chi-restraints excluded: chain Y residue 48 THR Chi-restraints excluded: chain Y residue 51 LEU Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain b residue 58 LYS Chi-restraints excluded: chain b residue 68 VAL Chi-restraints excluded: chain b residue 94 LYS Chi-restraints excluded: chain b residue 98 VAL Chi-restraints excluded: chain b residue 107 VAL Chi-restraints excluded: chain b residue 118 MET Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 119 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 105 optimal weight: 3.9990 chunk 82 optimal weight: 0.2980 chunk 137 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 42 ASN ** N 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 65 GLN ** T 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.059627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2439 r_free = 0.2439 target = 0.053210 restraints weight = 33382.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.055077 restraints weight = 14452.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2510 r_free = 0.2510 target = 0.056302 restraints weight = 7923.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.057126 restraints weight = 4908.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.057686 restraints weight = 3303.572| |-----------------------------------------------------------------------------| r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12384 Z= 0.119 Angle : 0.542 8.766 16734 Z= 0.285 Chirality : 0.048 0.157 1752 Planarity : 0.004 0.047 2214 Dihedral : 4.507 52.937 1695 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.91 % Allowed : 23.24 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.22), residues: 1488 helix: 2.25 (0.31), residues: 276 sheet: 0.67 (0.26), residues: 456 loop : -1.25 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 56 TYR 0.025 0.001 TYR b 17 PHE 0.013 0.001 PHE Q 123 TRP 0.007 0.001 TRP Q 38 HIS 0.004 0.001 HIS T 113 Details of bonding type rmsd covalent geometry : bond 0.00278 (12384) covalent geometry : angle 0.54241 (16734) hydrogen bonds : bond 0.03660 ( 472) hydrogen bonds : angle 5.48516 ( 1398) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 322 time to evaluate : 0.528 Fit side-chains REVERT: N 56 LYS cc_start: 0.9162 (mttt) cc_final: 0.7928 (tmtt) REVERT: Q 25 GLU cc_start: 0.8856 (mp0) cc_final: 0.8582 (mt-10) REVERT: Q 26 ASN cc_start: 0.8924 (t0) cc_final: 0.8612 (t0) REVERT: T 20 PHE cc_start: 0.9214 (OUTLIER) cc_final: 0.8386 (t80) REVERT: T 56 LYS cc_start: 0.9054 (mtmm) cc_final: 0.7962 (tmtt) REVERT: T 106 ILE cc_start: 0.9467 (mm) cc_final: 0.9205 (mm) REVERT: V 45 GLU cc_start: 0.8505 (mp0) cc_final: 0.8279 (mp0) REVERT: V 129 THR cc_start: 0.7987 (OUTLIER) cc_final: 0.7750 (p) REVERT: Y 10 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8785 (mtm-85) REVERT: Y 58 LYS cc_start: 0.8967 (ptmm) cc_final: 0.8692 (ptmm) REVERT: b 33 LYS cc_start: 0.9147 (mtmt) cc_final: 0.8587 (mtpp) REVERT: b 58 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8628 (ptmm) REVERT: A 58 ASN cc_start: 0.9206 (t0) cc_final: 0.8631 (t0) REVERT: A 91 ASP cc_start: 0.8196 (t0) cc_final: 0.7935 (t0) REVERT: A 104 GLN cc_start: 0.8506 (tp-100) cc_final: 0.8213 (tp-100) REVERT: C 1 MET cc_start: 0.8720 (mmm) cc_final: 0.7842 (tpp) REVERT: C 58 ASN cc_start: 0.9365 (t0) cc_final: 0.8973 (t0) REVERT: C 91 ASP cc_start: 0.8133 (t0) cc_final: 0.7904 (t0) REVERT: D 51 SER cc_start: 0.9278 (t) cc_final: 0.9066 (m) REVERT: D 58 ASN cc_start: 0.9220 (t0) cc_final: 0.8849 (t0) REVERT: D 104 GLN cc_start: 0.8633 (tp-100) cc_final: 0.8264 (tp-100) REVERT: G 1 MET cc_start: 0.8749 (mmm) cc_final: 0.7872 (tpp) REVERT: G 58 ASN cc_start: 0.9372 (t0) cc_final: 0.9000 (t0) REVERT: G 65 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8277 (mm-30) REVERT: G 84 GLU cc_start: 0.8429 (mp0) cc_final: 0.8145 (mp0) REVERT: G 91 ASP cc_start: 0.8154 (t0) cc_final: 0.7885 (t0) outliers start: 50 outliers final: 39 residues processed: 357 average time/residue: 0.1114 time to fit residues: 56.8069 Evaluate side-chains 354 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 311 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain Q residue 20 PHE Chi-restraints excluded: chain Q residue 30 THR Chi-restraints excluded: chain Q residue 33 LYS Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain T residue 20 PHE Chi-restraints excluded: chain T residue 48 THR Chi-restraints excluded: chain T residue 51 LEU Chi-restraints excluded: chain T residue 81 LEU Chi-restraints excluded: chain T residue 119 ILE Chi-restraints excluded: chain V residue 129 THR Chi-restraints excluded: chain Y residue 10 ARG Chi-restraints excluded: chain Y residue 51 LEU Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain b residue 58 LYS Chi-restraints excluded: chain b residue 68 VAL Chi-restraints excluded: chain b residue 94 LYS Chi-restraints excluded: chain b residue 98 VAL Chi-restraints excluded: chain b residue 107 VAL Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 118 MET Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain E residue 4 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 119 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 120 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 65 GLN ** T 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.058299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2409 r_free = 0.2409 target = 0.051945 restraints weight = 33545.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2452 r_free = 0.2452 target = 0.053759 restraints weight = 14598.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.054912 restraints weight = 8058.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.055738 restraints weight = 5146.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.056311 restraints weight = 3466.305| |-----------------------------------------------------------------------------| r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12384 Z= 0.160 Angle : 0.571 8.658 16734 Z= 0.302 Chirality : 0.048 0.151 1752 Planarity : 0.004 0.048 2214 Dihedral : 4.646 52.455 1695 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.15 % Allowed : 23.24 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.22), residues: 1488 helix: 2.21 (0.31), residues: 276 sheet: 0.87 (0.27), residues: 420 loop : -1.36 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 56 TYR 0.027 0.001 TYR b 17 PHE 0.014 0.001 PHE V 70 TRP 0.006 0.001 TRP Y 38 HIS 0.005 0.001 HIS T 113 Details of bonding type rmsd covalent geometry : bond 0.00375 (12384) covalent geometry : angle 0.57061 (16734) hydrogen bonds : bond 0.04098 ( 472) hydrogen bonds : angle 5.55220 ( 1398) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 312 time to evaluate : 0.482 Fit side-chains REVERT: N 56 LYS cc_start: 0.9245 (mttt) cc_final: 0.8181 (tmtt) REVERT: Q 26 ASN cc_start: 0.9062 (t0) cc_final: 0.8711 (t0) REVERT: T 20 PHE cc_start: 0.9249 (OUTLIER) cc_final: 0.8345 (t80) REVERT: T 56 LYS cc_start: 0.9082 (mtmm) cc_final: 0.7987 (tmtt) REVERT: T 106 ILE cc_start: 0.9513 (mm) cc_final: 0.9281 (mm) REVERT: Y 10 ARG cc_start: 0.9190 (OUTLIER) cc_final: 0.8708 (mtm-85) REVERT: Y 45 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7444 (mm-30) REVERT: Y 58 LYS cc_start: 0.9013 (ptmm) cc_final: 0.8719 (ptmm) REVERT: b 33 LYS cc_start: 0.9161 (mtmt) cc_final: 0.8587 (mtpp) REVERT: b 58 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8645 (ptmm) REVERT: A 58 ASN cc_start: 0.9195 (t0) cc_final: 0.8627 (t0) REVERT: A 91 ASP cc_start: 0.8203 (t0) cc_final: 0.7964 (t0) REVERT: A 104 GLN cc_start: 0.8542 (tp-100) cc_final: 0.8283 (tp-100) REVERT: C 1 MET cc_start: 0.8739 (mmm) cc_final: 0.7837 (tpp) REVERT: C 58 ASN cc_start: 0.9373 (t0) cc_final: 0.9008 (t0) REVERT: C 91 ASP cc_start: 0.8144 (t0) cc_final: 0.7879 (t0) REVERT: D 51 SER cc_start: 0.9306 (t) cc_final: 0.9098 (m) REVERT: D 58 ASN cc_start: 0.9220 (t0) cc_final: 0.8888 (t0) REVERT: D 91 ASP cc_start: 0.8172 (t0) cc_final: 0.7892 (t0) REVERT: D 104 GLN cc_start: 0.8531 (tp-100) cc_final: 0.8249 (tp-100) REVERT: G 1 MET cc_start: 0.8761 (mmm) cc_final: 0.7853 (tpp) REVERT: G 58 ASN cc_start: 0.9382 (t0) cc_final: 0.9008 (t0) REVERT: G 65 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8317 (mm-30) REVERT: G 84 GLU cc_start: 0.8465 (mp0) cc_final: 0.8129 (mp0) REVERT: G 91 ASP cc_start: 0.8155 (t0) cc_final: 0.7887 (t0) outliers start: 53 outliers final: 47 residues processed: 346 average time/residue: 0.1131 time to fit residues: 56.2806 Evaluate side-chains 358 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 307 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain Q residue 20 PHE Chi-restraints excluded: chain Q residue 30 THR Chi-restraints excluded: chain Q residue 33 LYS Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain T residue 20 PHE Chi-restraints excluded: chain T residue 48 THR Chi-restraints excluded: chain T residue 51 LEU Chi-restraints excluded: chain T residue 76 VAL Chi-restraints excluded: chain T residue 81 LEU Chi-restraints excluded: chain T residue 119 ILE Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 95 MET Chi-restraints excluded: chain Y residue 10 ARG Chi-restraints excluded: chain Y residue 45 GLU Chi-restraints excluded: chain Y residue 51 LEU Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain b residue 58 LYS Chi-restraints excluded: chain b residue 68 VAL Chi-restraints excluded: chain b residue 94 LYS Chi-restraints excluded: chain b residue 98 VAL Chi-restraints excluded: chain b residue 107 VAL Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 118 MET Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain E residue 4 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 119 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 84 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 21 optimal weight: 0.0020 chunk 108 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 overall best weight: 2.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 113 HIS ** 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 = 0.2558 r_free = 0.2558 target = 0.058110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2412 r_free = 0.2412 target = 0.051867 restraints weight = 33925.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2454 r_free = 0.2454 target = 0.053653 restraints weight = 15109.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.054870 restraints weight = 8442.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.055655 restraints weight = 5291.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.056208 restraints weight = 3593.048| |-----------------------------------------------------------------------------| r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12384 Z= 0.182 Angle : 0.584 8.720 16734 Z= 0.310 Chirality : 0.049 0.154 1752 Planarity : 0.004 0.048 2214 Dihedral : 4.736 51.828 1695 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 4.23 % Allowed : 23.08 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.22), residues: 1488 helix: 2.15 (0.31), residues: 276 sheet: 0.98 (0.26), residues: 444 loop : -1.39 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 56 TYR 0.025 0.001 TYR b 17 PHE 0.014 0.001 PHE Q 123 TRP 0.006 0.001 TRP Y 38 HIS 0.005 0.001 HIS T 113 Details of bonding type rmsd covalent geometry : bond 0.00426 (12384) covalent geometry : angle 0.58447 (16734) hydrogen bonds : bond 0.04318 ( 472) hydrogen bonds : angle 5.61894 ( 1398) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 308 time to evaluate : 0.520 Fit side-chains REVERT: N 56 LYS cc_start: 0.9224 (mttt) cc_final: 0.8300 (tmtt) REVERT: T 20 PHE cc_start: 0.9238 (OUTLIER) cc_final: 0.8374 (t80) REVERT: T 56 LYS cc_start: 0.9115 (mtmm) cc_final: 0.8108 (tmtt) REVERT: T 106 ILE cc_start: 0.9556 (mm) cc_final: 0.9335 (mm) REVERT: Y 10 ARG cc_start: 0.9226 (OUTLIER) cc_final: 0.8753 (mtm-85) REVERT: Y 45 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7308 (mm-30) REVERT: Y 58 LYS cc_start: 0.9045 (ptmm) cc_final: 0.8781 (ptmm) REVERT: b 58 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8605 (ptmm) REVERT: A 58 ASN cc_start: 0.9201 (t0) cc_final: 0.8639 (t0) REVERT: A 91 ASP cc_start: 0.8096 (t0) cc_final: 0.7855 (t0) REVERT: A 104 GLN cc_start: 0.8571 (tp-100) cc_final: 0.8306 (tp-100) REVERT: C 1 MET cc_start: 0.8723 (mmm) cc_final: 0.7831 (tpp) REVERT: C 58 ASN cc_start: 0.9368 (t0) cc_final: 0.9059 (t0) REVERT: C 91 ASP cc_start: 0.8019 (t0) cc_final: 0.7749 (t0) REVERT: D 51 SER cc_start: 0.9294 (t) cc_final: 0.9092 (m) REVERT: D 58 ASN cc_start: 0.9223 (t0) cc_final: 0.8927 (t0) REVERT: D 91 ASP cc_start: 0.8130 (t0) cc_final: 0.7857 (t0) REVERT: D 104 GLN cc_start: 0.8517 (tp-100) cc_final: 0.8266 (tp-100) REVERT: G 1 MET cc_start: 0.8705 (mmm) cc_final: 0.7822 (tpp) REVERT: G 58 ASN cc_start: 0.9391 (t0) cc_final: 0.9055 (t0) REVERT: G 84 GLU cc_start: 0.8468 (mp0) cc_final: 0.8153 (mp0) REVERT: G 91 ASP cc_start: 0.7940 (t0) cc_final: 0.7616 (t0) outliers start: 54 outliers final: 46 residues processed: 343 average time/residue: 0.1177 time to fit residues: 57.9130 Evaluate side-chains 354 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 304 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain Q residue 20 PHE Chi-restraints excluded: chain Q residue 30 THR Chi-restraints excluded: chain Q residue 33 LYS Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain T residue 20 PHE Chi-restraints excluded: chain T residue 48 THR Chi-restraints excluded: chain T residue 51 LEU Chi-restraints excluded: chain T residue 76 VAL Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain T residue 81 LEU Chi-restraints excluded: chain T residue 119 ILE Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 95 MET Chi-restraints excluded: chain Y residue 10 ARG Chi-restraints excluded: chain Y residue 45 GLU Chi-restraints excluded: chain Y residue 51 LEU Chi-restraints excluded: chain Y residue 110 ILE Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain b residue 58 LYS Chi-restraints excluded: chain b residue 68 VAL Chi-restraints excluded: chain b residue 94 LYS Chi-restraints excluded: chain b residue 98 VAL Chi-restraints excluded: chain b residue 118 MET Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain E residue 4 SER Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 143 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 47 optimal weight: 0.1980 chunk 40 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 34 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 18 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 113 HIS ** 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 = 0.2592 r_free = 0.2592 target = 0.059616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2446 r_free = 0.2446 target = 0.053327 restraints weight = 33712.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.055163 restraints weight = 14718.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.056405 restraints weight = 8117.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.057217 restraints weight = 5020.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.057778 restraints weight = 3367.654| |-----------------------------------------------------------------------------| r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12384 Z= 0.129 Angle : 0.576 8.867 16734 Z= 0.303 Chirality : 0.048 0.152 1752 Planarity : 0.004 0.047 2214 Dihedral : 4.615 51.839 1695 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.36 % Allowed : 23.94 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.22), residues: 1488 helix: 2.24 (0.31), residues: 276 sheet: 0.96 (0.26), residues: 450 loop : -1.39 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 56 TYR 0.022 0.001 TYR b 17 PHE 0.013 0.001 PHE V 70 TRP 0.009 0.001 TRP Q 38 HIS 0.003 0.001 HIS Y 113 Details of bonding type rmsd covalent geometry : bond 0.00301 (12384) covalent geometry : angle 0.57566 (16734) hydrogen bonds : bond 0.03783 ( 472) hydrogen bonds : angle 5.48792 ( 1398) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 312 time to evaluate : 0.517 Fit side-chains REVERT: N 56 LYS cc_start: 0.9259 (mttt) cc_final: 0.8168 (tmtt) REVERT: T 20 PHE cc_start: 0.9246 (OUTLIER) cc_final: 0.8350 (t80) REVERT: T 24 MET cc_start: 0.8959 (mmm) cc_final: 0.7851 (mtm) REVERT: T 56 LYS cc_start: 0.9089 (mtmm) cc_final: 0.8052 (tptt) REVERT: T 88 ASP cc_start: 0.8647 (m-30) cc_final: 0.8353 (m-30) REVERT: T 106 ILE cc_start: 0.9505 (mm) cc_final: 0.9300 (mm) REVERT: V 45 GLU cc_start: 0.8391 (mp0) cc_final: 0.8184 (mp0) REVERT: Y 10 ARG cc_start: 0.9201 (OUTLIER) cc_final: 0.8819 (mtm-85) REVERT: Y 45 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7296 (mm-30) REVERT: Y 58 LYS cc_start: 0.8989 (ptmm) cc_final: 0.8705 (ptmm) REVERT: Y 77 ASP cc_start: 0.8332 (m-30) cc_final: 0.7967 (m-30) REVERT: b 33 LYS cc_start: 0.9182 (mtmt) cc_final: 0.8652 (mtpp) REVERT: b 58 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8600 (ptmm) REVERT: A 58 ASN cc_start: 0.9183 (t0) cc_final: 0.8602 (t0) REVERT: A 91 ASP cc_start: 0.8130 (t0) cc_final: 0.7885 (t0) REVERT: A 104 GLN cc_start: 0.8518 (tp-100) cc_final: 0.8242 (tp-100) REVERT: C 1 MET cc_start: 0.8727 (mmm) cc_final: 0.7832 (tpp) REVERT: C 58 ASN cc_start: 0.9343 (t0) cc_final: 0.9017 (t0) REVERT: C 91 ASP cc_start: 0.8022 (t0) cc_final: 0.7719 (t0) REVERT: D 58 ASN cc_start: 0.9196 (t0) cc_final: 0.8842 (t0) REVERT: D 91 ASP cc_start: 0.8162 (t0) cc_final: 0.7895 (t0) REVERT: D 104 GLN cc_start: 0.8669 (tp-100) cc_final: 0.8311 (tp-100) REVERT: G 1 MET cc_start: 0.8716 (mmm) cc_final: 0.7829 (tpp) REVERT: G 58 ASN cc_start: 0.9364 (t0) cc_final: 0.8988 (t0) REVERT: G 84 GLU cc_start: 0.8501 (mp0) cc_final: 0.8184 (mp0) REVERT: G 91 ASP cc_start: 0.7996 (t0) cc_final: 0.7693 (t0) outliers start: 43 outliers final: 36 residues processed: 341 average time/residue: 0.1149 time to fit residues: 56.0765 Evaluate side-chains 341 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 301 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain Q residue 20 PHE Chi-restraints excluded: chain Q residue 30 THR Chi-restraints excluded: chain Q residue 33 LYS Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain T residue 20 PHE Chi-restraints excluded: chain T residue 48 THR Chi-restraints excluded: chain T residue 51 LEU Chi-restraints excluded: chain T residue 76 VAL Chi-restraints excluded: chain T residue 81 LEU Chi-restraints excluded: chain T residue 119 ILE Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain Y residue 10 ARG Chi-restraints excluded: chain Y residue 45 GLU Chi-restraints excluded: chain Y residue 48 THR Chi-restraints excluded: chain Y residue 51 LEU Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain b residue 58 LYS Chi-restraints excluded: chain b residue 68 VAL Chi-restraints excluded: chain b residue 94 LYS Chi-restraints excluded: chain b residue 118 MET Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain E residue 4 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 108 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 139 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 113 HIS ** 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 = 0.2524 r_free = 0.2524 target = 0.056530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2370 r_free = 0.2370 target = 0.050200 restraints weight = 33773.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2413 r_free = 0.2413 target = 0.051998 restraints weight = 14755.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2442 r_free = 0.2442 target = 0.053192 restraints weight = 8185.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2462 r_free = 0.2462 target = 0.054004 restraints weight = 5102.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2476 r_free = 0.2476 target = 0.054571 restraints weight = 3456.906| |-----------------------------------------------------------------------------| r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 12384 Z= 0.263 Angle : 0.634 8.353 16734 Z= 0.339 Chirality : 0.050 0.151 1752 Planarity : 0.005 0.064 2214 Dihedral : 4.876 50.665 1694 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 3.68 % Allowed : 24.02 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.22), residues: 1488 helix: 1.95 (0.30), residues: 276 sheet: 0.97 (0.26), residues: 444 loop : -1.39 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 56 TYR 0.025 0.002 TYR b 17 PHE 0.015 0.002 PHE Q 123 TRP 0.007 0.001 TRP T 117 HIS 0.006 0.001 HIS T 113 Details of bonding type rmsd covalent geometry : bond 0.00618 (12384) covalent geometry : angle 0.63365 (16734) hydrogen bonds : bond 0.04939 ( 472) hydrogen bonds : angle 5.79198 ( 1398) =============================================================================== Job complete usr+sys time: 2018.54 seconds wall clock time: 35 minutes 41.20 seconds (2141.20 seconds total)