Starting phenix.real_space_refine on Wed May 14 08:23:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l0e_62698/05_2025/9l0e_62698.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l0e_62698/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9l0e_62698/05_2025/9l0e_62698.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l0e_62698/05_2025/9l0e_62698.map" model { file = "/net/cci-nas-00/data/ceres_data/9l0e_62698/05_2025/9l0e_62698.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l0e_62698/05_2025/9l0e_62698.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.37, per 1000 atoms: 0.61 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: 2.71 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.26 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: 3.15 Time building geometry restraints manager: 3.19 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: 0.01 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: 3.440 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.040 Set scattering table: 0.100 Process input model: 27.560 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.470 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (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 TRP 0.009 0.001 TRP Y 117 HIS 0.004 0.001 HIS b 108 PHE 0.009 0.001 PHE b 41 TYR 0.016 0.001 TYR Q 23 ARG 0.003 0.000 ARG Q 122 Details of bonding type rmsd hydrogen bonds : bond 0.23030 ( 472) hydrogen bonds : angle 9.81288 ( 1398) covalent geometry : bond 0.00322 (12384) covalent geometry : angle 0.69392 (16734) *********************** 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 : 1.427 Fit side-chains REVERT: N 56 LYS cc_start: 0.7917 (mttt) cc_final: 0.7324 (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: 0.7571 (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: 0.6566 (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: 0.7232 (tmtt) REVERT: T 96 LEU cc_start: 0.8579 (mt) cc_final: 0.8203 (mt) REVERT: Y 40 ARG cc_start: 0.8026 (ttm170) cc_final: 0.7755 (ttm170) REVERT: Y 61 ILE cc_start: 0.8770 (mt) cc_final: 0.8546 (mt) REVERT: Y 119 ILE cc_start: 0.9187 (mt) cc_final: 0.8978 (tt) REVERT: b 33 LYS cc_start: 0.8265 (mtmt) cc_final: 0.7958 (mtpp) REVERT: A 70 SER cc_start: 0.7793 (p) cc_final: 0.7566 (p) REVERT: B 5 GLN cc_start: 0.7454 (tm-30) cc_final: 0.7108 (tm-30) REVERT: B 73 LEU cc_start: 0.8560 (mt) cc_final: 0.7728 (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: 0.7625 (mm-30) REVERT: D 58 ASN cc_start: 0.8002 (t0) cc_final: 0.7637 (t0) REVERT: E 5 GLN cc_start: 0.7473 (tm-30) cc_final: 0.7153 (tm-30) REVERT: G 46 GLN cc_start: 0.7666 (tt0) cc_final: 0.7272 (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: 0.2416 time to fit residues: 174.8980 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 : 1.436 ------------------------------------------------------------------------------- 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 121 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 26 ASN ** V 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 108 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.060006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2441 r_free = 0.2441 target = 0.053458 restraints weight = 33394.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2483 r_free = 0.2483 target = 0.055287 restraints weight = 14729.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.056493 restraints weight = 8186.575| |-----------------------------------------------------------------------------| r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 12384 Z= 0.285 Angle : 0.703 7.708 16734 Z= 0.381 Chirality : 0.053 0.157 1752 Planarity : 0.006 0.052 2214 Dihedral : 5.084 54.136 1695 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 5.63 % Allowed : 20.11 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.21), residues: 1488 helix: 1.93 (0.31), residues: 276 sheet: 1.26 (0.31), residues: 294 loop : -1.87 (0.18), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP Y 38 HIS 0.008 0.002 HIS T 113 PHE 0.017 0.002 PHE V 70 TYR 0.019 0.002 TYR Q 17 ARG 0.007 0.001 ARG E 22 Details of bonding type rmsd hydrogen bonds : bond 0.05515 ( 472) hydrogen bonds : angle 6.78242 ( 1398) covalent geometry : bond 0.00670 (12384) covalent geometry : angle 0.70298 (16734) *********************** 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 441 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 369 time to evaluate : 1.405 Fit side-chains REVERT: N 54 ASP cc_start: 0.8304 (p0) cc_final: 0.8058 (p0) REVERT: N 56 LYS cc_start: 0.9047 (mttt) cc_final: 0.7876 (tmtt) REVERT: N 103 GLU cc_start: 0.8814 (tt0) cc_final: 0.8611 (tt0) REVERT: Q 20 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.8602 (m-80) REVERT: Q 23 TYR cc_start: 0.8722 (t80) cc_final: 0.8359 (t80) REVERT: Q 26 ASN cc_start: 0.9037 (t0) cc_final: 0.8564 (t0) REVERT: Q 55 ARG cc_start: 0.9259 (mmt-90) cc_final: 0.7154 (mpp80) REVERT: Q 92 ASP cc_start: 0.9136 (OUTLIER) cc_final: 0.8487 (t0) REVERT: T 20 PHE cc_start: 0.9133 (OUTLIER) cc_final: 0.8258 (t80) REVERT: T 56 LYS cc_start: 0.9036 (mtmm) cc_final: 0.8009 (tmtt) REVERT: T 88 ASP cc_start: 0.8602 (m-30) cc_final: 0.8302 (m-30) REVERT: T 96 LEU cc_start: 0.9404 (mt) cc_final: 0.9200 (mt) REVERT: V 103 GLU cc_start: 0.8786 (tt0) cc_final: 0.8585 (tt0) REVERT: Y 40 ARG cc_start: 0.9351 (ttm170) cc_final: 0.9039 (ttm170) REVERT: Y 51 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8906 (pp) REVERT: Y 54 ASP cc_start: 0.8495 (p0) cc_final: 0.8275 (p0) REVERT: Y 58 LYS cc_start: 0.8964 (ptmm) cc_final: 0.8706 (ptmm) REVERT: b 33 LYS cc_start: 0.9327 (mtmt) cc_final: 0.8853 (mtpp) REVERT: b 58 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8645 (ptmm) REVERT: A 58 ASN cc_start: 0.9097 (t0) cc_final: 0.8673 (t0) REVERT: A 65 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8352 (mm-30) REVERT: A 93 ILE cc_start: 0.9383 (OUTLIER) cc_final: 0.8982 (mp) REVERT: B 58 ASN cc_start: 0.9190 (t0) cc_final: 0.8950 (t0) REVERT: B 71 ASP cc_start: 0.8671 (m-30) cc_final: 0.8341 (m-30) REVERT: B 99 ASP cc_start: 0.8435 (t0) cc_final: 0.8235 (t0) REVERT: C 58 ASN cc_start: 0.9409 (t0) cc_final: 0.9077 (t0) REVERT: C 65 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8661 (mm-30) REVERT: C 91 ASP cc_start: 0.8360 (t0) cc_final: 0.8090 (t0) REVERT: D 58 ASN cc_start: 0.9149 (t0) cc_final: 0.8490 (t0) REVERT: D 104 GLN cc_start: 0.8485 (tp-100) cc_final: 0.8231 (tp-100) REVERT: E 51 SER cc_start: 0.9401 (OUTLIER) cc_final: 0.9140 (m) REVERT: E 58 ASN cc_start: 0.9193 (t0) cc_final: 0.8968 (t0) REVERT: E 65 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8529 (mp0) REVERT: G 58 ASN cc_start: 0.9408 (t0) cc_final: 0.9096 (t0) REVERT: G 91 ASP cc_start: 0.8258 (t0) cc_final: 0.8042 (t0) outliers start: 72 outliers final: 44 residues processed: 415 average time/residue: 0.2242 time to fit residues: 133.0607 Evaluate side-chains 356 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 305 time to evaluate : 1.487 ------------------------------------------------------------------------------- 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 N residue 85 GLU Chi-restraints excluded: chain N residue 118 MET 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 92 ASP 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 V residue 110 ILE 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 58 LYS Chi-restraints excluded: chain b residue 68 VAL Chi-restraints excluded: chain b residue 98 VAL Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 93 ILE 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 119 VAL Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 98 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 51 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 97 VAL Chi-restraints excluded: chain G residue 98 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 125 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 26 ASN ** V 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.062159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.055615 restraints weight = 33181.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.057508 restraints weight = 14372.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.058743 restraints weight = 7877.425| |-----------------------------------------------------------------------------| r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12384 Z= 0.138 Angle : 0.576 7.080 16734 Z= 0.307 Chirality : 0.049 0.156 1752 Planarity : 0.004 0.043 2214 Dihedral : 4.746 53.856 1695 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 4.30 % Allowed : 20.42 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.21), residues: 1488 helix: 2.21 (0.31), residues: 276 sheet: 1.21 (0.31), residues: 294 loop : -1.72 (0.18), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Q 38 HIS 0.005 0.001 HIS Y 108 PHE 0.014 0.001 PHE V 70 TYR 0.013 0.001 TYR C 3 ARG 0.003 0.000 ARG C 101 Details of bonding type rmsd hydrogen bonds : bond 0.04520 ( 472) hydrogen bonds : angle 6.16215 ( 1398) covalent geometry : bond 0.00311 (12384) covalent geometry : angle 0.57605 (16734) *********************** 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 395 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 340 time to evaluate : 1.382 Fit side-chains REVERT: N 56 LYS cc_start: 0.9042 (mttt) cc_final: 0.7982 (tmtt) REVERT: Q 23 TYR cc_start: 0.8803 (t80) cc_final: 0.8257 (t80) REVERT: Q 26 ASN cc_start: 0.8899 (t0) cc_final: 0.8573 (t0) REVERT: Q 33 LYS cc_start: 0.8871 (ttpt) cc_final: 0.8503 (mtpp) REVERT: Q 55 ARG cc_start: 0.9101 (mmt-90) cc_final: 0.7211 (mpt180) REVERT: Q 92 ASP cc_start: 0.9104 (OUTLIER) cc_final: 0.8449 (t0) REVERT: T 20 PHE cc_start: 0.9173 (OUTLIER) cc_final: 0.8297 (t80) REVERT: T 56 LYS cc_start: 0.9057 (mtmm) cc_final: 0.7885 (tmtt) REVERT: T 88 ASP cc_start: 0.8576 (m-30) cc_final: 0.8254 (m-30) REVERT: T 96 LEU cc_start: 0.9412 (mt) cc_final: 0.9212 (mt) REVERT: V 103 GLU cc_start: 0.8805 (tt0) cc_final: 0.8582 (tt0) REVERT: Y 10 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.8627 (mtm-85) REVERT: Y 40 ARG cc_start: 0.9365 (ttm170) cc_final: 0.9066 (ttp80) REVERT: Y 58 LYS cc_start: 0.8959 (ptmm) cc_final: 0.8677 (ptmm) REVERT: b 33 LYS cc_start: 0.9240 (mtmt) cc_final: 0.8963 (mtpp) REVERT: b 54 ASP cc_start: 0.8379 (m-30) cc_final: 0.8074 (t0) REVERT: A 51 SER cc_start: 0.9246 (t) cc_final: 0.8917 (m) REVERT: A 58 ASN cc_start: 0.9147 (t0) cc_final: 0.8607 (t0) REVERT: B 71 ASP cc_start: 0.8623 (m-30) cc_final: 0.8333 (m-30) REVERT: C 58 ASN cc_start: 0.9394 (t0) cc_final: 0.9009 (t0) REVERT: C 91 ASP cc_start: 0.8225 (t0) cc_final: 0.7956 (t0) REVERT: D 51 SER cc_start: 0.9283 (t) cc_final: 0.8968 (m) REVERT: D 58 ASN cc_start: 0.9178 (t0) cc_final: 0.8634 (t0) REVERT: D 91 ASP cc_start: 0.8207 (t0) cc_final: 0.8002 (t0) REVERT: D 104 GLN cc_start: 0.8353 (tp-100) cc_final: 0.8121 (tp-100) REVERT: E 51 SER cc_start: 0.9387 (t) cc_final: 0.9130 (m) REVERT: G 58 ASN cc_start: 0.9394 (t0) cc_final: 0.8981 (t0) REVERT: G 91 ASP cc_start: 0.8246 (t0) cc_final: 0.8013 (t0) outliers start: 55 outliers final: 35 residues processed: 376 average time/residue: 0.2371 time to fit residues: 125.9726 Evaluate side-chains 365 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 327 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain Q residue 37 MET Chi-restraints excluded: chain Q residue 53 ILE Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 92 ASP Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain T residue 20 PHE Chi-restraints excluded: chain T residue 26 ASN 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 110 ILE Chi-restraints excluded: chain b residue 47 ASP Chi-restraints excluded: chain b residue 48 THR 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 93 ILE 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 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 119 VAL Chi-restraints excluded: chain G residue 61 GLU 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 58 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 5 optimal weight: 0.0370 chunk 130 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.9262 ------------------------------------------------------------------------------- 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 42 ASN A 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.061880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.055345 restraints weight = 32868.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.057239 restraints weight = 14153.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.058483 restraints weight = 7739.020| |-----------------------------------------------------------------------------| r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.3350 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= 0.115 Angle : 0.556 9.059 16734 Z= 0.291 Chirality : 0.048 0.148 1752 Planarity : 0.004 0.044 2214 Dihedral : 4.594 53.850 1695 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 4.38 % Allowed : 21.36 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.22), residues: 1488 helix: 2.25 (0.31), residues: 276 sheet: 0.94 (0.27), residues: 414 loop : -1.58 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Q 38 HIS 0.004 0.001 HIS Y 108 PHE 0.012 0.001 PHE V 70 TYR 0.024 0.001 TYR b 17 ARG 0.003 0.000 ARG T 27 Details of bonding type rmsd hydrogen bonds : bond 0.03917 ( 472) hydrogen bonds : angle 5.80541 ( 1398) covalent geometry : bond 0.00260 (12384) covalent geometry : angle 0.55587 (16734) *********************** 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 406 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 350 time to evaluate : 1.335 Fit side-chains REVERT: N 56 LYS cc_start: 0.9094 (mttt) cc_final: 0.7892 (tmtt) REVERT: Q 26 ASN cc_start: 0.8842 (t0) cc_final: 0.8538 (t0) REVERT: Q 55 ARG cc_start: 0.9065 (mmt-90) cc_final: 0.7211 (mpt180) REVERT: T 20 PHE cc_start: 0.9201 (OUTLIER) cc_final: 0.8290 (t80) REVERT: T 45 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8124 (mm-30) REVERT: T 56 LYS cc_start: 0.9046 (mtmm) cc_final: 0.7856 (tmtt) REVERT: T 88 ASP cc_start: 0.8579 (m-30) cc_final: 0.8276 (m-30) REVERT: T 96 LEU cc_start: 0.9386 (mt) cc_final: 0.9175 (mt) REVERT: V 103 GLU cc_start: 0.8802 (tt0) cc_final: 0.8588 (tt0) REVERT: Y 40 ARG cc_start: 0.9347 (ttm170) cc_final: 0.9134 (ttp80) REVERT: Y 58 LYS cc_start: 0.8837 (ptmm) cc_final: 0.8610 (ptmm) REVERT: b 33 LYS cc_start: 0.9212 (mtmt) cc_final: 0.8922 (mtpp) REVERT: b 54 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.8075 (t0) REVERT: A 51 SER cc_start: 0.9245 (OUTLIER) cc_final: 0.8938 (m) REVERT: A 58 ASN cc_start: 0.9159 (t0) cc_final: 0.8577 (t0) REVERT: B 58 ASN cc_start: 0.9155 (t0) cc_final: 0.8907 (t0) REVERT: B 71 ASP cc_start: 0.8600 (m-30) cc_final: 0.8325 (m-30) REVERT: C 58 ASN cc_start: 0.9408 (t0) cc_final: 0.9006 (t0) REVERT: C 65 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8419 (mm-30) REVERT: C 91 ASP cc_start: 0.8263 (t0) cc_final: 0.7964 (t0) REVERT: D 51 SER cc_start: 0.9274 (t) cc_final: 0.9009 (m) REVERT: D 58 ASN cc_start: 0.9188 (t0) cc_final: 0.8584 (t0) REVERT: D 104 GLN cc_start: 0.8498 (tp-100) cc_final: 0.8169 (tp-100) REVERT: E 51 SER cc_start: 0.9395 (t) cc_final: 0.9141 (m) REVERT: E 58 ASN cc_start: 0.9188 (t0) cc_final: 0.8933 (t0) REVERT: G 58 ASN cc_start: 0.9381 (t0) cc_final: 0.8964 (t0) REVERT: G 91 ASP cc_start: 0.8259 (t0) cc_final: 0.8018 (t0) outliers start: 56 outliers final: 36 residues processed: 385 average time/residue: 0.2245 time to fit residues: 123.4969 Evaluate side-chains 364 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 324 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 30 THR Chi-restraints excluded: chain Q residue 37 MET Chi-restraints excluded: chain Q residue 58 LYS Chi-restraints excluded: chain Q residue 69 VAL 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 58 LYS Chi-restraints excluded: chain V residue 76 VAL 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 54 ASP 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 51 SER Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 119 VAL 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 119 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 83 optimal weight: 7.9990 chunk 120 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 128 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 0.0060 chunk 33 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- 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 26 ASN ** 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 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.061446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2474 r_free = 0.2474 target = 0.054867 restraints weight = 33086.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.056753 restraints weight = 14381.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.057990 restraints weight = 7896.223| |-----------------------------------------------------------------------------| r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12384 Z= 0.119 Angle : 0.539 7.252 16734 Z= 0.285 Chirality : 0.048 0.150 1752 Planarity : 0.004 0.045 2214 Dihedral : 4.515 53.780 1695 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.99 % Allowed : 21.75 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.21), residues: 1488 helix: 2.24 (0.31), residues: 276 sheet: 1.33 (0.31), residues: 294 loop : -1.44 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Q 38 HIS 0.004 0.001 HIS T 113 PHE 0.013 0.001 PHE V 70 TYR 0.023 0.001 TYR b 17 ARG 0.006 0.000 ARG B 22 Details of bonding type rmsd hydrogen bonds : bond 0.03744 ( 472) hydrogen bonds : angle 5.62960 ( 1398) covalent geometry : bond 0.00273 (12384) covalent geometry : angle 0.53925 (16734) *********************** 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 384 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 333 time to evaluate : 1.426 Fit side-chains REVERT: N 33 LYS cc_start: 0.9154 (mmmm) cc_final: 0.8851 (mtpp) REVERT: N 56 LYS cc_start: 0.9049 (mttt) cc_final: 0.7946 (tmtt) REVERT: Q 26 ASN cc_start: 0.8817 (t0) cc_final: 0.8467 (t0) REVERT: Q 55 ARG cc_start: 0.9022 (mmt-90) cc_final: 0.7224 (mpt180) REVERT: T 20 PHE cc_start: 0.9210 (OUTLIER) cc_final: 0.8378 (t80) REVERT: T 45 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8071 (mm-30) REVERT: T 56 LYS cc_start: 0.9070 (mtmm) cc_final: 0.7864 (tmtt) REVERT: T 96 LEU cc_start: 0.9397 (mt) cc_final: 0.9193 (mt) REVERT: V 103 GLU cc_start: 0.8818 (tt0) cc_final: 0.8551 (tt0) REVERT: Y 10 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.8623 (mtm-85) REVERT: Y 58 LYS cc_start: 0.8849 (ptmm) cc_final: 0.8648 (ptmm) REVERT: b 33 LYS cc_start: 0.9209 (mtmt) cc_final: 0.8905 (mtpp) REVERT: b 55 ARG cc_start: 0.8874 (mmp-170) cc_final: 0.6288 (mpt180) REVERT: A 51 SER cc_start: 0.9245 (t) cc_final: 0.8984 (m) REVERT: A 58 ASN cc_start: 0.9155 (t0) cc_final: 0.8582 (t0) REVERT: B 71 ASP cc_start: 0.8579 (m-30) cc_final: 0.8304 (m-30) REVERT: C 1 MET cc_start: 0.8716 (mmm) cc_final: 0.7902 (tpp) REVERT: C 58 ASN cc_start: 0.9393 (t0) cc_final: 0.8996 (t0) REVERT: C 65 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8337 (mm-30) REVERT: C 91 ASP cc_start: 0.8324 (t0) cc_final: 0.8056 (t0) REVERT: D 51 SER cc_start: 0.9288 (t) cc_final: 0.9034 (m) REVERT: D 58 ASN cc_start: 0.9158 (t0) cc_final: 0.8736 (t0) REVERT: D 104 GLN cc_start: 0.8319 (tp-100) cc_final: 0.8032 (tp-100) REVERT: G 1 MET cc_start: 0.8692 (mmm) cc_final: 0.7884 (tpp) REVERT: G 58 ASN cc_start: 0.9384 (t0) cc_final: 0.8986 (t0) REVERT: G 91 ASP cc_start: 0.8251 (t0) cc_final: 0.7988 (t0) outliers start: 51 outliers final: 38 residues processed: 364 average time/residue: 0.2355 time to fit residues: 121.7016 Evaluate side-chains 362 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 321 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 37 MET Chi-restraints excluded: chain Q residue 58 LYS Chi-restraints excluded: chain Q residue 69 VAL 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 58 LYS 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 37 MET 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 96 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 119 VAL 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 119 VAL 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 111 optimal weight: 5.9990 chunk 126 optimal weight: 8.9990 chunk 117 optimal weight: 8.9990 chunk 131 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 108 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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 26 ASN 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** A 104 GLN C 46 GLN G 46 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.058961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2421 r_free = 0.2421 target = 0.052482 restraints weight = 33682.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2463 r_free = 0.2463 target = 0.054326 restraints weight = 14519.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.055540 restraints weight = 7970.750| |-----------------------------------------------------------------------------| r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12384 Z= 0.176 Angle : 0.576 8.432 16734 Z= 0.306 Chirality : 0.049 0.146 1752 Planarity : 0.004 0.048 2214 Dihedral : 4.665 52.938 1695 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 4.77 % Allowed : 21.05 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.21), residues: 1488 helix: 2.10 (0.31), residues: 276 sheet: 1.21 (0.31), residues: 294 loop : -1.39 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Y 38 HIS 0.006 0.001 HIS T 113 PHE 0.013 0.002 PHE Q 123 TYR 0.013 0.001 TYR Q 3 ARG 0.008 0.001 ARG D 56 Details of bonding type rmsd hydrogen bonds : bond 0.04360 ( 472) hydrogen bonds : angle 5.70543 ( 1398) covalent geometry : bond 0.00411 (12384) covalent geometry : angle 0.57570 (16734) *********************** 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 374 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 313 time to evaluate : 1.428 Fit side-chains revert: symmetry clash REVERT: N 33 LYS cc_start: 0.9202 (mmmm) cc_final: 0.8888 (mtpp) REVERT: N 56 LYS cc_start: 0.9093 (mttt) cc_final: 0.8107 (tmtt) REVERT: Q 26 ASN cc_start: 0.8844 (t0) cc_final: 0.8560 (t0) REVERT: Q 92 ASP cc_start: 0.9168 (OUTLIER) cc_final: 0.8455 (t0) REVERT: T 20 PHE cc_start: 0.9240 (OUTLIER) cc_final: 0.8409 (t80) REVERT: T 45 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8053 (mm-30) REVERT: T 56 LYS cc_start: 0.9083 (mtmm) cc_final: 0.7962 (tmtt) REVERT: T 106 ILE cc_start: 0.9480 (mm) cc_final: 0.9200 (mm) REVERT: V 103 GLU cc_start: 0.8834 (tt0) cc_final: 0.8553 (tt0) REVERT: Y 10 ARG cc_start: 0.9183 (OUTLIER) cc_final: 0.8713 (mtm-85) REVERT: Y 58 LYS cc_start: 0.8987 (ptmm) cc_final: 0.8704 (ptmm) REVERT: b 33 LYS cc_start: 0.9189 (mtmt) cc_final: 0.8867 (mtpp) REVERT: b 45 GLU cc_start: 0.8646 (mp0) cc_final: 0.8393 (mp0) REVERT: b 55 ARG cc_start: 0.8915 (mmp-170) cc_final: 0.6338 (mpt180) REVERT: A 51 SER cc_start: 0.9292 (t) cc_final: 0.9051 (m) REVERT: A 58 ASN cc_start: 0.9183 (t0) cc_final: 0.8637 (t0) REVERT: C 1 MET cc_start: 0.8760 (mmm) cc_final: 0.7907 (tpp) REVERT: C 58 ASN cc_start: 0.9382 (t0) cc_final: 0.9009 (t0) REVERT: C 91 ASP cc_start: 0.8247 (t0) cc_final: 0.8008 (t0) REVERT: D 51 SER cc_start: 0.9321 (t) cc_final: 0.9088 (m) REVERT: D 58 ASN cc_start: 0.9177 (t0) cc_final: 0.8763 (t0) REVERT: D 104 GLN cc_start: 0.8397 (tp-100) cc_final: 0.8151 (tp-100) REVERT: E 51 SER cc_start: 0.9466 (t) cc_final: 0.9215 (m) REVERT: G 1 MET cc_start: 0.8732 (mmm) cc_final: 0.7888 (tpp) REVERT: G 58 ASN cc_start: 0.9392 (t0) cc_final: 0.9029 (t0) REVERT: G 91 ASP cc_start: 0.8275 (t0) cc_final: 0.8020 (t0) outliers start: 61 outliers final: 45 residues processed: 350 average time/residue: 0.2230 time to fit residues: 111.3393 Evaluate side-chains 357 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 308 time to evaluate : 1.290 ------------------------------------------------------------------------------- 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 58 LYS Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 92 ASP Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain T residue 20 PHE Chi-restraints excluded: chain T residue 26 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 76 VAL Chi-restraints excluded: chain T residue 81 LEU Chi-restraints excluded: chain T residue 119 ILE 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 37 MET 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 54 THR 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 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 97 VAL 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 31 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 138 optimal weight: 0.6980 chunk 12 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 55 optimal weight: 0.0870 chunk 126 optimal weight: 0.8980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 26 ASN T 65 GLN ** T 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 113 HIS ** Y 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.061318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2477 r_free = 0.2477 target = 0.054827 restraints weight = 32927.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2518 r_free = 0.2518 target = 0.056688 restraints weight = 14195.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.057932 restraints weight = 7798.343| |-----------------------------------------------------------------------------| r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12384 Z= 0.107 Angle : 0.552 9.337 16734 Z= 0.290 Chirality : 0.048 0.154 1752 Planarity : 0.004 0.046 2214 Dihedral : 4.496 53.000 1695 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.60 % Allowed : 23.08 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.22), residues: 1488 helix: 2.33 (0.31), residues: 276 sheet: 0.93 (0.27), residues: 420 loop : -1.31 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Q 38 HIS 0.003 0.001 HIS V 108 PHE 0.012 0.001 PHE Q 123 TYR 0.012 0.001 TYR V 17 ARG 0.006 0.000 ARG T 27 Details of bonding type rmsd hydrogen bonds : bond 0.03500 ( 472) hydrogen bonds : angle 5.45606 ( 1398) covalent geometry : bond 0.00244 (12384) covalent geometry : angle 0.55175 (16734) *********************** 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 373 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 327 time to evaluate : 1.433 Fit side-chains REVERT: N 33 LYS cc_start: 0.9157 (mmmm) cc_final: 0.8827 (mtpp) REVERT: N 56 LYS cc_start: 0.9057 (mttt) cc_final: 0.7917 (tptp) REVERT: Q 25 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8691 (mt-10) REVERT: Q 26 ASN cc_start: 0.8818 (t0) cc_final: 0.8617 (t0) REVERT: Q 92 ASP cc_start: 0.9152 (OUTLIER) cc_final: 0.8496 (t0) REVERT: T 20 PHE cc_start: 0.9238 (OUTLIER) cc_final: 0.8367 (t80) REVERT: T 56 LYS cc_start: 0.9061 (mtmm) cc_final: 0.7981 (tmtt) REVERT: T 106 ILE cc_start: 0.9431 (mm) cc_final: 0.9171 (mm) REVERT: V 103 GLU cc_start: 0.8816 (tt0) cc_final: 0.8554 (tt0) REVERT: Y 10 ARG cc_start: 0.9168 (OUTLIER) cc_final: 0.8586 (mtm-85) REVERT: Y 58 LYS cc_start: 0.8891 (ptmm) cc_final: 0.8653 (ptmm) REVERT: b 33 LYS cc_start: 0.9151 (mtmt) cc_final: 0.8659 (mtpp) REVERT: A 51 SER cc_start: 0.9251 (t) cc_final: 0.9032 (m) REVERT: A 58 ASN cc_start: 0.9193 (t0) cc_final: 0.8646 (t0) REVERT: C 1 MET cc_start: 0.8747 (mmm) cc_final: 0.7903 (tpp) REVERT: C 58 ASN cc_start: 0.9354 (t0) cc_final: 0.8949 (t0) REVERT: C 91 ASP cc_start: 0.8185 (t0) cc_final: 0.7943 (t0) REVERT: D 51 SER cc_start: 0.9281 (t) cc_final: 0.9067 (m) REVERT: D 58 ASN cc_start: 0.9188 (t0) cc_final: 0.8780 (t0) REVERT: D 91 ASP cc_start: 0.8209 (t0) cc_final: 0.7958 (t0) REVERT: D 104 GLN cc_start: 0.8449 (tp-100) cc_final: 0.8152 (tp-100) REVERT: G 1 MET cc_start: 0.8711 (mmm) cc_final: 0.7873 (tpp) REVERT: G 58 ASN cc_start: 0.9367 (t0) cc_final: 0.8966 (t0) outliers start: 46 outliers final: 32 residues processed: 357 average time/residue: 0.2375 time to fit residues: 120.2276 Evaluate side-chains 348 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 313 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain Q residue 20 PHE Chi-restraints excluded: chain Q residue 30 THR Chi-restraints excluded: chain Q residue 58 LYS Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 92 ASP Chi-restraints excluded: chain T residue 20 PHE Chi-restraints excluded: chain T residue 26 ASN 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 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 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 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 54 THR Chi-restraints excluded: chain B residue 119 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 119 VAL 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 64 optimal weight: 9.9990 chunk 143 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 99 optimal weight: 9.9990 chunk 3 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 139 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- 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 26 ASN T 65 GLN ** T 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 GLN A 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.058924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2420 r_free = 0.2420 target = 0.052420 restraints weight = 33801.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2463 r_free = 0.2463 target = 0.054251 restraints weight = 14642.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.055471 restraints weight = 8081.359| |-----------------------------------------------------------------------------| r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.4007 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= 0.173 Angle : 0.581 9.859 16734 Z= 0.308 Chirality : 0.049 0.154 1752 Planarity : 0.004 0.048 2214 Dihedral : 4.622 52.301 1695 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 3.83 % Allowed : 22.93 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.22), residues: 1488 helix: 2.23 (0.31), residues: 276 sheet: 1.22 (0.28), residues: 378 loop : -1.34 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Y 38 HIS 0.005 0.001 HIS T 113 PHE 0.013 0.001 PHE V 70 TYR 0.013 0.001 TYR V 17 ARG 0.006 0.000 ARG T 27 Details of bonding type rmsd hydrogen bonds : bond 0.04131 ( 472) hydrogen bonds : angle 5.55715 ( 1398) covalent geometry : bond 0.00405 (12384) covalent geometry : angle 0.58143 (16734) *********************** 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 358 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 309 time to evaluate : 1.455 Fit side-chains REVERT: N 33 LYS cc_start: 0.9162 (mmmm) cc_final: 0.8839 (mtpp) REVERT: N 56 LYS cc_start: 0.9175 (mttt) cc_final: 0.8037 (tmtt) REVERT: N 112 LYS cc_start: 0.9062 (mtmt) cc_final: 0.8812 (mtmt) REVERT: Q 25 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8735 (mt-10) REVERT: Q 26 ASN cc_start: 0.8890 (t0) cc_final: 0.8578 (t0) REVERT: Q 92 ASP cc_start: 0.9255 (OUTLIER) cc_final: 0.8593 (t0) REVERT: T 20 PHE cc_start: 0.9269 (OUTLIER) cc_final: 0.8434 (t80) REVERT: T 56 LYS cc_start: 0.9096 (mtmm) cc_final: 0.7975 (tmtt) REVERT: T 106 ILE cc_start: 0.9481 (mm) cc_final: 0.9225 (mm) REVERT: V 103 GLU cc_start: 0.8852 (tt0) cc_final: 0.8600 (tt0) REVERT: Y 10 ARG cc_start: 0.9181 (OUTLIER) cc_final: 0.8712 (mtm-85) REVERT: Y 58 LYS cc_start: 0.8998 (ptmm) cc_final: 0.8726 (ptmm) REVERT: b 33 LYS cc_start: 0.9154 (mtmt) cc_final: 0.8838 (mtpp) REVERT: A 51 SER cc_start: 0.9270 (t) cc_final: 0.9067 (m) REVERT: A 58 ASN cc_start: 0.9189 (t0) cc_final: 0.8625 (t0) REVERT: C 1 MET cc_start: 0.8772 (mmm) cc_final: 0.7895 (tpp) REVERT: C 58 ASN cc_start: 0.9352 (t0) cc_final: 0.8994 (t0) REVERT: C 91 ASP cc_start: 0.8195 (t0) cc_final: 0.7931 (t0) REVERT: D 51 SER cc_start: 0.9312 (t) cc_final: 0.9102 (m) REVERT: D 58 ASN cc_start: 0.9194 (t0) cc_final: 0.8809 (t0) REVERT: D 91 ASP cc_start: 0.8257 (t0) cc_final: 0.7979 (t0) REVERT: D 104 GLN cc_start: 0.8439 (tp-100) cc_final: 0.8191 (tp-100) REVERT: G 1 MET cc_start: 0.8789 (mmm) cc_final: 0.7890 (tpp) REVERT: G 58 ASN cc_start: 0.9378 (t0) cc_final: 0.9004 (t0) outliers start: 49 outliers final: 40 residues processed: 339 average time/residue: 0.2343 time to fit residues: 113.3273 Evaluate side-chains 349 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 306 time to evaluate : 1.410 ------------------------------------------------------------------------------- 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 58 LYS Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 92 ASP 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 95 MET 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 37 MET Chi-restraints excluded: chain b residue 51 LEU 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 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 54 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain C residue 4 SER 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 98 VAL Chi-restraints excluded: chain E residue 119 VAL 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 40 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 135 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 55 optimal weight: 0.0570 chunk 44 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 overall best weight: 1.6902 ------------------------------------------------------------------------------- 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 = 0.2599 r_free = 0.2599 target = 0.059934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2448 r_free = 0.2448 target = 0.053495 restraints weight = 33612.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2492 r_free = 0.2492 target = 0.055367 restraints weight = 14777.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.056614 restraints weight = 8179.871| |-----------------------------------------------------------------------------| r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12384 Z= 0.141 Angle : 0.568 8.940 16734 Z= 0.300 Chirality : 0.048 0.152 1752 Planarity : 0.004 0.047 2214 Dihedral : 4.619 52.193 1695 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 3.68 % Allowed : 22.61 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.22), residues: 1488 helix: 2.28 (0.31), residues: 276 sheet: 1.23 (0.28), residues: 378 loop : -1.30 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Y 38 HIS 0.004 0.001 HIS T 113 PHE 0.013 0.001 PHE Q 123 TYR 0.021 0.001 TYR Y 17 ARG 0.005 0.000 ARG C 56 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 472) hydrogen bonds : angle 5.51104 ( 1398) covalent geometry : bond 0.00329 (12384) covalent geometry : angle 0.56781 (16734) *********************** 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 361 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 314 time to evaluate : 1.322 Fit side-chains REVERT: N 33 LYS cc_start: 0.9154 (mmmm) cc_final: 0.8826 (mtpp) REVERT: N 56 LYS cc_start: 0.9238 (mttt) cc_final: 0.8161 (tmtt) REVERT: N 112 LYS cc_start: 0.9088 (mtmt) cc_final: 0.8830 (mtmt) REVERT: Q 25 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8702 (mt-10) REVERT: Q 26 ASN cc_start: 0.8960 (t0) cc_final: 0.8660 (t0) REVERT: Q 92 ASP cc_start: 0.9270 (OUTLIER) cc_final: 0.8738 (t0) REVERT: T 20 PHE cc_start: 0.9261 (OUTLIER) cc_final: 0.8388 (t80) REVERT: T 56 LYS cc_start: 0.9092 (mtmm) cc_final: 0.7976 (tmtt) REVERT: T 106 ILE cc_start: 0.9466 (mm) cc_final: 0.9211 (mm) REVERT: V 103 GLU cc_start: 0.8828 (tt0) cc_final: 0.8575 (tt0) REVERT: Y 10 ARG cc_start: 0.9172 (OUTLIER) cc_final: 0.8687 (mtm-85) REVERT: Y 58 LYS cc_start: 0.8990 (ptmm) cc_final: 0.8714 (ptmm) REVERT: b 33 LYS cc_start: 0.9125 (mtmt) cc_final: 0.8599 (mtpp) REVERT: b 58 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8534 (ptmm) REVERT: A 58 ASN cc_start: 0.9180 (t0) cc_final: 0.8627 (t0) REVERT: B 70 SER cc_start: 0.9122 (m) cc_final: 0.8921 (p) REVERT: C 1 MET cc_start: 0.8767 (mmm) cc_final: 0.7898 (tpp) REVERT: C 58 ASN cc_start: 0.9349 (t0) cc_final: 0.9018 (t0) REVERT: C 91 ASP cc_start: 0.8111 (t0) cc_final: 0.7800 (t0) REVERT: D 51 SER cc_start: 0.9304 (t) cc_final: 0.9093 (m) REVERT: D 58 ASN cc_start: 0.9186 (t0) cc_final: 0.8798 (t0) REVERT: D 91 ASP cc_start: 0.8259 (t0) cc_final: 0.7978 (t0) REVERT: D 104 GLN cc_start: 0.8392 (tp-100) cc_final: 0.8173 (tp-100) REVERT: G 1 MET cc_start: 0.8766 (mmm) cc_final: 0.7881 (tpp) REVERT: G 58 ASN cc_start: 0.9373 (t0) cc_final: 0.9047 (t0) outliers start: 47 outliers final: 39 residues processed: 344 average time/residue: 0.2355 time to fit residues: 114.9714 Evaluate side-chains 349 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 306 time to evaluate : 1.488 ------------------------------------------------------------------------------- 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 58 LYS Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 92 ASP 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 76 VAL Chi-restraints excluded: chain T residue 81 LEU Chi-restraints excluded: chain T residue 119 ILE Chi-restraints excluded: chain V residue 95 MET 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 54 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain C residue 4 SER 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 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 3 optimal weight: 0.0670 chunk 123 optimal weight: 8.9990 chunk 70 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 124 optimal weight: 0.0980 overall best weight: 0.9722 ------------------------------------------------------------------------------- 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 ** Y 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 104 GLN ** 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 = 0.2609 r_free = 0.2609 target = 0.060412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2459 r_free = 0.2459 target = 0.054008 restraints weight = 33630.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.055879 restraints weight = 14731.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.057130 restraints weight = 8126.546| |-----------------------------------------------------------------------------| r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.4160 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= 0.116 Angle : 0.563 8.932 16734 Z= 0.295 Chirality : 0.048 0.152 1752 Planarity : 0.004 0.047 2214 Dihedral : 4.510 52.296 1695 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.29 % Allowed : 23.16 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.22), residues: 1488 helix: 2.33 (0.31), residues: 276 sheet: 0.64 (0.26), residues: 462 loop : -1.20 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Q 38 HIS 0.003 0.001 HIS T 113 PHE 0.013 0.001 PHE Q 123 TYR 0.012 0.001 TYR V 17 ARG 0.005 0.000 ARG C 56 Details of bonding type rmsd hydrogen bonds : bond 0.03523 ( 472) hydrogen bonds : angle 5.40685 ( 1398) covalent geometry : bond 0.00271 (12384) covalent geometry : angle 0.56280 (16734) ********************** 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 357 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 315 time to evaluate : 1.420 Fit side-chains REVERT: N 33 LYS cc_start: 0.9145 (mmmm) cc_final: 0.8815 (mtpp) REVERT: N 56 LYS cc_start: 0.9228 (mttt) cc_final: 0.8164 (tmtt) REVERT: N 112 LYS cc_start: 0.9080 (mtmt) cc_final: 0.8841 (mtmt) REVERT: Q 25 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8670 (mt-10) REVERT: Q 26 ASN cc_start: 0.8899 (t0) cc_final: 0.8603 (t0) REVERT: Q 92 ASP cc_start: 0.9295 (OUTLIER) cc_final: 0.8708 (t0) REVERT: T 20 PHE cc_start: 0.9264 (OUTLIER) cc_final: 0.8386 (t80) REVERT: T 56 LYS cc_start: 0.9082 (mtmm) cc_final: 0.7974 (tmtt) REVERT: T 88 ASP cc_start: 0.8607 (m-30) cc_final: 0.8353 (m-30) REVERT: T 106 ILE cc_start: 0.9465 (mm) cc_final: 0.9244 (mm) REVERT: V 45 GLU cc_start: 0.8365 (mp0) cc_final: 0.8155 (mp0) REVERT: V 103 GLU cc_start: 0.8817 (tt0) cc_final: 0.8570 (tt0) REVERT: Y 10 ARG cc_start: 0.9204 (OUTLIER) cc_final: 0.8625 (mtm-85) REVERT: Y 58 LYS cc_start: 0.8956 (ptmm) cc_final: 0.8704 (ptmm) REVERT: b 33 LYS cc_start: 0.9139 (mtmt) cc_final: 0.8645 (mtpp) REVERT: b 58 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8571 (ptmm) REVERT: A 58 ASN cc_start: 0.9168 (t0) cc_final: 0.8578 (t0) REVERT: A 91 ASP cc_start: 0.8226 (t0) cc_final: 0.7974 (t0) REVERT: B 70 SER cc_start: 0.9113 (m) cc_final: 0.8895 (p) REVERT: C 1 MET cc_start: 0.8755 (mmm) cc_final: 0.7900 (tpp) REVERT: C 58 ASN cc_start: 0.9333 (t0) cc_final: 0.9005 (t0) REVERT: C 91 ASP cc_start: 0.8097 (t0) cc_final: 0.7792 (t0) REVERT: D 58 ASN cc_start: 0.9165 (t0) cc_final: 0.8778 (t0) REVERT: D 91 ASP cc_start: 0.8223 (t0) cc_final: 0.7938 (t0) REVERT: D 104 GLN cc_start: 0.8459 (tp-100) cc_final: 0.8237 (tp-100) REVERT: G 1 MET cc_start: 0.8769 (mmm) cc_final: 0.7888 (tpp) REVERT: G 58 ASN cc_start: 0.9343 (t0) cc_final: 0.8993 (t0) outliers start: 42 outliers final: 33 residues processed: 341 average time/residue: 0.2422 time to fit residues: 117.0238 Evaluate side-chains 340 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 303 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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 58 LYS Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 92 ASP 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 95 MET Chi-restraints excluded: chain Y residue 10 ARG Chi-restraints excluded: chain Y residue 44 ILE Chi-restraints excluded: chain Y residue 51 LEU Chi-restraints excluded: chain b residue 37 MET 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 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 119 VAL Chi-restraints excluded: chain C residue 4 SER 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 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 2 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 51 optimal weight: 0.0670 chunk 30 optimal weight: 8.9990 chunk 99 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 109 GLN ** N 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 65 GLN Y 113 HIS A 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.062333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2506 r_free = 0.2506 target = 0.055946 restraints weight = 33364.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.057842 restraints weight = 14688.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.059091 restraints weight = 8048.879| |-----------------------------------------------------------------------------| r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12384 Z= 0.109 Angle : 0.561 8.812 16734 Z= 0.291 Chirality : 0.048 0.154 1752 Planarity : 0.004 0.047 2214 Dihedral : 4.394 52.499 1694 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.05 % Allowed : 23.63 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.22), residues: 1488 helix: 2.37 (0.30), residues: 276 sheet: 1.20 (0.28), residues: 384 loop : -1.23 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Q 38 HIS 0.003 0.001 HIS V 108 PHE 0.014 0.001 PHE V 70 TYR 0.023 0.001 TYR Y 17 ARG 0.005 0.000 ARG C 56 Details of bonding type rmsd hydrogen bonds : bond 0.03324 ( 472) hydrogen bonds : angle 5.30446 ( 1398) covalent geometry : bond 0.00255 (12384) covalent geometry : angle 0.56071 (16734) =============================================================================== Job complete usr+sys time: 3665.56 seconds wall clock time: 64 minutes 59.81 seconds (3899.81 seconds total)