Starting phenix.real_space_refine on Fri Mar 6 17:31:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wub_21909/03_2026/6wub_21909.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wub_21909/03_2026/6wub_21909.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6wub_21909/03_2026/6wub_21909.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wub_21909/03_2026/6wub_21909.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wub_21909/03_2026/6wub_21909.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wub_21909/03_2026/6wub_21909.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.005 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: 5 Type Number sf(0) Gaussians P 1121 5.49 5 S 26 5.16 5 C 16918 2.51 5 N 6288 2.21 5 O 9596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33949 Number of models: 1 Model: "" Number of chains: 12 Chain: "a" Number of atoms: 24077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 24077 Classifications: {'RNA': 1121} Modifications used: {'rna2p_pur': 85, 'rna2p_pyr': 50, 'rna3p_pur': 562, 'rna3p_pyr': 424} Link IDs: {'rna2p': 135, 'rna3p': 985} Chain breaks: 3 Chain: "d" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1620 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 8, 'TRANS': 192} Chain: "e" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1204 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "f" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 795 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "h" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1041 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 125} Chain: "k" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 863 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain: "l" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1065 Classifications: {'peptide': 136} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 127} Chain: "o" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 741 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "p" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 708 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "q" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 681 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "r" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 537 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "t" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 617 Classifications: {'peptide': 82} Link IDs: {'TRANS': 81} Time building chain proxies: 6.63, per 1000 atoms: 0.20 Number of scatterers: 33949 At special positions: 0 Unit cell: (161.259, 189.781, 173.326, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 P 1121 15.00 O 9596 8.00 N 6288 7.00 C 16918 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: 2.31 Conformation dependent library (CDL) restraints added in 608.0 milliseconds 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2322 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 12 sheets defined 36.5% alpha, 21.3% beta 375 base pairs and 632 stacking pairs defined. Time for finding SS restraints: 4.77 Creating SS restraints... Processing helix chain 'd' and resid 9 through 16 Processing helix chain 'd' and resid 45 through 61 removed outlier: 3.510A pdb=" N MET d 49 " --> pdb=" O SER d 45 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN d 50 " --> pdb=" O GLU d 46 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR d 61 " --> pdb=" O LEU d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 76 Processing helix chain 'd' and resid 83 through 91 removed outlier: 3.589A pdb=" N PHE d 87 " --> pdb=" O HIS d 83 " (cutoff:3.500A) Processing helix chain 'd' and resid 94 through 103 Processing helix chain 'd' and resid 107 through 117 removed outlier: 3.806A pdb=" N ALA d 111 " --> pdb=" O THR d 107 " (cutoff:3.500A) Processing helix chain 'd' and resid 149 through 158 removed outlier: 3.586A pdb=" N GLU d 157 " --> pdb=" O LYS d 153 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA d 158 " --> pdb=" O GLU d 154 " (cutoff:3.500A) Processing helix chain 'd' and resid 182 through 186 Processing helix chain 'd' and resid 193 through 199 removed outlier: 3.540A pdb=" N TYR d 199 " --> pdb=" O VAL d 195 " (cutoff:3.500A) Processing helix chain 'e' and resid 55 through 69 removed outlier: 3.838A pdb=" N LYS e 69 " --> pdb=" O GLU e 65 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 117 removed outlier: 3.643A pdb=" N ALA e 113 " --> pdb=" O GLY e 109 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL e 114 " --> pdb=" O PRO e 110 " (cutoff:3.500A) Processing helix chain 'e' and resid 132 through 145 Processing helix chain 'e' and resid 149 through 157 removed outlier: 3.666A pdb=" N VAL e 153 " --> pdb=" O ARG e 149 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA e 154 " --> pdb=" O ALA e 150 " (cutoff:3.500A) Processing helix chain 'f' and resid 20 through 35 Processing helix chain 'f' and resid 76 through 85 removed outlier: 3.738A pdb=" N ASP f 81 " --> pdb=" O ILE f 77 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 20 Processing helix chain 'h' and resid 30 through 43 Processing helix chain 'h' and resid 115 through 122 Processing helix chain 'k' and resid 48 through 51 Processing helix chain 'k' and resid 53 through 58 Processing helix chain 'k' and resid 59 through 75 removed outlier: 3.747A pdb=" N ALA k 63 " --> pdb=" O THR k 59 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL k 73 " --> pdb=" O ALA k 69 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 102 removed outlier: 3.667A pdb=" N ILE k 97 " --> pdb=" O ARG k 93 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 10 Processing helix chain 'l' and resid 21 through 25 Processing helix chain 'o' and resid 4 through 13 removed outlier: 3.901A pdb=" N ASN o 9 " --> pdb=" O GLN o 5 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 46 removed outlier: 3.938A pdb=" N GLN o 28 " --> pdb=" O SER o 24 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.667A pdb=" N ARG o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) Processing helix chain 'o' and resid 74 through 86 removed outlier: 3.713A pdb=" N GLY o 86 " --> pdb=" O ILE o 82 " (cutoff:3.500A) Processing helix chain 'p' and resid 55 through 61 removed outlier: 3.551A pdb=" N SER p 61 " --> pdb=" O LEU p 57 " (cutoff:3.500A) Processing helix chain 'p' and resid 67 through 76 Processing helix chain 'p' and resid 78 through 88 removed outlier: 3.937A pdb=" N LYS p 82 " --> pdb=" O GLY p 78 " (cutoff:3.500A) Processing helix chain 'r' and resid 15 through 20 removed outlier: 3.722A pdb=" N ASN r 20 " --> pdb=" O TYR r 16 " (cutoff:3.500A) Processing helix chain 'r' and resid 29 through 34 Processing helix chain 'r' and resid 45 through 50 removed outlier: 3.643A pdb=" N THR r 49 " --> pdb=" O PRO r 45 " (cutoff:3.500A) Processing helix chain 'r' and resid 52 through 69 removed outlier: 3.565A pdb=" N ARG r 57 " --> pdb=" O ALA r 53 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE r 68 " --> pdb=" O LYS r 64 " (cutoff:3.500A) Processing helix chain 't' and resid 4 through 40 removed outlier: 3.524A pdb=" N ILE t 8 " --> pdb=" O ILE t 4 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS t 9 " --> pdb=" O GLU t 5 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG t 10 " --> pdb=" O SER t 6 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL t 11 " --> pdb=" O ALA t 7 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG t 12 " --> pdb=" O ILE t 8 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA t 38 " --> pdb=" O LYS t 34 " (cutoff:3.500A) Processing helix chain 't' and resid 46 through 63 removed outlier: 3.648A pdb=" N TYR t 50 " --> pdb=" O VAL t 46 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 80 Processing sheet with id=AA1, first strand: chain 'd' and resid 125 through 126 Processing sheet with id=AA2, first strand: chain 'd' and resid 166 through 169 Processing sheet with id=AA3, first strand: chain 'e' and resid 14 through 24 removed outlier: 5.688A pdb=" N VAL e 15 " --> pdb=" O VAL e 38 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL e 38 " --> pdb=" O VAL e 15 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA e 17 " --> pdb=" O LEU e 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'e' and resid 85 through 88 Processing sheet with id=AA5, first strand: chain 'f' and resid 39 through 50 removed outlier: 6.062A pdb=" N ASN f 67 " --> pdb=" O ILE f 41 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N SER f 43 " --> pdb=" O ILE f 65 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE f 65 " --> pdb=" O SER f 43 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ASP f 45 " --> pdb=" O TYR f 63 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N TYR f 63 " --> pdb=" O ASP f 45 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLU f 47 " --> pdb=" O GLY f 61 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY f 61 " --> pdb=" O GLU f 47 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL f 68 " --> pdb=" O TYR f 7 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N MET f 10 " --> pdb=" O HIS f 93 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N HIS f 93 " --> pdb=" O MET f 10 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE f 12 " --> pdb=" O ILE f 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'f' and resid 39 through 50 removed outlier: 6.062A pdb=" N ASN f 67 " --> pdb=" O ILE f 41 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N SER f 43 " --> pdb=" O ILE f 65 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE f 65 " --> pdb=" O SER f 43 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ASP f 45 " --> pdb=" O TYR f 63 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N TYR f 63 " --> pdb=" O ASP f 45 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLU f 47 " --> pdb=" O GLY f 61 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY f 61 " --> pdb=" O GLU f 47 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL f 68 " --> pdb=" O TYR f 7 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LYS f 6 " --> pdb=" O VAL f 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'h' and resid 25 through 27 removed outlier: 3.650A pdb=" N ASP h 48 " --> pdb=" O PHE h 63 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'h' and resid 77 through 79 removed outlier: 6.805A pdb=" N ILE h 105 " --> pdb=" O ILE h 128 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N TYR h 130 " --> pdb=" O ILE h 103 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ILE h 103 " --> pdb=" O TYR h 130 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY h 111 " --> pdb=" O THR h 108 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'k' and resid 41 through 46 removed outlier: 6.344A pdb=" N VAL k 82 " --> pdb=" O VAL k 107 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA k 109 " --> pdb=" O VAL k 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'l' and resid 43 through 53 removed outlier: 5.875A pdb=" N CYS l 47 " --> pdb=" O ARG l 69 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG l 69 " --> pdb=" O CYS l 47 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG l 49 " --> pdb=" O ARG l 67 " (cutoff:3.500A) removed outlier: 13.538A pdb=" N GLU l 75 " --> pdb=" O VAL l 106 " (cutoff:3.500A) removed outlier: 10.192A pdb=" N TYR l 108 " --> pdb=" O GLU l 75 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N THR l 77 " --> pdb=" O TYR l 108 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE l 110 " --> pdb=" O THR l 77 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N TYR l 79 " --> pdb=" O ILE l 110 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'p' and resid 48 through 50 removed outlier: 3.595A pdb=" N GLU p 48 " --> pdb=" O ASN p 41 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU p 35 " --> pdb=" O VAL p 22 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE p 20 " --> pdb=" O VAL p 37 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N THR p 39 " --> pdb=" O TYR p 18 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N TYR p 18 " --> pdb=" O THR p 39 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'q' and resid 10 through 17 removed outlier: 17.366A pdb=" N VAL q 10 " --> pdb=" O LYS q 31 " (cutoff:3.500A) removed outlier: 14.270A pdb=" N LYS q 31 " --> pdb=" O VAL q 10 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N GLN q 12 " --> pdb=" O GLU q 29 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLU q 29 " --> pdb=" O GLN q 12 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR q 25 " --> pdb=" O VAL q 16 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LEU q 78 " --> pdb=" O MET q 65 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N MET q 65 " --> pdb=" O LEU q 78 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU q 80 " --> pdb=" O LYS q 63 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE q 61 " --> pdb=" O VAL q 82 " (cutoff:3.500A) 414 hydrogen bonds defined for protein. 1167 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 946 hydrogen bonds 1510 hydrogen bond angles 0 basepair planarities 375 basepair parallelities 632 stacking parallelities Total time for adding SS restraints: 12.95 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3684 1.32 - 1.44: 16134 1.44 - 1.56: 14868 1.56 - 1.68: 2238 1.68 - 1.81: 50 Bond restraints: 36974 Sorted by residual: bond pdb=" C ARG q 68 " pdb=" N PRO q 69 " ideal model delta sigma weight residual 1.332 1.307 0.025 1.12e-02 7.97e+03 5.04e+00 bond pdb=" N9 G a 183 " pdb=" C4 G a 183 " ideal model delta sigma weight residual 1.375 1.333 0.042 2.00e-02 2.50e+03 4.41e+00 bond pdb=" P G a 35 " pdb=" O5' G a 35 " ideal model delta sigma weight residual 1.593 1.564 0.029 1.50e-02 4.44e+03 3.73e+00 bond pdb=" CB VAL p 37 " pdb=" CG1 VAL p 37 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.27e+00 bond pdb=" C2 G a 183 " pdb=" N3 G a 183 " ideal model delta sigma weight residual 1.323 1.287 0.036 2.00e-02 2.50e+03 3.21e+00 ... (remaining 36969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 54388 2.71 - 5.42: 1050 5.42 - 8.13: 58 8.13 - 10.84: 9 10.84 - 13.55: 4 Bond angle restraints: 55509 Sorted by residual: angle pdb=" O3' U a 34 " pdb=" P G a 35 " pdb=" O5' G a 35 " ideal model delta sigma weight residual 104.00 112.98 -8.98 1.50e+00 4.44e-01 3.59e+01 angle pdb=" C3' U a 34 " pdb=" O3' U a 34 " pdb=" P G a 35 " ideal model delta sigma weight residual 120.20 111.59 8.61 1.50e+00 4.44e-01 3.29e+01 angle pdb=" C2' C a 31 " pdb=" C1' C a 31 " pdb=" N1 C a 31 " ideal model delta sigma weight residual 114.00 106.92 7.08 1.50e+00 4.44e-01 2.23e+01 angle pdb=" OP1 G a 35 " pdb=" P G a 35 " pdb=" O5' G a 35 " ideal model delta sigma weight residual 108.00 94.45 13.55 3.00e+00 1.11e-01 2.04e+01 angle pdb=" C2' C a 201 " pdb=" C1' C a 201 " pdb=" N1 C a 201 " ideal model delta sigma weight residual 112.00 118.53 -6.53 1.50e+00 4.44e-01 1.89e+01 ... (remaining 55504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.08: 20647 34.08 - 68.15: 2758 68.15 - 102.23: 323 102.23 - 136.30: 5 136.30 - 170.38: 11 Dihedral angle restraints: 23744 sinusoidal: 20143 harmonic: 3601 Sorted by residual: dihedral pdb=" O4' U a 586 " pdb=" C1' U a 586 " pdb=" N1 U a 586 " pdb=" C2 U a 586 " ideal model delta sinusoidal sigma weight residual 200.00 29.62 170.38 1 1.50e+01 4.44e-03 8.47e+01 dihedral pdb=" O4' U a 579 " pdb=" C1' U a 579 " pdb=" N1 U a 579 " pdb=" C2 U a 579 " ideal model delta sinusoidal sigma weight residual -160.00 9.15 -169.15 1 1.50e+01 4.44e-03 8.46e+01 dihedral pdb=" C4' G a1447 " pdb=" C3' G a1447 " pdb=" C2' G a1447 " pdb=" C1' G a1447 " ideal model delta sinusoidal sigma weight residual 36.00 -24.66 60.66 1 8.00e+00 1.56e-02 7.65e+01 ... (remaining 23741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 6312 0.082 - 0.165: 739 0.165 - 0.247: 63 0.247 - 0.329: 8 0.329 - 0.411: 2 Chirality restraints: 7124 Sorted by residual: chirality pdb=" C1' C a 201 " pdb=" O4' C a 201 " pdb=" C2' C a 201 " pdb=" N1 C a 201 " both_signs ideal model delta sigma weight residual False 2.47 2.05 0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" C3' U a 214 " pdb=" C4' U a 214 " pdb=" O3' U a 214 " pdb=" C2' U a 214 " both_signs ideal model delta sigma weight residual False -2.48 -2.11 -0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" C3' C a 37 " pdb=" C4' C a 37 " pdb=" O3' C a 37 " pdb=" C2' C a 37 " both_signs ideal model delta sigma weight residual False -2.48 -2.15 -0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 7121 not shown) Planarity restraints: 2853 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C a 31 " -0.068 2.00e-02 2.50e+03 3.64e-02 2.99e+01 pdb=" N1 C a 31 " 0.081 2.00e-02 2.50e+03 pdb=" C2 C a 31 " 0.005 2.00e-02 2.50e+03 pdb=" O2 C a 31 " 0.004 2.00e-02 2.50e+03 pdb=" N3 C a 31 " -0.005 2.00e-02 2.50e+03 pdb=" C4 C a 31 " -0.016 2.00e-02 2.50e+03 pdb=" N4 C a 31 " -0.013 2.00e-02 2.50e+03 pdb=" C5 C a 31 " -0.004 2.00e-02 2.50e+03 pdb=" C6 C a 31 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U a 255 " 0.064 2.00e-02 2.50e+03 3.51e-02 2.77e+01 pdb=" N1 U a 255 " -0.080 2.00e-02 2.50e+03 pdb=" C2 U a 255 " -0.005 2.00e-02 2.50e+03 pdb=" O2 U a 255 " -0.005 2.00e-02 2.50e+03 pdb=" N3 U a 255 " 0.008 2.00e-02 2.50e+03 pdb=" C4 U a 255 " 0.017 2.00e-02 2.50e+03 pdb=" O4 U a 255 " 0.011 2.00e-02 2.50e+03 pdb=" C5 U a 255 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U a 255 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G a1447 " 0.061 2.00e-02 2.50e+03 2.77e-02 2.30e+01 pdb=" N9 G a1447 " -0.070 2.00e-02 2.50e+03 pdb=" C8 G a1447 " -0.008 2.00e-02 2.50e+03 pdb=" N7 G a1447 " 0.008 2.00e-02 2.50e+03 pdb=" C5 G a1447 " 0.011 2.00e-02 2.50e+03 pdb=" C6 G a1447 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G a1447 " 0.008 2.00e-02 2.50e+03 pdb=" N1 G a1447 " 0.011 2.00e-02 2.50e+03 pdb=" C2 G a1447 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G a1447 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G a1447 " -0.007 2.00e-02 2.50e+03 pdb=" C4 G a1447 " -0.013 2.00e-02 2.50e+03 ... (remaining 2850 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 631 2.60 - 3.18: 24582 3.18 - 3.75: 61162 3.75 - 4.33: 89739 4.33 - 4.90: 118572 Nonbonded interactions: 294686 Sorted by model distance: nonbonded pdb=" O2 U a 858 " pdb=" N4 C a 860 " model vdw 2.029 3.120 nonbonded pdb=" O2' A a 26 " pdb=" O2 C a 27 " model vdw 2.108 3.040 nonbonded pdb=" NH1 ARG e 61 " pdb=" OE2 GLU e 65 " model vdw 2.125 3.120 nonbonded pdb=" O2' C a 483 " pdb=" O4' U a 484 " model vdw 2.137 3.040 nonbonded pdb=" O2' A a1508 " pdb=" O5' A a1509 " model vdw 2.142 3.040 ... (remaining 294681 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 37.350 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 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 : 0.009 0.072 36974 Z= 0.461 Angle : 0.966 13.545 55509 Z= 0.486 Chirality : 0.054 0.411 7124 Planarity : 0.007 0.060 2853 Dihedral : 23.658 170.377 21422 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.41 % Allowed : 13.40 % Favored : 86.19 % Rotamer: Outliers : 18.19 % Allowed : 15.65 % Favored : 66.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.06 (0.20), residues: 1231 helix: -2.07 (0.21), residues: 419 sheet: -1.85 (0.29), residues: 250 loop : -3.62 (0.22), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG l 12 TYR 0.029 0.004 TYR l 28 PHE 0.020 0.003 PHE d 72 TRP 0.020 0.004 TRP d 9 HIS 0.010 0.002 HIS h 22 Details of bonding type rmsd covalent geometry : bond 0.00915 (36974) covalent geometry : angle 0.96582 (55509) hydrogen bonds : bond 0.16103 ( 1348) hydrogen bonds : angle 5.06640 ( 2677) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 268 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: d 9 TRP cc_start: 0.7149 (OUTLIER) cc_final: 0.6912 (t60) REVERT: d 28 ARG cc_start: 0.6992 (OUTLIER) cc_final: 0.6178 (mpt90) REVERT: d 29 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7769 (ptt180) REVERT: d 65 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7464 (mm-30) REVERT: d 114 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8705 (mt) REVERT: d 143 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7280 (ttt-90) REVERT: d 159 THR cc_start: 0.6294 (OUTLIER) cc_final: 0.6022 (p) REVERT: e 41 ASP cc_start: 0.8209 (p0) cc_final: 0.8006 (p0) REVERT: e 101 GLU cc_start: 0.6005 (OUTLIER) cc_final: 0.5531 (mm-30) REVERT: e 112 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7952 (ttm-80) REVERT: h 49 VAL cc_start: 0.8799 (OUTLIER) cc_final: 0.8570 (t) REVERT: h 74 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7978 (mt) REVERT: k 40 ASN cc_start: 0.7599 (OUTLIER) cc_final: 0.7393 (m110) REVERT: k 112 ASP cc_start: 0.7267 (t0) cc_final: 0.7048 (t70) REVERT: k 113 VAL cc_start: 0.8463 (OUTLIER) cc_final: 0.8238 (m) REVERT: l 32 LYS cc_start: 0.6799 (OUTLIER) cc_final: 0.6456 (mtmt) REVERT: l 35 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.6575 (pp30) REVERT: l 63 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7715 (mtt90) REVERT: o 7 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.7068 (tmt170) REVERT: o 12 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7558 (pt) REVERT: o 89 ARG cc_start: 0.3224 (OUTLIER) cc_final: 0.0814 (ptt180) REVERT: t 36 GLU cc_start: 0.6487 (OUTLIER) cc_final: 0.6257 (mm-30) outliers start: 193 outliers final: 108 residues processed: 401 average time/residue: 0.2307 time to fit residues: 143.0673 Evaluate side-chains 329 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 201 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 9 TRP Chi-restraints excluded: chain d residue 14 ARG Chi-restraints excluded: chain d residue 25 GLU Chi-restraints excluded: chain d residue 28 ARG Chi-restraints excluded: chain d residue 29 ARG Chi-restraints excluded: chain d residue 53 GLU Chi-restraints excluded: chain d residue 58 ARG Chi-restraints excluded: chain d residue 63 MET Chi-restraints excluded: chain d residue 65 GLU Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 139 VAL Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 143 ARG Chi-restraints excluded: chain d residue 159 THR Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain d residue 189 GLU Chi-restraints excluded: chain d residue 192 GLU Chi-restraints excluded: chain d residue 202 LYS Chi-restraints excluded: chain e residue 22 THR Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 76 MET Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 101 GLU Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 112 ARG Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 123 ILE Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain e residue 160 SER Chi-restraints excluded: chain e residue 165 ILE Chi-restraints excluded: chain f residue 3 GLN Chi-restraints excluded: chain f residue 4 ASP Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 33 LEU Chi-restraints excluded: chain f residue 36 ASN Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 68 VAL Chi-restraints excluded: chain f residue 77 ILE Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 11 LEU Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 52 ILE Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 57 GLN Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 73 VAL Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 113 ILE Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 40 ASN Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 32 LYS Chi-restraints excluded: chain l residue 35 GLN Chi-restraints excluded: chain l residue 37 ASN Chi-restraints excluded: chain l residue 42 GLN Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 63 ARG Chi-restraints excluded: chain l residue 64 LYS Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 122 ASP Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 12 ILE Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 54 ARG Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 32 ARG Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 44 LYS Chi-restraints excluded: chain p residue 56 VAL Chi-restraints excluded: chain p residue 73 ILE Chi-restraints excluded: chain q residue 10 VAL Chi-restraints excluded: chain q residue 14 ARG Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 30 THR Chi-restraints excluded: chain q residue 42 LYS Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 79 LEU Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 20 ASN Chi-restraints excluded: chain r residue 22 ILE Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain t residue 13 THR Chi-restraints excluded: chain t residue 20 LYS Chi-restraints excluded: chain t residue 36 GLU Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 44 ASP Chi-restraints excluded: chain t residue 62 THR Chi-restraints excluded: chain t residue 81 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 0.2980 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 4.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 55 GLN d 59 HIS d 113 GLN d 147 GLN e 8 HIS e 43 ASN h 57 GLN l 5 ASN l 109 HIS l 125 GLN o 38 GLN o 42 HIS o 46 HIS p 41 ASN p 65 GLN p 72 ASN q 34 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.081677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.068799 restraints weight = 70930.903| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 0.39 r_work: 0.2664 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2583 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 36974 Z= 0.173 Angle : 0.629 9.085 55509 Z= 0.330 Chirality : 0.038 0.278 7124 Planarity : 0.005 0.060 2853 Dihedral : 23.235 170.019 19157 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.53 % Favored : 91.39 % Rotamer: Outliers : 12.25 % Allowed : 19.79 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.22), residues: 1231 helix: -0.51 (0.24), residues: 429 sheet: -1.36 (0.31), residues: 239 loop : -3.11 (0.23), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG o 71 TYR 0.018 0.002 TYR r 27 PHE 0.013 0.002 PHE d 72 TRP 0.015 0.002 TRP d 9 HIS 0.006 0.001 HIS h 22 Details of bonding type rmsd covalent geometry : bond 0.00337 (36974) covalent geometry : angle 0.62889 (55509) hydrogen bonds : bond 0.06715 ( 1348) hydrogen bonds : angle 3.31290 ( 2677) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 204 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: d 114 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8645 (mt) REVERT: d 143 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.6887 (ttt-90) REVERT: e 41 ASP cc_start: 0.8249 (p0) cc_final: 0.7977 (p0) REVERT: e 101 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.6153 (mm-30) REVERT: f 6 LYS cc_start: 0.8034 (mtmt) cc_final: 0.7507 (tttt) REVERT: f 33 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.6906 (tp) REVERT: k 113 VAL cc_start: 0.8495 (OUTLIER) cc_final: 0.8254 (m) REVERT: l 35 GLN cc_start: 0.7442 (OUTLIER) cc_final: 0.7110 (pp30) REVERT: l 53 MET cc_start: 0.8374 (ptp) cc_final: 0.8005 (ptp) REVERT: l 80 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8366 (mt) REVERT: o 29 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8148 (mt) REVERT: o 56 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8608 (tp) REVERT: q 42 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8494 (mttt) outliers start: 130 outliers final: 81 residues processed: 298 average time/residue: 0.2197 time to fit residues: 103.2758 Evaluate side-chains 270 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 179 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 14 ARG Chi-restraints excluded: chain d residue 53 GLU Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 139 VAL Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 143 ARG Chi-restraints excluded: chain d residue 190 ILE Chi-restraints excluded: chain d residue 192 GLU Chi-restraints excluded: chain d residue 202 LYS Chi-restraints excluded: chain e residue 9 LEU Chi-restraints excluded: chain e residue 22 THR Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 79 SER Chi-restraints excluded: chain e residue 84 GLU Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 101 GLU Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain e residue 165 ILE Chi-restraints excluded: chain f residue 3 GLN Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 33 LEU Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 60 GLU Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 68 VAL Chi-restraints excluded: chain f residue 77 ILE Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 52 ILE Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 126 GLU Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 35 GLN Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 60 SER Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 122 ASP Chi-restraints excluded: chain o residue 12 ILE Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 38 GLN Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 32 ARG Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain p residue 56 VAL Chi-restraints excluded: chain q residue 10 VAL Chi-restraints excluded: chain q residue 42 LYS Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 48 VAL Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 44 ASP Chi-restraints excluded: chain t residue 62 THR Chi-restraints excluded: chain t residue 81 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 109 optimal weight: 10.0000 chunk 224 optimal weight: 5.9990 chunk 220 optimal weight: 0.2980 chunk 228 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 211 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 overall best weight: 4.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 87 ASN l 37 ASN o 9 ASN o 38 GLN p 41 ASN p 65 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.079023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 114)---------------| | r_work = 0.2765 r_free = 0.2765 target = 0.062430 restraints weight = 70754.482| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 0.59 r_work: 0.2585 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2499 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 36974 Z= 0.287 Angle : 0.761 9.994 55509 Z= 0.389 Chirality : 0.044 0.304 7124 Planarity : 0.006 0.066 2853 Dihedral : 23.289 172.852 19027 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.89 % Favored : 89.03 % Rotamer: Outliers : 11.78 % Allowed : 20.36 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.22), residues: 1231 helix: -0.24 (0.24), residues: 434 sheet: -0.98 (0.31), residues: 239 loop : -2.98 (0.23), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG l 12 TYR 0.022 0.002 TYR r 27 PHE 0.019 0.002 PHE d 72 TRP 0.019 0.003 TRP d 9 HIS 0.010 0.002 HIS h 22 Details of bonding type rmsd covalent geometry : bond 0.00571 (36974) covalent geometry : angle 0.76102 (55509) hydrogen bonds : bond 0.08611 ( 1348) hydrogen bonds : angle 3.30549 ( 2677) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 173 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: d 17 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7652 (mp) REVERT: d 114 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8682 (mt) REVERT: d 143 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7250 (ttt-90) REVERT: e 41 ASP cc_start: 0.8280 (p0) cc_final: 0.8061 (p0) REVERT: e 101 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6429 (mm-30) REVERT: f 99 GLU cc_start: 0.6714 (OUTLIER) cc_final: 0.6301 (mm-30) REVERT: k 113 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8319 (m) REVERT: l 86 ASN cc_start: 0.8094 (p0) cc_final: 0.7888 (p0) REVERT: o 12 ILE cc_start: 0.7887 (OUTLIER) cc_final: 0.7569 (pt) REVERT: o 29 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8189 (mt) REVERT: t 58 ASP cc_start: 0.7771 (m-30) cc_final: 0.7531 (m-30) outliers start: 125 outliers final: 103 residues processed: 265 average time/residue: 0.2135 time to fit residues: 90.4856 Evaluate side-chains 286 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 175 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 14 ARG Chi-restraints excluded: chain d residue 17 ILE Chi-restraints excluded: chain d residue 53 GLU Chi-restraints excluded: chain d residue 63 MET Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 139 VAL Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 143 ARG Chi-restraints excluded: chain d residue 150 SER Chi-restraints excluded: chain d residue 189 GLU Chi-restraints excluded: chain d residue 190 ILE Chi-restraints excluded: chain d residue 192 GLU Chi-restraints excluded: chain d residue 202 LYS Chi-restraints excluded: chain e residue 9 LEU Chi-restraints excluded: chain e residue 22 THR Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 76 MET Chi-restraints excluded: chain e residue 79 SER Chi-restraints excluded: chain e residue 84 GLU Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 96 MET Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 101 GLU Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain f residue 3 GLN Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 60 GLU Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 68 VAL Chi-restraints excluded: chain f residue 77 ILE Chi-restraints excluded: chain f residue 87 ASN Chi-restraints excluded: chain f residue 99 GLU Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 52 ILE Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 107 VAL Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 35 GLN Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 60 SER Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 122 ASP Chi-restraints excluded: chain o residue 11 ILE Chi-restraints excluded: chain o residue 12 ILE Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 73 THR Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 32 ARG Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain p residue 56 VAL Chi-restraints excluded: chain q residue 10 VAL Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 30 THR Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 32 LEU Chi-restraints excluded: chain r residue 48 VAL Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain t residue 13 THR Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 44 ASP Chi-restraints excluded: chain t residue 62 THR Chi-restraints excluded: chain t residue 81 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 192 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 178 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 116 optimal weight: 8.9990 chunk 49 optimal weight: 8.9990 chunk 138 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 chunk 210 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 142 optimal weight: 7.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 87 ASN l 37 ASN o 9 ASN o 38 GLN p 65 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.080103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.064827 restraints weight = 70532.275| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 0.48 r_work: 0.2616 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2535 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 36974 Z= 0.216 Angle : 0.661 9.161 55509 Z= 0.343 Chirality : 0.040 0.290 7124 Planarity : 0.005 0.051 2853 Dihedral : 23.114 171.962 19017 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.94 % Favored : 90.98 % Rotamer: Outliers : 10.84 % Allowed : 21.68 % Favored : 67.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.23), residues: 1231 helix: 0.24 (0.25), residues: 428 sheet: -0.65 (0.32), residues: 232 loop : -2.75 (0.24), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG l 12 TYR 0.021 0.002 TYR r 27 PHE 0.014 0.002 PHE d 72 TRP 0.017 0.002 TRP d 9 HIS 0.009 0.001 HIS h 22 Details of bonding type rmsd covalent geometry : bond 0.00426 (36974) covalent geometry : angle 0.66070 (55509) hydrogen bonds : bond 0.07330 ( 1348) hydrogen bonds : angle 3.10596 ( 2677) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 177 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 17 ILE cc_start: 0.7793 (OUTLIER) cc_final: 0.7511 (mp) REVERT: d 94 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.6931 (ptm-80) REVERT: d 114 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8695 (mt) REVERT: d 143 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.6407 (ttm-80) REVERT: e 41 ASP cc_start: 0.8233 (p0) cc_final: 0.7968 (p0) REVERT: f 3 GLN cc_start: 0.6461 (OUTLIER) cc_final: 0.5821 (pp30) REVERT: h 36 ILE cc_start: 0.8334 (pt) cc_final: 0.7961 (mt) REVERT: k 113 VAL cc_start: 0.8546 (OUTLIER) cc_final: 0.8297 (m) REVERT: l 63 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.6760 (mtt90) REVERT: o 29 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8100 (mt) REVERT: t 58 ASP cc_start: 0.7758 (m-30) cc_final: 0.7558 (m-30) outliers start: 115 outliers final: 96 residues processed: 258 average time/residue: 0.2200 time to fit residues: 90.6917 Evaluate side-chains 279 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 175 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 14 ARG Chi-restraints excluded: chain d residue 17 ILE Chi-restraints excluded: chain d residue 53 GLU Chi-restraints excluded: chain d residue 63 MET Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 94 ARG Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 139 VAL Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 143 ARG Chi-restraints excluded: chain d residue 150 SER Chi-restraints excluded: chain d residue 189 GLU Chi-restraints excluded: chain d residue 190 ILE Chi-restraints excluded: chain d residue 192 GLU Chi-restraints excluded: chain e residue 22 THR Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 76 MET Chi-restraints excluded: chain e residue 79 SER Chi-restraints excluded: chain e residue 84 GLU Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 96 MET Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain f residue 3 GLN Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 60 GLU Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 68 VAL Chi-restraints excluded: chain f residue 77 ILE Chi-restraints excluded: chain f residue 99 GLU Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 52 ILE Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 126 GLU Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 107 VAL Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 35 GLN Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 63 ARG Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 122 ASP Chi-restraints excluded: chain o residue 11 ILE Chi-restraints excluded: chain o residue 12 ILE Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 38 GLN Chi-restraints excluded: chain o residue 73 THR Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 32 ARG Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain p residue 73 ILE Chi-restraints excluded: chain q residue 10 VAL Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 32 LEU Chi-restraints excluded: chain r residue 34 LYS Chi-restraints excluded: chain r residue 48 VAL Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain t residue 13 THR Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 81 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 152 optimal weight: 0.6980 chunk 74 optimal weight: 10.0000 chunk 228 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 180 optimal weight: 8.9990 chunk 134 optimal weight: 0.7980 chunk 18 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 overall best weight: 4.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 37 ASN p 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.079395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.2770 r_free = 0.2770 target = 0.062689 restraints weight = 70800.675| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 0.58 r_work: 0.2593 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2514 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 36974 Z= 0.254 Angle : 0.707 9.540 55509 Z= 0.364 Chirality : 0.042 0.296 7124 Planarity : 0.005 0.056 2853 Dihedral : 23.144 172.528 19006 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.59 % Favored : 90.25 % Rotamer: Outliers : 12.25 % Allowed : 21.21 % Favored : 66.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.23), residues: 1231 helix: 0.23 (0.25), residues: 433 sheet: -0.55 (0.33), residues: 232 loop : -2.76 (0.24), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG l 12 TYR 0.022 0.002 TYR r 27 PHE 0.016 0.002 PHE d 72 TRP 0.019 0.002 TRP d 9 HIS 0.008 0.002 HIS h 22 Details of bonding type rmsd covalent geometry : bond 0.00502 (36974) covalent geometry : angle 0.70681 (55509) hydrogen bonds : bond 0.08014 ( 1348) hydrogen bonds : angle 3.15380 ( 2677) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 172 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 17 ILE cc_start: 0.7825 (OUTLIER) cc_final: 0.7551 (mp) REVERT: d 94 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.6712 (ptm-80) REVERT: d 114 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8718 (mt) REVERT: d 143 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.6946 (ttt-90) REVERT: e 41 ASP cc_start: 0.8238 (p0) cc_final: 0.7982 (p0) REVERT: e 101 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6473 (mm-30) REVERT: h 36 ILE cc_start: 0.8351 (pt) cc_final: 0.7972 (mt) REVERT: k 113 VAL cc_start: 0.8555 (OUTLIER) cc_final: 0.8291 (m) REVERT: l 63 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.6745 (mtt90) REVERT: o 29 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8165 (mt) REVERT: p 32 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7008 (ptp-170) REVERT: t 58 ASP cc_start: 0.7733 (m-30) cc_final: 0.7525 (m-30) outliers start: 130 outliers final: 104 residues processed: 266 average time/residue: 0.2170 time to fit residues: 91.6868 Evaluate side-chains 285 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 172 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 14 ARG Chi-restraints excluded: chain d residue 17 ILE Chi-restraints excluded: chain d residue 53 GLU Chi-restraints excluded: chain d residue 63 MET Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 94 ARG Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 139 VAL Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 143 ARG Chi-restraints excluded: chain d residue 150 SER Chi-restraints excluded: chain d residue 152 ILE Chi-restraints excluded: chain d residue 189 GLU Chi-restraints excluded: chain d residue 190 ILE Chi-restraints excluded: chain d residue 192 GLU Chi-restraints excluded: chain e residue 4 ILE Chi-restraints excluded: chain e residue 9 LEU Chi-restraints excluded: chain e residue 22 THR Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 76 MET Chi-restraints excluded: chain e residue 79 SER Chi-restraints excluded: chain e residue 84 GLU Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 96 MET Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 101 GLU Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain f residue 3 GLN Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 60 GLU Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 68 VAL Chi-restraints excluded: chain f residue 77 ILE Chi-restraints excluded: chain f residue 87 ASN Chi-restraints excluded: chain f residue 99 GLU Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 52 ILE Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 107 VAL Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 35 GLN Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 63 ARG Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 122 ASP Chi-restraints excluded: chain o residue 11 ILE Chi-restraints excluded: chain o residue 12 ILE Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 73 THR Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 32 ARG Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain p residue 73 ILE Chi-restraints excluded: chain q residue 10 VAL Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 30 THR Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 32 LEU Chi-restraints excluded: chain r residue 34 LYS Chi-restraints excluded: chain r residue 48 VAL Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain t residue 13 THR Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 81 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 214 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 53 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 226 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 220 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 18 ASN l 37 ASN o 9 ASN p 65 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.079162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.064080 restraints weight = 70451.941| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 0.46 r_work: 0.2600 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 36974 Z= 0.269 Angle : 0.722 9.691 55509 Z= 0.372 Chirality : 0.043 0.301 7124 Planarity : 0.006 0.058 2853 Dihedral : 23.152 172.661 19006 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.42 % Favored : 90.41 % Rotamer: Outliers : 12.44 % Allowed : 21.11 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.23), residues: 1231 helix: 0.26 (0.25), residues: 433 sheet: -0.62 (0.33), residues: 238 loop : -2.70 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG l 12 TYR 0.022 0.002 TYR r 27 PHE 0.017 0.002 PHE d 72 TRP 0.020 0.003 TRP d 9 HIS 0.008 0.002 HIS h 22 Details of bonding type rmsd covalent geometry : bond 0.00534 (36974) covalent geometry : angle 0.72244 (55509) hydrogen bonds : bond 0.08184 ( 1348) hydrogen bonds : angle 3.15973 ( 2677) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 173 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 17 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7573 (mp) REVERT: d 94 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.6659 (ptm-80) REVERT: d 114 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8711 (mt) REVERT: d 143 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.6504 (ttm-80) REVERT: e 101 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6459 (mm-30) REVERT: h 36 ILE cc_start: 0.8363 (pt) cc_final: 0.7968 (mt) REVERT: k 113 VAL cc_start: 0.8560 (OUTLIER) cc_final: 0.8297 (m) REVERT: l 63 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.6766 (mtt90) REVERT: o 29 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8184 (mt) REVERT: p 32 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.6985 (ptp-170) REVERT: t 58 ASP cc_start: 0.7753 (m-30) cc_final: 0.7511 (m-30) outliers start: 132 outliers final: 111 residues processed: 269 average time/residue: 0.2146 time to fit residues: 92.0570 Evaluate side-chains 290 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 170 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 14 ARG Chi-restraints excluded: chain d residue 17 ILE Chi-restraints excluded: chain d residue 53 GLU Chi-restraints excluded: chain d residue 63 MET Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 94 ARG Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 139 VAL Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 143 ARG Chi-restraints excluded: chain d residue 150 SER Chi-restraints excluded: chain d residue 152 ILE Chi-restraints excluded: chain d residue 189 GLU Chi-restraints excluded: chain d residue 190 ILE Chi-restraints excluded: chain d residue 192 GLU Chi-restraints excluded: chain e residue 4 ILE Chi-restraints excluded: chain e residue 9 LEU Chi-restraints excluded: chain e residue 22 THR Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 76 MET Chi-restraints excluded: chain e residue 79 SER Chi-restraints excluded: chain e residue 84 GLU Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 96 MET Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 101 GLU Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain e residue 165 ILE Chi-restraints excluded: chain f residue 3 GLN Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 33 LEU Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 54 GLU Chi-restraints excluded: chain f residue 60 GLU Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 68 VAL Chi-restraints excluded: chain f residue 77 ILE Chi-restraints excluded: chain f residue 87 ASN Chi-restraints excluded: chain f residue 99 GLU Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 52 ILE Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 73 VAL Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 107 VAL Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 34 THR Chi-restraints excluded: chain l residue 35 GLN Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 63 ARG Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 122 ASP Chi-restraints excluded: chain o residue 11 ILE Chi-restraints excluded: chain o residue 12 ILE Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 73 THR Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 32 ARG Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain p residue 73 ILE Chi-restraints excluded: chain q residue 10 VAL Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 30 THR Chi-restraints excluded: chain q residue 32 LYS Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 32 LEU Chi-restraints excluded: chain r residue 34 LYS Chi-restraints excluded: chain r residue 48 VAL Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain t residue 13 THR Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 81 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 146 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 chunk 106 optimal weight: 10.0000 chunk 154 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 205 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 38 GLN p 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.079586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.063000 restraints weight = 70759.400| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 0.57 r_work: 0.2592 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 36974 Z= 0.207 Angle : 0.681 9.590 55509 Z= 0.354 Chirality : 0.040 0.294 7124 Planarity : 0.005 0.053 2853 Dihedral : 23.145 172.664 19006 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.26 % Favored : 90.58 % Rotamer: Outliers : 12.06 % Allowed : 21.77 % Favored : 66.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.23), residues: 1231 helix: 0.36 (0.25), residues: 433 sheet: -0.61 (0.33), residues: 238 loop : -2.67 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG r 40 TYR 0.022 0.002 TYR r 27 PHE 0.014 0.002 PHE d 72 TRP 0.018 0.002 TRP d 9 HIS 0.008 0.001 HIS h 22 Details of bonding type rmsd covalent geometry : bond 0.00406 (36974) covalent geometry : angle 0.68060 (55509) hydrogen bonds : bond 0.07736 ( 1348) hydrogen bonds : angle 3.12206 ( 2677) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 172 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 17 ILE cc_start: 0.7830 (OUTLIER) cc_final: 0.7549 (mp) REVERT: d 94 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.6630 (ptm-80) REVERT: d 114 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8703 (mt) REVERT: d 143 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.6485 (ttm-80) REVERT: e 101 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6530 (mm-30) REVERT: f 3 GLN cc_start: 0.6433 (OUTLIER) cc_final: 0.5894 (pp30) REVERT: h 36 ILE cc_start: 0.8354 (pt) cc_final: 0.7968 (mt) REVERT: k 113 VAL cc_start: 0.8552 (OUTLIER) cc_final: 0.8289 (m) REVERT: l 63 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.6758 (mtt90) REVERT: o 29 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8156 (mt) REVERT: r 33 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8490 (mp) REVERT: t 58 ASP cc_start: 0.7767 (m-30) cc_final: 0.7525 (m-30) outliers start: 128 outliers final: 108 residues processed: 267 average time/residue: 0.2109 time to fit residues: 90.0670 Evaluate side-chains 289 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 171 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 14 ARG Chi-restraints excluded: chain d residue 17 ILE Chi-restraints excluded: chain d residue 53 GLU Chi-restraints excluded: chain d residue 63 MET Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 94 ARG Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 139 VAL Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 143 ARG Chi-restraints excluded: chain d residue 150 SER Chi-restraints excluded: chain d residue 152 ILE Chi-restraints excluded: chain d residue 189 GLU Chi-restraints excluded: chain d residue 190 ILE Chi-restraints excluded: chain d residue 192 GLU Chi-restraints excluded: chain e residue 4 ILE Chi-restraints excluded: chain e residue 9 LEU Chi-restraints excluded: chain e residue 22 THR Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain e residue 76 MET Chi-restraints excluded: chain e residue 79 SER Chi-restraints excluded: chain e residue 84 GLU Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 96 MET Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 101 GLU Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain e residue 165 ILE Chi-restraints excluded: chain f residue 3 GLN Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 54 GLU Chi-restraints excluded: chain f residue 60 GLU Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 68 VAL Chi-restraints excluded: chain f residue 77 ILE Chi-restraints excluded: chain f residue 87 ASN Chi-restraints excluded: chain f residue 99 GLU Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 52 ILE Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 73 VAL Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 107 VAL Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 35 GLN Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 63 ARG Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 122 ASP Chi-restraints excluded: chain o residue 11 ILE Chi-restraints excluded: chain o residue 12 ILE Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 38 GLN Chi-restraints excluded: chain o residue 73 THR Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 32 ARG Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain q residue 10 VAL Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 30 THR Chi-restraints excluded: chain q residue 32 LYS Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 32 LEU Chi-restraints excluded: chain r residue 33 LEU Chi-restraints excluded: chain r residue 48 VAL Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain t residue 13 THR Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 81 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 86 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 56 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 201 optimal weight: 8.9990 chunk 147 optimal weight: 9.9990 chunk 184 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 218 optimal weight: 0.3980 overall best weight: 6.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 9 ASN o 38 GLN p 65 GLN ** r 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.077899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.064634 restraints weight = 70492.974| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 0.47 r_work: 0.2564 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2488 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 36974 Z= 0.368 Angle : 0.845 11.400 55509 Z= 0.427 Chirality : 0.048 0.340 7124 Planarity : 0.007 0.081 2853 Dihedral : 23.301 172.980 19006 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.37 % Favored : 88.46 % Rotamer: Outliers : 12.16 % Allowed : 22.15 % Favored : 65.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.23), residues: 1231 helix: 0.05 (0.24), residues: 435 sheet: -0.68 (0.32), residues: 245 loop : -2.75 (0.24), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG l 12 TYR 0.024 0.003 TYR r 27 PHE 0.021 0.003 PHE d 72 TRP 0.024 0.003 TRP d 9 HIS 0.009 0.002 HIS h 22 Details of bonding type rmsd covalent geometry : bond 0.00735 (36974) covalent geometry : angle 0.84510 (55509) hydrogen bonds : bond 0.09692 ( 1348) hydrogen bonds : angle 3.32905 ( 2677) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 175 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 17 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7705 (mp) REVERT: d 114 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8706 (mt) REVERT: d 143 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7307 (ttt-90) REVERT: e 101 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6545 (mm-30) REVERT: k 113 VAL cc_start: 0.8535 (OUTLIER) cc_final: 0.8295 (m) REVERT: l 63 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.6837 (mtt90) REVERT: o 12 ILE cc_start: 0.7932 (OUTLIER) cc_final: 0.7653 (pt) REVERT: o 29 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8294 (mt) REVERT: p 54 ASP cc_start: 0.6715 (p0) cc_final: 0.6425 (p0) REVERT: r 17 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8676 (mm) REVERT: r 33 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8522 (mp) REVERT: t 58 ASP cc_start: 0.7792 (m-30) cc_final: 0.7549 (m-30) outliers start: 129 outliers final: 109 residues processed: 268 average time/residue: 0.2206 time to fit residues: 94.2173 Evaluate side-chains 292 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 173 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 14 ARG Chi-restraints excluded: chain d residue 17 ILE Chi-restraints excluded: chain d residue 63 MET Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 139 VAL Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 143 ARG Chi-restraints excluded: chain d residue 150 SER Chi-restraints excluded: chain d residue 152 ILE Chi-restraints excluded: chain d residue 189 GLU Chi-restraints excluded: chain d residue 190 ILE Chi-restraints excluded: chain d residue 192 GLU Chi-restraints excluded: chain e residue 4 ILE Chi-restraints excluded: chain e residue 9 LEU Chi-restraints excluded: chain e residue 22 THR Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 76 MET Chi-restraints excluded: chain e residue 79 SER Chi-restraints excluded: chain e residue 84 GLU Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 96 MET Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 101 GLU Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain f residue 3 GLN Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 33 LEU Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 54 GLU Chi-restraints excluded: chain f residue 60 GLU Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 68 VAL Chi-restraints excluded: chain f residue 77 ILE Chi-restraints excluded: chain f residue 87 ASN Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain f residue 99 GLU Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 52 ILE Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 73 VAL Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 107 VAL Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 34 THR Chi-restraints excluded: chain l residue 35 GLN Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 63 ARG Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 122 ASP Chi-restraints excluded: chain o residue 11 ILE Chi-restraints excluded: chain o residue 12 ILE Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 32 ARG Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain p residue 73 ILE Chi-restraints excluded: chain q residue 10 VAL Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 30 THR Chi-restraints excluded: chain q residue 32 LYS Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 17 ILE Chi-restraints excluded: chain r residue 32 LEU Chi-restraints excluded: chain r residue 33 LEU Chi-restraints excluded: chain r residue 34 LYS Chi-restraints excluded: chain r residue 48 VAL Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain t residue 13 THR Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 81 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 105 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 197 optimal weight: 0.9990 chunk 153 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 208 optimal weight: 1.9990 chunk 184 optimal weight: 0.8980 chunk 214 optimal weight: 5.9990 chunk 118 optimal weight: 0.7980 chunk 48 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 38 GLN p 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.083636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.072033 restraints weight = 70790.913| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 0.34 r_work: 0.2742 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 36974 Z= 0.122 Angle : 0.554 7.856 55509 Z= 0.290 Chirality : 0.034 0.264 7124 Planarity : 0.004 0.048 2853 Dihedral : 22.939 170.720 19003 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.88 % Favored : 92.04 % Rotamer: Outliers : 8.86 % Allowed : 24.98 % Favored : 66.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.24), residues: 1231 helix: 0.77 (0.26), residues: 428 sheet: -0.43 (0.33), residues: 229 loop : -2.46 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG r 40 TYR 0.020 0.001 TYR r 27 PHE 0.009 0.001 PHE f 58 TRP 0.016 0.002 TRP d 9 HIS 0.005 0.001 HIS h 22 Details of bonding type rmsd covalent geometry : bond 0.00232 (36974) covalent geometry : angle 0.55352 (55509) hydrogen bonds : bond 0.05827 ( 1348) hydrogen bonds : angle 2.85665 ( 2677) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 190 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 17 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7437 (mp) REVERT: d 114 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8656 (mt) REVERT: d 192 GLU cc_start: 0.5951 (OUTLIER) cc_final: 0.5584 (pm20) REVERT: e 4 ILE cc_start: 0.6747 (OUTLIER) cc_final: 0.6423 (pt) REVERT: e 101 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6172 (mm-30) REVERT: e 165 ILE cc_start: 0.6676 (pp) cc_final: 0.6464 (pt) REVERT: f 3 GLN cc_start: 0.6334 (OUTLIER) cc_final: 0.5849 (pp30) REVERT: f 99 GLU cc_start: 0.6289 (OUTLIER) cc_final: 0.5862 (tp30) REVERT: h 36 ILE cc_start: 0.8194 (pt) cc_final: 0.7935 (mt) REVERT: h 68 LYS cc_start: 0.8052 (mmmt) cc_final: 0.7679 (pttt) REVERT: o 12 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.7676 (pt) REVERT: o 29 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.7826 (mt) REVERT: q 57 LYS cc_start: 0.7006 (mmtm) cc_final: 0.6796 (mptt) outliers start: 94 outliers final: 71 residues processed: 260 average time/residue: 0.2161 time to fit residues: 90.4735 Evaluate side-chains 257 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 177 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 14 ARG Chi-restraints excluded: chain d residue 17 ILE Chi-restraints excluded: chain d residue 53 GLU Chi-restraints excluded: chain d residue 63 MET Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 189 GLU Chi-restraints excluded: chain d residue 192 GLU Chi-restraints excluded: chain e residue 4 ILE Chi-restraints excluded: chain e residue 22 THR Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 79 SER Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 96 MET Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 101 GLU Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain f residue 3 GLN Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 60 GLU Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 68 VAL Chi-restraints excluded: chain f residue 87 ASN Chi-restraints excluded: chain f residue 99 GLU Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 107 VAL Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 122 ASP Chi-restraints excluded: chain o residue 12 ILE Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 32 ARG Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain q residue 10 VAL Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 32 LYS Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 34 LYS Chi-restraints excluded: chain r residue 48 VAL Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 81 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 5 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 217 optimal weight: 6.9990 chunk 198 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 180 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 38 GLN t 45 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.079255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.064300 restraints weight = 70764.080| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 0.47 r_work: 0.2585 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2501 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 36974 Z= 0.270 Angle : 0.727 9.662 55509 Z= 0.372 Chirality : 0.042 0.297 7124 Planarity : 0.006 0.060 2853 Dihedral : 23.070 172.519 18986 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.83 % Favored : 90.09 % Rotamer: Outliers : 8.20 % Allowed : 25.92 % Favored : 65.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.23), residues: 1231 helix: 0.46 (0.25), residues: 433 sheet: -0.48 (0.33), residues: 240 loop : -2.52 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG l 12 TYR 0.022 0.002 TYR r 27 PHE 0.020 0.003 PHE k 61 TRP 0.020 0.002 TRP d 9 HIS 0.009 0.001 HIS h 22 Details of bonding type rmsd covalent geometry : bond 0.00538 (36974) covalent geometry : angle 0.72658 (55509) hydrogen bonds : bond 0.08219 ( 1348) hydrogen bonds : angle 3.10493 ( 2677) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 177 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 17 ILE cc_start: 0.7830 (OUTLIER) cc_final: 0.7504 (mp) REVERT: d 114 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8684 (mt) REVERT: e 4 ILE cc_start: 0.6555 (OUTLIER) cc_final: 0.6281 (pt) REVERT: e 43 ASN cc_start: 0.7765 (t0) cc_final: 0.7487 (t0) REVERT: e 101 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6608 (mm-30) REVERT: f 3 GLN cc_start: 0.6329 (OUTLIER) cc_final: 0.5696 (pp30) REVERT: h 36 ILE cc_start: 0.8341 (pt) cc_final: 0.7966 (mt) REVERT: o 29 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8164 (mt) REVERT: p 32 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.6951 (ptp-170) REVERT: p 54 ASP cc_start: 0.6725 (p0) cc_final: 0.6485 (p0) REVERT: q 57 LYS cc_start: 0.7369 (mmtm) cc_final: 0.7101 (mptt) REVERT: t 58 ASP cc_start: 0.7725 (m-30) cc_final: 0.7467 (m-30) outliers start: 87 outliers final: 79 residues processed: 247 average time/residue: 0.2122 time to fit residues: 84.0624 Evaluate side-chains 259 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 173 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 14 ARG Chi-restraints excluded: chain d residue 17 ILE Chi-restraints excluded: chain d residue 53 GLU Chi-restraints excluded: chain d residue 63 MET Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 189 GLU Chi-restraints excluded: chain d residue 192 GLU Chi-restraints excluded: chain e residue 4 ILE Chi-restraints excluded: chain e residue 22 THR Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 79 SER Chi-restraints excluded: chain e residue 84 GLU Chi-restraints excluded: chain e residue 95 LEU Chi-restraints excluded: chain e residue 96 MET Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 101 GLU Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain f residue 3 GLN Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 54 GLU Chi-restraints excluded: chain f residue 60 GLU Chi-restraints excluded: chain f residue 65 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 68 VAL Chi-restraints excluded: chain f residue 87 ASN Chi-restraints excluded: chain f residue 99 GLU Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 89 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 107 VAL Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 122 ASP Chi-restraints excluded: chain o residue 11 ILE Chi-restraints excluded: chain o residue 12 ILE Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 38 GLN Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 32 ARG Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain q residue 10 VAL Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 32 LYS Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 34 LYS Chi-restraints excluded: chain r residue 48 VAL Chi-restraints excluded: chain r residue 63 ILE Chi-restraints excluded: chain t residue 13 THR Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 81 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 227 optimal weight: 3.9990 chunk 229 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 120 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 210 optimal weight: 0.4980 chunk 126 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 37 ASN o 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.081787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.065471 restraints weight = 70471.461| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 0.57 r_work: 0.2650 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.110 36974 Z= 0.123 Angle : 0.596 10.930 55509 Z= 0.316 Chirality : 0.036 0.256 7124 Planarity : 0.005 0.058 2853 Dihedral : 23.022 171.746 18986 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.61 % Favored : 91.31 % Rotamer: Outliers : 7.73 % Allowed : 26.30 % Favored : 65.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.24), residues: 1231 helix: 0.75 (0.26), residues: 427 sheet: -0.30 (0.34), residues: 233 loop : -2.35 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG r 40 TYR 0.018 0.001 TYR r 27 PHE 0.039 0.002 PHE k 61 TRP 0.018 0.002 TRP d 9 HIS 0.006 0.001 HIS e 83 Details of bonding type rmsd covalent geometry : bond 0.00234 (36974) covalent geometry : angle 0.59649 (55509) hydrogen bonds : bond 0.06407 ( 1348) hydrogen bonds : angle 2.97922 ( 2677) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7777.23 seconds wall clock time: 133 minutes 40.16 seconds (8020.16 seconds total)