Starting phenix.real_space_refine on Mon Jul 6 09:19:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7bgd_12178/07_2026/7bgd_12178.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bgd_12178/07_2026/7bgd_12178.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/7bgd_12178/07_2026/7bgd_12178.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bgd_12178/07_2026/7bgd_12178.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bgd_12178/07_2026/7bgd_12178.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bgd_12178/07_2026/7bgd_12178.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7bgd_12178/07_2026/7bgd_12178.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7bgd_12178/07_2026/7bgd_12178.cif" } 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= 0.008 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 1128 5.49 5 S 30 5.16 5 C 17806 2.51 5 N 6522 2.21 5 O 9878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35364 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 693 Classifications: {'RNA': 32} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 4, 'rna3p_pur': 13, 'rna3p_pyr': 5} Link IDs: {'rna2p': 14, 'rna3p': 17} Chain: "a" Number of atoms: 23497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1096, 23497 Classifications: {'RNA': 1096} Modifications used: {'rna2p_pur': 81, 'rna2p_pyr': 59, 'rna3p_pur': 542, 'rna3p_pyr': 414} Link IDs: {'rna2p': 140, 'rna3p': 955} Chain breaks: 1 Chain: "b" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1299 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 6, 'TRANS': 156} Chain breaks: 2 Chain: "d" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1595 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 187} Chain breaks: 1 Chain: "e" Number of atoms: 1169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1169 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain: "f" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 798 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 1, 'TRANS': 94} Chain: "h" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1032 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "k" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 880 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain: "l" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1058 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "o" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 738 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "p" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 712 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 84} Chain: "q" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 707 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "r" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 580 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "t" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 606 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Time building chain proxies: 7.21, per 1000 atoms: 0.20 Number of scatterers: 35364 At special positions: 0 Unit cell: (145.18, 183.26, 172.55, 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 30 16.00 P 1128 15.00 O 9878 8.00 N 6522 7.00 C 17806 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: 3.12 Conformation dependent library (CDL) restraints added in 735.0 milliseconds 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2616 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 14 sheets defined 34.7% alpha, 17.7% beta 359 base pairs and 687 stacking pairs defined. Time for finding SS restraints: 6.04 Creating SS restraints... Processing helix chain 'b' and resid 27 through 29 No H-bonds generated for 'chain 'b' and resid 27 through 29' Processing helix chain 'b' and resid 43 through 60 Processing helix chain 'b' and resid 61 through 63 No H-bonds generated for 'chain 'b' and resid 61 through 63' Processing helix chain 'b' and resid 77 through 82 Processing helix chain 'b' and resid 206 through 223 removed outlier: 3.631A pdb=" N VAL b 210 " --> pdb=" O ALA b 206 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU b 213 " --> pdb=" O ALA b 209 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA b 218 " --> pdb=" O THR b 214 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 14 removed outlier: 3.633A pdb=" N ARG d 14 " --> pdb=" O LYS d 10 " (cutoff:3.500A) Processing helix chain 'd' and resid 45 through 62 removed outlier: 3.597A pdb=" N LEU d 60 " --> pdb=" O LYS d 56 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR d 61 " --> pdb=" O LEU d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 74 Processing helix chain 'd' and resid 81 through 91 removed outlier: 3.604A pdb=" N ALA d 91 " --> pdb=" O MET d 87 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 101 Processing helix chain 'd' and resid 106 through 116 Processing helix chain 'd' and resid 142 through 146 removed outlier: 4.203A pdb=" N GLN d 146 " --> pdb=" O GLU d 143 " (cutoff:3.500A) Processing helix chain 'd' and resid 148 through 157 removed outlier: 3.751A pdb=" N GLU d 156 " --> pdb=" O VAL d 152 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE d 157 " --> pdb=" O GLU d 153 " (cutoff:3.500A) Processing helix chain 'd' and resid 191 through 196 removed outlier: 3.575A pdb=" N VAL d 195 " --> pdb=" O GLU d 191 " (cutoff:3.500A) Processing helix chain 'e' and resid 55 through 68 Processing helix chain 'e' and resid 109 through 116 removed outlier: 3.668A pdb=" N ALA e 113 " --> pdb=" O GLY e 109 " (cutoff:3.500A) Processing helix chain 'e' and resid 132 through 146 Processing helix chain 'e' and resid 149 through 157 Processing helix chain 'f' and resid 15 through 30 removed outlier: 3.512A pdb=" N LYS f 20 " --> pdb=" O GLU f 16 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA f 21 " --> pdb=" O ASP f 17 " (cutoff:3.500A) Processing helix chain 'f' and resid 72 through 83 removed outlier: 3.785A pdb=" N LYS f 81 " --> pdb=" O GLN f 77 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE f 82 " --> pdb=" O ARG f 78 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 20 removed outlier: 3.811A pdb=" N VAL h 20 " --> pdb=" O ASN h 16 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 43 Processing helix chain 'h' and resid 96 through 101 Processing helix chain 'h' and resid 114 through 121 removed outlier: 3.766A pdb=" N ARG h 121 " --> pdb=" O GLU h 117 " (cutoff:3.500A) Processing helix chain 'k' and resid 46 through 51 removed outlier: 3.792A pdb=" N LEU k 50 " --> pdb=" O ALA k 47 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY k 51 " --> pdb=" O GLY k 48 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 57 removed outlier: 3.667A pdb=" N LYS k 57 " --> pdb=" O GLY k 54 " (cutoff:3.500A) Processing helix chain 'k' and resid 59 through 78 removed outlier: 3.771A pdb=" N ALA k 63 " --> pdb=" O THR k 59 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER k 73 " --> pdb=" O THR k 69 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 103 removed outlier: 3.812A pdb=" N ALA k 96 " --> pdb=" O GLY k 92 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE k 97 " --> pdb=" O ARG k 93 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG k 98 " --> pdb=" O GLU k 94 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 8 Processing helix chain 'o' and resid 4 through 12 Processing helix chain 'o' and resid 24 through 46 removed outlier: 3.621A pdb=" N ARG o 44 " --> pdb=" O ASN o 40 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N THR o 45 " --> pdb=" O GLU o 41 " (cutoff:3.500A) Processing helix chain 'o' and resid 50 through 74 removed outlier: 4.021A pdb=" N ARG o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) Processing helix chain 'o' and resid 74 through 86 removed outlier: 3.571A pdb=" N GLY o 86 " --> pdb=" O ILE o 82 " (cutoff:3.500A) Processing helix chain 'p' and resid 55 through 63 removed outlier: 3.569A pdb=" N ASP p 63 " --> pdb=" O LYS p 59 " (cutoff:3.500A) Processing helix chain 'p' and resid 68 through 78 Processing helix chain 'p' and resid 79 through 89 removed outlier: 3.517A pdb=" N LYS p 83 " --> pdb=" O GLY p 79 " (cutoff:3.500A) Processing helix chain 'r' and resid 30 through 35 removed outlier: 3.644A pdb=" N LEU r 34 " --> pdb=" O ASP r 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 46 through 51 Processing helix chain 'r' and resid 53 through 70 Processing helix chain 't' and resid 8 through 38 removed outlier: 3.849A pdb=" N LYS t 12 " --> pdb=" O ILE t 8 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN t 24 " --> pdb=" O ARG t 20 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA t 27 " --> pdb=" O SER t 23 " (cutoff:3.500A) Processing helix chain 't' and resid 45 through 63 removed outlier: 3.797A pdb=" N LEU t 49 " --> pdb=" O ASN t 45 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER t 51 " --> pdb=" O ASN t 47 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS t 55 " --> pdb=" O SER t 51 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL t 57 " --> pdb=" O ALA t 53 " (cutoff:3.500A) Processing helix chain 't' and resid 74 through 79 Processing sheet with id=AA1, first strand: chain 'b' and resid 31 through 35 removed outlier: 4.087A pdb=" N THR b 33 " --> pdb=" O ILE b 40 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE b 38 " --> pdb=" O ARG b 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'b' and resid 90 through 91 removed outlier: 3.936A pdb=" N PHE b 69 " --> pdb=" O PHE b 90 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LEU b 68 " --> pdb=" O PHE b 162 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL b 163 " --> pdb=" O ILE b 186 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLY b 185 " --> pdb=" O ILE b 200 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'd' and resid 124 through 126 removed outlier: 3.946A pdb=" N VAL d 126 " --> pdb=" O ILE d 119 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ILE d 119 " --> pdb=" O VAL d 126 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN d 166 " --> pdb=" O THR d 175 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'e' and resid 14 through 24 removed outlier: 5.017A pdb=" N VAL e 15 " --> pdb=" O VAL e 38 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL e 38 " --> pdb=" O VAL e 15 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'e' and resid 85 through 87 removed outlier: 6.369A pdb=" N ILE e 106 " --> pdb=" O SER e 125 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N SER e 127 " --> pdb=" O ILE e 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'f' and resid 36 through 40 removed outlier: 5.653A pdb=" N VAL f 37 " --> pdb=" O LYS f 66 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LYS f 66 " --> pdb=" O VAL f 37 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'f' and resid 36 through 40 removed outlier: 5.653A pdb=" N VAL f 37 " --> pdb=" O LYS f 66 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LYS f 66 " --> pdb=" O VAL f 37 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG f 88 " --> pdb=" O ILE f 9 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'h' and resid 24 through 26 removed outlier: 3.745A pdb=" N ASN h 48 " --> pdb=" O PHE h 63 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'h' and resid 76 through 79 Processing sheet with id=AB1, first strand: chain 'h' and resid 76 through 79 removed outlier: 6.944A pdb=" N LEU h 105 " --> pdb=" O ILE h 128 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N TYR h 130 " --> pdb=" O ILE h 103 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ILE h 103 " --> pdb=" O TYR h 130 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'k' and resid 41 through 45 removed outlier: 6.550A pdb=" N GLY k 19 " --> pdb=" O GLU k 83 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N THR k 85 " --> pdb=" O GLY k 19 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ALA k 21 " --> pdb=" O THR k 85 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N LYS k 87 " --> pdb=" O ALA k 21 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE k 23 " --> pdb=" O LYS k 87 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL k 82 " --> pdb=" O VAL k 107 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ALA k 109 " --> pdb=" O VAL k 82 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'l' and resid 92 through 95 removed outlier: 6.864A pdb=" N ARG l 67 " --> pdb=" O THR l 48 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N VAL l 50 " --> pdb=" O TYR l 65 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N TYR l 65 " --> pdb=" O VAL l 50 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR l 108 " --> pdb=" O ASN l 77 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'p' and resid 5 through 11 removed outlier: 6.319A pdb=" N ASN p 41 " --> pdb=" O PRO p 16 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N TYR p 18 " --> pdb=" O THR p 39 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N THR p 39 " --> pdb=" O TYR p 18 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ILE p 20 " --> pdb=" O ILE p 37 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'q' and resid 41 through 48 removed outlier: 3.571A pdb=" N TYR q 42 " --> pdb=" O THR q 29 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR q 29 " --> pdb=" O TYR q 42 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N THR q 22 " --> pdb=" O ASP q 17 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ASP q 17 " --> pdb=" O THR q 22 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N THR q 24 " --> pdb=" O VAL q 15 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLU q 28 " --> pdb=" O VAL q 11 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N VAL q 11 " --> pdb=" O GLU q 28 " (cutoff:3.500A) removed outlier: 13.031A pdb=" N TYR q 30 " --> pdb=" O VAL q 9 " (cutoff:3.500A) removed outlier: 16.569A pdb=" N VAL q 9 " --> pdb=" O TYR q 30 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ILE q 60 " --> pdb=" O ILE q 80 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ILE q 80 " --> pdb=" O ILE q 60 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LYS q 62 " --> pdb=" O VAL q 78 " (cutoff:3.500A) 417 hydrogen bonds defined for protein. 1191 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 894 hydrogen bonds 1446 hydrogen bond angles 0 basepair planarities 359 basepair parallelities 687 stacking parallelities Total time for adding SS restraints: 15.06 Time building geometry restraints manager: 4.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4586 1.32 - 1.45: 16148 1.45 - 1.57: 15375 1.57 - 1.69: 2254 1.69 - 1.81: 56 Bond restraints: 38419 Sorted by residual: bond pdb=" C SER l 118 " pdb=" N GLY l 119 " ideal model delta sigma weight residual 1.330 1.440 -0.110 8.80e-03 1.29e+04 1.55e+02 bond pdb=" C THR l 117 " pdb=" N SER l 118 " ideal model delta sigma weight residual 1.330 1.487 -0.157 1.45e-02 4.76e+03 1.17e+02 bond pdb=" C PHE b 90 " pdb=" N TYR b 91 " ideal model delta sigma weight residual 1.330 1.455 -0.125 1.47e-02 4.63e+03 7.18e+01 bond pdb=" C TYR b 91 " pdb=" N ILE b 92 " ideal model delta sigma weight residual 1.332 1.420 -0.088 1.36e-02 5.41e+03 4.18e+01 bond pdb=" CG1 ILE d 128 " pdb=" CD1 ILE d 128 " ideal model delta sigma weight residual 1.513 1.365 0.148 3.90e-02 6.57e+02 1.45e+01 ... (remaining 38414 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.08: 56585 4.08 - 8.15: 794 8.15 - 12.23: 68 12.23 - 16.30: 3 16.30 - 20.38: 1 Bond angle restraints: 57451 Sorted by residual: angle pdb=" C SER l 118 " pdb=" N GLY l 119 " pdb=" CA GLY l 119 " ideal model delta sigma weight residual 119.92 129.97 -10.05 9.60e-01 1.09e+00 1.10e+02 angle pdb=" CA PHE b 90 " pdb=" C PHE b 90 " pdb=" N TYR b 91 " ideal model delta sigma weight residual 116.45 106.52 9.93 1.23e+00 6.61e-01 6.52e+01 angle pdb=" N SER l 128 " pdb=" CA SER l 128 " pdb=" C SER l 128 " ideal model delta sigma weight residual 111.14 102.70 8.44 1.08e+00 8.57e-01 6.10e+01 angle pdb=" O SER l 118 " pdb=" C SER l 118 " pdb=" N GLY l 119 " ideal model delta sigma weight residual 123.16 114.44 8.72 1.16e+00 7.43e-01 5.65e+01 angle pdb=" C3' A a 540 " pdb=" O3' A a 540 " pdb=" P A a 541 " ideal model delta sigma weight residual 120.20 130.72 -10.52 1.50e+00 4.44e-01 4.92e+01 ... (remaining 57446 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.22: 19616 35.22 - 70.43: 872 70.43 - 105.65: 71 105.65 - 140.86: 6 140.86 - 176.08: 12 Dihedral angle restraints: 20577 sinusoidal: 16523 harmonic: 4054 Sorted by residual: dihedral pdb=" O4' U a 477 " pdb=" C1' U a 477 " pdb=" N1 U a 477 " pdb=" C2 U a 477 " ideal model delta sinusoidal sigma weight residual 200.00 23.92 176.08 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U a 315 " pdb=" C1' U a 315 " pdb=" N1 U a 315 " pdb=" C2 U a 315 " ideal model delta sinusoidal sigma weight residual -160.00 11.70 -171.70 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" O4' U a 851 " pdb=" C1' U a 851 " pdb=" N1 U a 851 " pdb=" C2 U a 851 " ideal model delta sinusoidal sigma weight residual 200.00 35.92 164.08 1 1.50e+01 4.44e-03 8.37e+01 ... (remaining 20574 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 6669 0.101 - 0.201: 597 0.201 - 0.302: 63 0.302 - 0.402: 11 0.402 - 0.503: 5 Chirality restraints: 7345 Sorted by residual: chirality pdb=" CB ILE h 127 " pdb=" CA ILE h 127 " pdb=" CG1 ILE h 127 " pdb=" CG2 ILE h 127 " both_signs ideal model delta sigma weight residual False 2.64 2.14 0.50 2.00e-01 2.50e+01 6.33e+00 chirality pdb=" CB VAL d 141 " pdb=" CA VAL d 141 " pdb=" CG1 VAL d 141 " pdb=" CG2 VAL d 141 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" C1' A a 61 " pdb=" O4' A a 61 " pdb=" C2' A a 61 " pdb=" N9 A a 61 " both_signs ideal model delta sigma weight residual False 2.44 1.97 0.46 2.00e-01 2.50e+01 5.35e+00 ... (remaining 7342 not shown) Planarity restraints: 3085 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR b 91 " 0.030 2.00e-02 2.50e+03 6.39e-02 4.08e+01 pdb=" C TYR b 91 " -0.110 2.00e-02 2.50e+03 pdb=" O TYR b 91 " 0.045 2.00e-02 2.50e+03 pdb=" N ILE b 92 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE b 90 " 0.028 2.00e-02 2.50e+03 6.07e-02 3.68e+01 pdb=" C PHE b 90 " -0.105 2.00e-02 2.50e+03 pdb=" O PHE b 90 " 0.044 2.00e-02 2.50e+03 pdb=" N TYR b 91 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY l 119 " 0.027 2.00e-02 2.50e+03 5.83e-02 3.40e+01 pdb=" C GLY l 119 " -0.101 2.00e-02 2.50e+03 pdb=" O GLY l 119 " 0.040 2.00e-02 2.50e+03 pdb=" N VAL l 120 " 0.033 2.00e-02 2.50e+03 ... (remaining 3082 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 10539 2.84 - 3.36: 26884 3.36 - 3.87: 80066 3.87 - 4.39: 89718 4.39 - 4.90: 119146 Nonbonded interactions: 326353 Sorted by model distance: nonbonded pdb=" OP1 A a 212 " pdb=" O2' C a 229 " model vdw 2.327 3.040 nonbonded pdb=" O2' G a 262 " pdb=" O ASP q 20 " model vdw 2.329 3.040 nonbonded pdb=" O2' G a 900 " pdb=" O6 G a 916 " model vdw 2.331 3.040 nonbonded pdb=" OP1 U a 383 " pdb=" OG1 THR p 70 " model vdw 2.334 3.040 nonbonded pdb=" O ILE o 29 " pdb=" OG1 THR o 33 " model vdw 2.336 3.040 ... (remaining 326348 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=0.00 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: 1.770 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: 0.040 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 44.040 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 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 : 0.008 0.157 38419 Z= 0.420 Angle : 1.300 20.379 57451 Z= 0.629 Chirality : 0.062 0.503 7345 Planarity : 0.009 0.102 3085 Dihedral : 16.197 176.081 17961 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.97 % Favored : 91.74 % Rotamer: Outliers : 2.16 % Allowed : 10.70 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -5.26 (0.16), residues: 1380 helix: -4.32 (0.10), residues: 475 sheet: -2.84 (0.30), residues: 229 loop : -3.02 (0.19), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG l 127 TYR 0.032 0.004 TYR q 30 PHE 0.025 0.003 PHE e 31 TRP 0.047 0.005 TRP b 96 HIS 0.048 0.004 HIS k 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00796 / 0.42 (38419) covalent geometry : angle 1.29991 / 0.63 (57451) hydrogen bonds : bond 0.12081 / 7.18 ( 1305) hydrogen bonds : angle 5.69283 / 3.39 ( 2637) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 409 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 24 ASN cc_start: 0.8124 (t0) cc_final: 0.7921 (t0) REVERT: b 27 MET cc_start: 0.7285 (mmm) cc_final: 0.6707 (mmm) REVERT: b 59 GLN cc_start: 0.7837 (tp40) cc_final: 0.7536 (mm-40) REVERT: b 73 LYS cc_start: 0.7724 (tptt) cc_final: 0.7523 (tptm) REVERT: b 77 GLN cc_start: 0.7228 (pt0) cc_final: 0.6675 (pm20) REVERT: b 188 ASP cc_start: 0.5682 (m-30) cc_final: 0.4688 (t0) REVERT: e 32 ARG cc_start: 0.7392 (mtm180) cc_final: 0.7169 (mtm-85) REVERT: e 88 ARG cc_start: 0.8005 (mtt-85) cc_final: 0.7596 (mtt180) REVERT: f 5 GLU cc_start: 0.7090 (tt0) cc_final: 0.6744 (tt0) REVERT: f 70 ASN cc_start: 0.7400 (p0) cc_final: 0.7093 (p0) REVERT: f 74 ASP cc_start: 0.8072 (p0) cc_final: 0.7859 (p0) REVERT: f 79 LEU cc_start: 0.8108 (mm) cc_final: 0.7880 (mt) REVERT: h 21 ARG cc_start: 0.7846 (mmt-90) cc_final: 0.7592 (mpt180) REVERT: h 105 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8817 (pp) REVERT: l 25 ASN cc_start: 0.8907 (p0) cc_final: 0.8623 (p0) REVERT: l 53 MET cc_start: 0.8684 (ptm) cc_final: 0.8447 (ptm) REVERT: l 60 SER cc_start: 0.7870 (t) cc_final: 0.7361 (t) REVERT: o 59 MET cc_start: 0.8020 (mtt) cc_final: 0.7783 (mtt) REVERT: p 62 ASN cc_start: 0.8065 (m-40) cc_final: 0.7736 (m110) REVERT: p 77 LYS cc_start: 0.8602 (mtmt) cc_final: 0.8371 (mtmt) REVERT: q 70 SER cc_start: 0.8910 (t) cc_final: 0.8507 (t) outliers start: 26 outliers final: 8 residues processed: 424 average time/residue: 0.2466 time to fit residues: 162.4381 Evaluate side-chains 330 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 321 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 105 LEU Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain r residue 76 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 6.9990 chunk 247 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 44 GLN b 66 GLN ** b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 159 GLN b 190 ASN ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 118 HIS ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 18 ASN h 22 HIS k 18 ASN k 64 GLN l 5 ASN l 6 GLN ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 37 ASN o 50 HIS p 46 ASN p 87 GLN t 42 ASN t 64 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.104839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.087447 restraints weight = 74365.183| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.60 r_work: 0.2805 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 38419 Z= 0.315 Angle : 0.707 12.164 57451 Z= 0.363 Chirality : 0.041 0.376 7345 Planarity : 0.006 0.074 3085 Dihedral : 15.177 177.367 15101 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 5.31 % Allowed : 18.24 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.63 (0.19), residues: 1380 helix: -2.05 (0.19), residues: 482 sheet: -2.72 (0.30), residues: 240 loop : -2.49 (0.21), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG b 95 TYR 0.019 0.002 TYR p 40 PHE 0.030 0.002 PHE k 61 TRP 0.017 0.002 TRP k 44 HIS 0.009 0.002 HIS o 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00610 / 0.32 (38419) covalent geometry : angle 0.70653 / 0.36 (57451) hydrogen bonds : bond 0.06315 / 3.72 ( 1305) hydrogen bonds : angle 3.91707 / 2.32 ( 2637) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 328 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 59 GLN cc_start: 0.7805 (tp40) cc_final: 0.7605 (mm-40) REVERT: b 77 GLN cc_start: 0.7166 (pt0) cc_final: 0.6567 (pm20) REVERT: b 151 ILE cc_start: 0.6763 (OUTLIER) cc_final: 0.6494 (pp) REVERT: d 119 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8236 (pt) REVERT: d 149 ASN cc_start: 0.7205 (t0) cc_final: 0.6445 (t0) REVERT: f 5 GLU cc_start: 0.7821 (tt0) cc_final: 0.7545 (tt0) REVERT: f 74 ASP cc_start: 0.8311 (p0) cc_final: 0.7841 (p0) REVERT: f 79 LEU cc_start: 0.8356 (mm) cc_final: 0.8080 (mt) REVERT: h 22 HIS cc_start: 0.8812 (OUTLIER) cc_final: 0.8190 (m-70) REVERT: h 39 ILE cc_start: 0.9264 (mm) cc_final: 0.9033 (mt) REVERT: h 98 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8597 (mp) REVERT: k 24 ARG cc_start: 0.8141 (tpt-90) cc_final: 0.7788 (tpt-90) REVERT: k 65 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7670 (mmp) REVERT: k 125 LYS cc_start: 0.8233 (tmmt) cc_final: 0.7637 (tptm) REVERT: l 60 SER cc_start: 0.8305 (t) cc_final: 0.7842 (t) REVERT: o 64 ARG cc_start: 0.8202 (tpm170) cc_final: 0.7955 (tpm170) REVERT: p 21 VAL cc_start: 0.9413 (OUTLIER) cc_final: 0.9164 (m) REVERT: p 62 ASN cc_start: 0.8349 (m-40) cc_final: 0.7961 (m110) REVERT: q 28 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7641 (mm-30) REVERT: q 70 SER cc_start: 0.9229 (t) cc_final: 0.8998 (t) REVERT: r 27 ASP cc_start: 0.8449 (OUTLIER) cc_final: 0.7744 (t0) outliers start: 64 outliers final: 44 residues processed: 366 average time/residue: 0.2430 time to fit residues: 140.3331 Evaluate side-chains 373 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 322 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain d residue 31 TYR Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain e residue 31 PHE Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 61 LYS Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 61 ASN Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 12 THR Chi-restraints excluded: chain h residue 22 HIS Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 105 LEU Chi-restraints excluded: chain h residue 127 ILE Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 90 HIS Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain o residue 50 HIS Chi-restraints excluded: chain p residue 12 SER Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 76 SER Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain r residue 15 VAL Chi-restraints excluded: chain r residue 26 ILE Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 40 SER Chi-restraints excluded: chain t residue 57 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 142 optimal weight: 9.9990 chunk 216 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 154 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 208 optimal weight: 0.4980 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 109 GLN d 112 GLN ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 50 HIS p 73 ASN p 87 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.103372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.084888 restraints weight = 74350.222| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.76 r_work: 0.2790 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 38419 Z= 0.348 Angle : 0.711 11.889 57451 Z= 0.363 Chirality : 0.042 0.305 7345 Planarity : 0.006 0.071 3085 Dihedral : 15.135 178.135 15101 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 7.21 % Allowed : 18.57 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.03 (0.21), residues: 1380 helix: -1.23 (0.21), residues: 491 sheet: -2.63 (0.30), residues: 244 loop : -2.31 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG d 5 TYR 0.018 0.002 TYR p 40 PHE 0.024 0.002 PHE k 61 TRP 0.014 0.002 TRP k 44 HIS 0.017 0.002 HIS o 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00674 / 0.35 (38419) covalent geometry : angle 0.71071 / 0.36 (57451) hydrogen bonds : bond 0.06447 / 3.79 ( 1305) hydrogen bonds : angle 3.76125 / 2.22 ( 2637) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 333 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 59 GLN cc_start: 0.7730 (tp40) cc_final: 0.7510 (mm-40) REVERT: b 73 LYS cc_start: 0.7498 (tptt) cc_final: 0.7294 (ttpt) REVERT: b 77 GLN cc_start: 0.7093 (pt0) cc_final: 0.6637 (pm20) REVERT: b 151 ILE cc_start: 0.6788 (OUTLIER) cc_final: 0.6517 (pp) REVERT: d 47 TYR cc_start: 0.9250 (t80) cc_final: 0.8983 (t80) REVERT: d 119 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8299 (pt) REVERT: e 14 ARG cc_start: 0.8446 (tpp-160) cc_final: 0.8225 (tpp80) REVERT: f 5 GLU cc_start: 0.7764 (tt0) cc_final: 0.7447 (tt0) REVERT: f 60 TYR cc_start: 0.8705 (m-80) cc_final: 0.8320 (m-80) REVERT: f 74 ASP cc_start: 0.8250 (p0) cc_final: 0.7684 (p0) REVERT: f 78 ARG cc_start: 0.8345 (tmm-80) cc_final: 0.8103 (tmm-80) REVERT: f 79 LEU cc_start: 0.8473 (mm) cc_final: 0.8209 (mt) REVERT: h 39 ILE cc_start: 0.9290 (mm) cc_final: 0.9058 (mt) REVERT: h 98 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8569 (mp) REVERT: k 24 ARG cc_start: 0.8140 (tpt-90) cc_final: 0.7825 (tpt-90) REVERT: k 65 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7680 (mmt) REVERT: k 125 LYS cc_start: 0.8326 (tmmt) cc_final: 0.7702 (tptm) REVERT: l 18 LYS cc_start: 0.7605 (ttpp) cc_final: 0.7283 (ttpp) REVERT: l 60 SER cc_start: 0.8219 (t) cc_final: 0.7776 (t) REVERT: o 26 GLU cc_start: 0.8635 (mp0) cc_final: 0.8386 (mp0) REVERT: p 50 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8619 (pt) REVERT: q 28 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7656 (mm-30) REVERT: q 39 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7988 (mtp85) REVERT: q 70 SER cc_start: 0.9213 (t) cc_final: 0.8935 (t) REVERT: r 27 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.7703 (t70) REVERT: r 70 MET cc_start: 0.8164 (mmp) cc_final: 0.7961 (mmp) outliers start: 87 outliers final: 61 residues processed: 385 average time/residue: 0.2338 time to fit residues: 141.2828 Evaluate side-chains 387 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 319 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain b residue 221 ILE Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 112 GLN Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain e residue 31 PHE Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 160 THR Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 61 ASN Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 12 THR Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 105 LEU Chi-restraints excluded: chain h residue 127 ILE Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 36 THR Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 90 HIS Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain o residue 31 VAL Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 50 HIS Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain p residue 12 SER Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 50 ILE Chi-restraints excluded: chain p residue 53 ASP Chi-restraints excluded: chain p residue 76 SER Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 39 ARG Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain q residue 59 ASP Chi-restraints excluded: chain r residue 15 VAL Chi-restraints excluded: chain r residue 25 HIS Chi-restraints excluded: chain r residue 26 ILE Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 40 SER Chi-restraints excluded: chain t residue 57 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 31 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 129 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 180 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 173 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 106 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 112 GLN ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 149 ASN ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 50 HIS p 73 ASN p 87 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.104004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.086003 restraints weight = 73969.644| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.58 r_work: 0.2806 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 38419 Z= 0.296 Angle : 0.667 11.968 57451 Z= 0.341 Chirality : 0.040 0.265 7345 Planarity : 0.005 0.070 3085 Dihedral : 15.030 179.438 15101 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 7.05 % Allowed : 20.73 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.21), residues: 1380 helix: -0.78 (0.22), residues: 488 sheet: -2.47 (0.31), residues: 246 loop : -2.10 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG k 93 TYR 0.019 0.002 TYR f 60 PHE 0.020 0.002 PHE k 61 TRP 0.012 0.002 TRP k 44 HIS 0.016 0.002 HIS o 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.30 (38419) covalent geometry : angle 0.66655 / 0.34 (57451) hydrogen bonds : bond 0.06039 / 3.56 ( 1305) hydrogen bonds : angle 3.63121 / 2.16 ( 2637) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 326 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 59 GLN cc_start: 0.7954 (tp40) cc_final: 0.7647 (mm-40) REVERT: b 73 LYS cc_start: 0.7471 (tptt) cc_final: 0.7234 (ttpt) REVERT: b 77 GLN cc_start: 0.7095 (pt0) cc_final: 0.6576 (pm20) REVERT: b 151 ILE cc_start: 0.6778 (OUTLIER) cc_final: 0.6516 (pp) REVERT: d 47 TYR cc_start: 0.9255 (t80) cc_final: 0.9015 (t80) REVERT: d 119 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8343 (pt) REVERT: f 66 LYS cc_start: 0.8386 (tptp) cc_final: 0.8149 (tptp) REVERT: f 74 ASP cc_start: 0.8406 (p0) cc_final: 0.7894 (p0) REVERT: f 79 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8249 (mt) REVERT: h 39 ILE cc_start: 0.9250 (mm) cc_final: 0.9019 (mt) REVERT: h 61 ARG cc_start: 0.8442 (ttm110) cc_final: 0.8007 (ttm170) REVERT: h 98 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8568 (mp) REVERT: k 24 ARG cc_start: 0.8127 (tpt-90) cc_final: 0.7918 (tpt-90) REVERT: k 65 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7709 (mmt) REVERT: k 87 LYS cc_start: 0.8346 (ttmt) cc_final: 0.8110 (ttpt) REVERT: k 125 LYS cc_start: 0.8402 (tmmt) cc_final: 0.7728 (tptm) REVERT: l 60 SER cc_start: 0.8172 (t) cc_final: 0.7663 (t) REVERT: o 26 GLU cc_start: 0.8590 (mp0) cc_final: 0.8345 (mp0) REVERT: p 50 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8480 (pt) REVERT: q 4 ARG cc_start: 0.7031 (tpm170) cc_final: 0.6773 (tpm170) REVERT: q 28 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7691 (mm-30) REVERT: q 70 SER cc_start: 0.9234 (t) cc_final: 0.8954 (t) REVERT: r 27 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7532 (t70) outliers start: 85 outliers final: 66 residues processed: 373 average time/residue: 0.2360 time to fit residues: 138.6823 Evaluate side-chains 388 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 315 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain b residue 221 ILE Chi-restraints excluded: chain d residue 31 TYR Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain e residue 31 PHE Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 115 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 130 SER Chi-restraints excluded: chain e residue 160 THR Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 61 ASN Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 12 THR Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 105 LEU Chi-restraints excluded: chain h residue 127 ILE Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 36 THR Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 74 ILE Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain o residue 13 LYS Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 50 HIS Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain p residue 12 SER Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 50 ILE Chi-restraints excluded: chain p residue 76 SER Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 39 ARG Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain q residue 59 ASP Chi-restraints excluded: chain r residue 15 VAL Chi-restraints excluded: chain r residue 25 HIS Chi-restraints excluded: chain r residue 26 ILE Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 62 THR Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 40 SER Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 58 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 223 optimal weight: 0.3980 chunk 228 optimal weight: 0.6980 chunk 166 optimal weight: 4.9990 chunk 176 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 192 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 246 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 208 optimal weight: 7.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 89 GLN ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 50 HIS p 87 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.104132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.086487 restraints weight = 73968.246| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.51 r_work: 0.2812 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 38419 Z= 0.284 Angle : 0.653 11.610 57451 Z= 0.334 Chirality : 0.039 0.260 7345 Planarity : 0.005 0.068 3085 Dihedral : 14.953 178.340 15101 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 7.55 % Allowed : 21.14 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.22), residues: 1380 helix: -0.56 (0.22), residues: 491 sheet: -2.38 (0.31), residues: 243 loop : -2.07 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG k 93 TYR 0.022 0.002 TYR f 60 PHE 0.018 0.002 PHE k 61 TRP 0.011 0.002 TRP k 44 HIS 0.015 0.002 HIS o 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.28 (38419) covalent geometry : angle 0.65306 / 0.33 (57451) hydrogen bonds : bond 0.05940 / 3.50 ( 1305) hydrogen bonds : angle 3.58824 / 2.14 ( 2637) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 323 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 59 GLN cc_start: 0.7988 (tp40) cc_final: 0.7691 (mm-40) REVERT: b 73 LYS cc_start: 0.7471 (tptt) cc_final: 0.7216 (ttpt) REVERT: b 77 GLN cc_start: 0.7082 (pt0) cc_final: 0.6645 (pm20) REVERT: b 151 ILE cc_start: 0.6881 (OUTLIER) cc_final: 0.6633 (pp) REVERT: d 47 TYR cc_start: 0.9263 (t80) cc_final: 0.9037 (t80) REVERT: d 119 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8385 (pt) REVERT: d 198 TYR cc_start: 0.8965 (m-80) cc_final: 0.8739 (m-80) REVERT: f 1 MET cc_start: 0.6539 (tpt) cc_final: 0.6317 (tpp) REVERT: f 2 ARG cc_start: 0.8055 (mtt-85) cc_final: 0.7842 (mtt-85) REVERT: f 66 LYS cc_start: 0.8131 (tptp) cc_final: 0.7786 (tptt) REVERT: f 74 ASP cc_start: 0.8519 (p0) cc_final: 0.7954 (p0) REVERT: f 79 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8011 (mt) REVERT: h 39 ILE cc_start: 0.9255 (mm) cc_final: 0.9027 (mt) REVERT: h 98 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8558 (mp) REVERT: k 24 ARG cc_start: 0.8111 (tpt-90) cc_final: 0.7891 (tpt-90) REVERT: k 65 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7627 (mmt) REVERT: k 76 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7537 (pp20) REVERT: k 87 LYS cc_start: 0.8325 (ttmt) cc_final: 0.8102 (ttpt) REVERT: k 125 LYS cc_start: 0.8412 (tmmt) cc_final: 0.7754 (tptm) REVERT: l 60 SER cc_start: 0.8056 (t) cc_final: 0.7567 (t) REVERT: p 50 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8542 (pt) REVERT: q 4 ARG cc_start: 0.7016 (tpm170) cc_final: 0.6775 (tpm170) REVERT: q 70 SER cc_start: 0.9260 (t) cc_final: 0.8975 (t) REVERT: r 27 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7443 (t70) REVERT: r 35 LYS cc_start: 0.8773 (mptt) cc_final: 0.8284 (mptt) REVERT: r 39 SER cc_start: 0.8890 (t) cc_final: 0.8644 (p) REVERT: t 58 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7385 (m-30) outliers start: 91 outliers final: 67 residues processed: 375 average time/residue: 0.2361 time to fit residues: 138.9709 Evaluate side-chains 383 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 307 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 97 LEU Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain b residue 221 ILE Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain e residue 31 PHE Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 115 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 160 THR Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain f residue 61 ASN Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 12 THR Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 105 LEU Chi-restraints excluded: chain h residue 127 ILE Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 76 GLU Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 36 THR Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 74 ILE Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain o residue 13 LYS Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 50 HIS Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain p residue 12 SER Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 50 ILE Chi-restraints excluded: chain p residue 76 SER Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain q residue 59 ASP Chi-restraints excluded: chain r residue 15 VAL Chi-restraints excluded: chain r residue 25 HIS Chi-restraints excluded: chain r residue 26 ILE Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 31 THR Chi-restraints excluded: chain r residue 62 THR Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 58 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 97 optimal weight: 10.0000 chunk 243 optimal weight: 10.0000 chunk 167 optimal weight: 0.3980 chunk 106 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 10 optimal weight: 30.0000 chunk 148 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 overall best weight: 6.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** b 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 22 HIS k 40 ASN ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 73 ASN p 87 GLN t 77 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.100820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.083653 restraints weight = 74810.222| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.88 r_work: 0.2725 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.079 38419 Z= 0.511 Angle : 0.841 11.726 57451 Z= 0.422 Chirality : 0.049 0.336 7345 Planarity : 0.006 0.068 3085 Dihedral : 15.268 178.446 15101 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.80 % Favored : 89.20 % Rotamer: Outliers : 8.13 % Allowed : 21.06 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.21), residues: 1380 helix: -0.76 (0.22), residues: 485 sheet: -2.40 (0.31), residues: 245 loop : -2.14 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG e 45 TYR 0.030 0.003 TYR d 197 PHE 0.019 0.003 PHE l 28 TRP 0.012 0.003 TRP d 9 HIS 0.014 0.002 HIS o 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00993 / 0.51 (38419) covalent geometry : angle 0.84092 / 0.42 (57451) hydrogen bonds : bond 0.07291 / 4.31 ( 1305) hydrogen bonds : angle 3.85385 / 2.29 ( 2637) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 302 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 27 MET cc_start: 0.7773 (mmm) cc_final: 0.7367 (mmm) REVERT: b 73 LYS cc_start: 0.7632 (tptt) cc_final: 0.7325 (ttpt) REVERT: b 77 GLN cc_start: 0.7144 (pt0) cc_final: 0.6516 (pm20) REVERT: b 151 ILE cc_start: 0.6818 (OUTLIER) cc_final: 0.6578 (pp) REVERT: d 47 TYR cc_start: 0.9347 (t80) cc_final: 0.9127 (t80) REVERT: d 119 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8395 (pt) REVERT: e 43 ASN cc_start: 0.8065 (p0) cc_final: 0.7865 (p0) REVERT: f 66 LYS cc_start: 0.8437 (tptp) cc_final: 0.8158 (tptt) REVERT: f 79 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8112 (mt) REVERT: h 39 ILE cc_start: 0.9297 (mm) cc_final: 0.9089 (mt) REVERT: h 98 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8558 (mp) REVERT: k 24 ARG cc_start: 0.8140 (tpt-90) cc_final: 0.7922 (tpt-90) REVERT: k 65 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7691 (mmt) REVERT: k 76 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7770 (pp20) REVERT: k 87 LYS cc_start: 0.8517 (ttmt) cc_final: 0.8296 (ttpt) REVERT: k 125 LYS cc_start: 0.8462 (tmmt) cc_final: 0.7750 (tptm) REVERT: l 60 SER cc_start: 0.8360 (t) cc_final: 0.7984 (t) REVERT: l 75 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8197 (mp0) REVERT: p 50 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8815 (pt) REVERT: q 16 SER cc_start: 0.9432 (t) cc_final: 0.9187 (m) REVERT: r 27 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.7634 (t70) REVERT: r 35 LYS cc_start: 0.8883 (mptt) cc_final: 0.8559 (mptt) REVERT: r 39 SER cc_start: 0.8974 (t) cc_final: 0.8683 (p) REVERT: t 58 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7314 (m-30) outliers start: 98 outliers final: 79 residues processed: 364 average time/residue: 0.2345 time to fit residues: 135.8071 Evaluate side-chains 382 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 293 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain b residue 97 LEU Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain b residue 221 ILE Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 31 TYR Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain e residue 31 PHE Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 115 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 130 SER Chi-restraints excluded: chain e residue 160 THR Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 61 ASN Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 12 THR Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 105 LEU Chi-restraints excluded: chain h residue 127 ILE Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 76 GLU Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 36 THR Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 74 ILE Chi-restraints excluded: chain l residue 75 GLU Chi-restraints excluded: chain l residue 90 HIS Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain o residue 12 ILE Chi-restraints excluded: chain o residue 13 LYS Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 50 HIS Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain p residue 12 SER Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 50 ILE Chi-restraints excluded: chain p residue 76 SER Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain q residue 59 ASP Chi-restraints excluded: chain r residue 15 VAL Chi-restraints excluded: chain r residue 25 HIS Chi-restraints excluded: chain r residue 26 ILE Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 31 THR Chi-restraints excluded: chain r residue 62 THR Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 37 THR Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 40 SER Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 58 ASP Chi-restraints excluded: chain t residue 77 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 100 optimal weight: 10.0000 chunk 221 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 165 optimal weight: 7.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 131 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** b 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 18 ASN ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 50 HIS p 73 ASN p 87 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.104228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.078322 restraints weight = 74308.545| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 0.92 r_work: 0.2913 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 38419 Z= 0.240 Angle : 0.638 11.577 57451 Z= 0.327 Chirality : 0.038 0.259 7345 Planarity : 0.005 0.070 3085 Dihedral : 14.961 178.193 15100 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 7.21 % Allowed : 22.72 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.22), residues: 1380 helix: -0.26 (0.23), residues: 480 sheet: -2.40 (0.31), residues: 237 loop : -1.97 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG e 45 TYR 0.026 0.002 TYR d 197 PHE 0.016 0.002 PHE d 79 TRP 0.009 0.002 TRP f 43 HIS 0.010 0.002 HIS k 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.24 (38419) covalent geometry : angle 0.63811 / 0.33 (57451) hydrogen bonds : bond 0.05780 / 3.41 ( 1305) hydrogen bonds : angle 3.61237 / 2.16 ( 2637) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 322 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 27 MET cc_start: 0.7880 (mmm) cc_final: 0.7395 (mmm) REVERT: b 73 LYS cc_start: 0.7522 (tptt) cc_final: 0.7198 (ttpt) REVERT: d 120 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8558 (mt) REVERT: f 74 ASP cc_start: 0.8537 (p0) cc_final: 0.7795 (p0) REVERT: f 79 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8266 (mt) REVERT: h 39 ILE cc_start: 0.9275 (mm) cc_final: 0.9067 (mt) REVERT: h 61 ARG cc_start: 0.8494 (ttm110) cc_final: 0.8082 (ttm170) REVERT: h 98 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8602 (mp) REVERT: k 65 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7546 (mmt) REVERT: k 76 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7565 (pp20) REVERT: k 87 LYS cc_start: 0.8355 (ttmt) cc_final: 0.8154 (ttpt) REVERT: k 125 LYS cc_start: 0.8475 (tmmt) cc_final: 0.7762 (tptm) REVERT: l 60 SER cc_start: 0.8050 (t) cc_final: 0.7565 (t) REVERT: l 75 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8087 (mp0) REVERT: p 50 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8565 (pt) REVERT: p 62 ASN cc_start: 0.8242 (m-40) cc_final: 0.7817 (m110) REVERT: q 16 SER cc_start: 0.9359 (t) cc_final: 0.9135 (m) REVERT: r 27 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7578 (t70) REVERT: r 35 LYS cc_start: 0.8816 (mptt) cc_final: 0.8439 (mptt) REVERT: t 58 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.7244 (m-30) outliers start: 87 outliers final: 65 residues processed: 370 average time/residue: 0.2348 time to fit residues: 137.1514 Evaluate side-chains 381 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 307 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 97 LEU Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 31 TYR Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain e residue 31 PHE Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 115 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 130 SER Chi-restraints excluded: chain e residue 160 THR Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 61 ASN Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 105 LEU Chi-restraints excluded: chain h residue 127 ILE Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 76 GLU Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 74 ILE Chi-restraints excluded: chain l residue 75 GLU Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain o residue 13 LYS Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 50 HIS Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain p residue 10 LEU Chi-restraints excluded: chain p residue 12 SER Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 50 ILE Chi-restraints excluded: chain p residue 76 SER Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain r residue 15 VAL Chi-restraints excluded: chain r residue 26 ILE Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 31 THR Chi-restraints excluded: chain r residue 62 THR Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 37 THR Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 40 SER Chi-restraints excluded: chain t residue 58 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 225 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 2 optimal weight: 40.0000 chunk 17 optimal weight: 10.0000 chunk 216 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 213 optimal weight: 0.9990 chunk 111 optimal weight: 10.0000 chunk 160 optimal weight: 0.9990 chunk 238 optimal weight: 0.8980 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** b 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 89 GLN ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 87 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.107241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.082927 restraints weight = 74165.707| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 0.89 r_work: 0.2993 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 38419 Z= 0.148 Angle : 0.570 10.944 57451 Z= 0.293 Chirality : 0.034 0.255 7345 Planarity : 0.004 0.061 3085 Dihedral : 14.745 179.363 15100 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 5.89 % Allowed : 24.30 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.22), residues: 1380 helix: 0.13 (0.23), residues: 481 sheet: -2.29 (0.32), residues: 233 loop : -1.80 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG f 78 TYR 0.032 0.002 TYR l 65 PHE 0.015 0.001 PHE k 61 TRP 0.012 0.002 TRP f 43 HIS 0.020 0.002 HIS o 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 (38419) covalent geometry : angle 0.57041 / 0.29 (57451) hydrogen bonds : bond 0.05134 / 3.01 ( 1305) hydrogen bonds : angle 3.42074 / 2.03 ( 2637) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 324 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 24 ASN cc_start: 0.8160 (t0) cc_final: 0.7924 (t0) REVERT: b 27 MET cc_start: 0.7899 (mmm) cc_final: 0.7416 (mmm) REVERT: d 119 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8314 (pt) REVERT: e 41 ASP cc_start: 0.8059 (p0) cc_final: 0.7566 (p0) REVERT: e 45 ARG cc_start: 0.8371 (mtp-110) cc_final: 0.8169 (ttp-110) REVERT: f 74 ASP cc_start: 0.8466 (p0) cc_final: 0.7823 (p0) REVERT: f 79 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8080 (mt) REVERT: h 39 ILE cc_start: 0.9217 (mm) cc_final: 0.8996 (mt) REVERT: h 61 ARG cc_start: 0.8414 (ttm110) cc_final: 0.8081 (ttm170) REVERT: k 65 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7470 (mmt) REVERT: k 76 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7558 (pp20) REVERT: k 125 LYS cc_start: 0.8406 (tmmt) cc_final: 0.7764 (tptm) REVERT: l 60 SER cc_start: 0.7745 (t) cc_final: 0.7324 (t) REVERT: o 47 LYS cc_start: 0.8648 (ptpp) cc_final: 0.8429 (ptpp) REVERT: p 50 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8542 (pt) REVERT: p 62 ASN cc_start: 0.8071 (m-40) cc_final: 0.7655 (m110) REVERT: q 4 ARG cc_start: 0.6847 (tpm170) cc_final: 0.6607 (tpm170) REVERT: q 16 SER cc_start: 0.9254 (t) cc_final: 0.9037 (m) REVERT: q 70 SER cc_start: 0.9213 (t) cc_final: 0.8802 (t) REVERT: r 27 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7352 (t70) outliers start: 71 outliers final: 50 residues processed: 369 average time/residue: 0.2279 time to fit residues: 132.5680 Evaluate side-chains 361 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 305 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain e residue 31 PHE Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 115 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 130 SER Chi-restraints excluded: chain e residue 160 THR Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 103 ILE Chi-restraints excluded: chain h residue 105 LEU Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 76 GLU Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 50 HIS Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain p residue 10 LEU Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 50 ILE Chi-restraints excluded: chain p residue 76 SER Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain r residue 15 VAL Chi-restraints excluded: chain r residue 23 ILE Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 37 THR Chi-restraints excluded: chain t residue 57 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 234 optimal weight: 9.9990 chunk 119 optimal weight: 8.9990 chunk 231 optimal weight: 3.9990 chunk 139 optimal weight: 0.0970 chunk 4 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 chunk 163 optimal weight: 3.9990 chunk 146 optimal weight: 0.6980 chunk 237 optimal weight: 0.9980 chunk 186 optimal weight: 20.0000 chunk 111 optimal weight: 10.0000 overall best weight: 1.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** b 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.106171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.080945 restraints weight = 74046.049| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 0.89 r_work: 0.2960 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 38419 Z= 0.193 Angle : 0.587 10.915 57451 Z= 0.301 Chirality : 0.035 0.248 7345 Planarity : 0.005 0.069 3085 Dihedral : 14.676 179.809 15100 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 5.56 % Allowed : 25.21 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.74 (0.22), residues: 1380 helix: 0.23 (0.24), residues: 481 sheet: -2.25 (0.31), residues: 238 loop : -1.75 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG f 93 TYR 0.029 0.002 TYR d 47 PHE 0.019 0.002 PHE d 79 TRP 0.009 0.002 TRP k 44 HIS 0.009 0.002 HIS o 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.19 (38419) covalent geometry : angle 0.58666 / 0.30 (57451) hydrogen bonds : bond 0.05351 / 3.15 ( 1305) hydrogen bonds : angle 3.42234 / 2.05 ( 2637) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 310 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 24 ASN cc_start: 0.8168 (t0) cc_final: 0.7935 (t0) REVERT: b 27 MET cc_start: 0.7875 (mmm) cc_final: 0.7354 (mmm) REVERT: d 119 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8305 (pt) REVERT: f 74 ASP cc_start: 0.8396 (p0) cc_final: 0.7831 (p0) REVERT: f 79 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8105 (mt) REVERT: h 21 ARG cc_start: 0.8694 (mmt180) cc_final: 0.8362 (mmt180) REVERT: h 39 ILE cc_start: 0.9223 (mm) cc_final: 0.9013 (mt) REVERT: k 65 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7509 (mmt) REVERT: k 76 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7561 (pp20) REVERT: k 125 LYS cc_start: 0.8430 (tmmt) cc_final: 0.7774 (tptm) REVERT: l 60 SER cc_start: 0.7801 (t) cc_final: 0.7376 (t) REVERT: l 75 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8045 (mp0) REVERT: p 62 ASN cc_start: 0.8123 (m-40) cc_final: 0.7605 (m110) REVERT: q 4 ARG cc_start: 0.6869 (tpm170) cc_final: 0.6631 (tpm170) REVERT: q 70 SER cc_start: 0.9256 (t) cc_final: 0.8965 (t) REVERT: r 27 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7290 (t70) outliers start: 67 outliers final: 56 residues processed: 350 average time/residue: 0.2271 time to fit residues: 126.3580 Evaluate side-chains 360 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 298 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 97 LEU Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain b residue 221 ILE Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain e residue 31 PHE Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 115 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 160 THR Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 103 ILE Chi-restraints excluded: chain h residue 105 LEU Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 76 GLU Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 75 GLU Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 115 LEU Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 50 HIS Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain p residue 10 LEU Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 76 SER Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain q residue 42 TYR Chi-restraints excluded: chain q residue 59 ASP Chi-restraints excluded: chain r residue 15 VAL Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 37 THR Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 57 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 88 optimal weight: 10.0000 chunk 242 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 144 optimal weight: 9.9990 chunk 151 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** b 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 50 HIS p 87 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.103397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.086329 restraints weight = 74411.591| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.54 r_work: 0.2784 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 38419 Z= 0.326 Angle : 0.691 11.133 57451 Z= 0.352 Chirality : 0.040 0.259 7345 Planarity : 0.005 0.062 3085 Dihedral : 14.829 177.585 15100 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.78 % Favored : 90.22 % Rotamer: Outliers : 5.56 % Allowed : 25.62 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.22), residues: 1380 helix: 0.01 (0.23), residues: 485 sheet: -2.26 (0.31), residues: 242 loop : -1.92 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG k 24 TYR 0.034 0.003 TYR d 47 PHE 0.019 0.002 PHE f 59 TRP 0.011 0.002 TRP d 9 HIS 0.011 0.002 HIS l 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00635 / 0.33 (38419) covalent geometry : angle 0.69069 / 0.35 (57451) hydrogen bonds : bond 0.06246 / 3.69 ( 1305) hydrogen bonds : angle 3.60541 / 2.15 ( 2637) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 300 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 24 ASN cc_start: 0.8247 (t0) cc_final: 0.7956 (t0) REVERT: b 27 MET cc_start: 0.7864 (mmm) cc_final: 0.7296 (mmm) REVERT: d 119 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8319 (pt) REVERT: f 66 LYS cc_start: 0.8633 (tptt) cc_final: 0.8366 (tptm) REVERT: f 74 ASP cc_start: 0.8538 (p0) cc_final: 0.7912 (p0) REVERT: f 79 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8089 (mt) REVERT: h 21 ARG cc_start: 0.8771 (mmt180) cc_final: 0.8428 (mmt180) REVERT: h 39 ILE cc_start: 0.9261 (mm) cc_final: 0.9048 (mt) REVERT: h 55 ASP cc_start: 0.7560 (t0) cc_final: 0.7352 (t0) REVERT: h 61 ARG cc_start: 0.8573 (ttm110) cc_final: 0.8210 (ttm110) REVERT: k 65 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7663 (mmt) REVERT: k 76 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7535 (pp20) REVERT: k 125 LYS cc_start: 0.8503 (tmmt) cc_final: 0.7773 (tptm) REVERT: l 60 SER cc_start: 0.8068 (t) cc_final: 0.7636 (t) REVERT: l 75 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8090 (mp0) REVERT: p 62 ASN cc_start: 0.8225 (m-40) cc_final: 0.7669 (m110) REVERT: r 27 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7181 (t70) REVERT: r 35 LYS cc_start: 0.8822 (mptt) cc_final: 0.8358 (mptt) outliers start: 67 outliers final: 57 residues processed: 345 average time/residue: 0.2407 time to fit residues: 130.8114 Evaluate side-chains 359 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 296 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 97 LEU Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain b residue 221 ILE Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 31 TYR Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain e residue 31 PHE Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 115 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 160 THR Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 105 LEU Chi-restraints excluded: chain h residue 127 ILE Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 76 GLU Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 75 GLU Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 50 HIS Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 76 SER Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain q residue 59 ASP Chi-restraints excluded: chain r residue 15 VAL Chi-restraints excluded: chain r residue 23 ILE Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 37 THR Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 57 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 61 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 207 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 185 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** b 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 50 HIS p 87 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.102487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.085432 restraints weight = 74507.135| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.65 r_work: 0.2772 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 38419 Z= 0.385 Angle : 0.737 11.284 57451 Z= 0.374 Chirality : 0.043 0.283 7345 Planarity : 0.006 0.069 3085 Dihedral : 14.947 179.263 15100 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 5.47 % Allowed : 25.70 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.22), residues: 1380 helix: -0.20 (0.23), residues: 490 sheet: -2.36 (0.31), residues: 242 loop : -2.03 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG e 45 TYR 0.038 0.003 TYR d 47 PHE 0.021 0.003 PHE f 59 TRP 0.011 0.002 TRP d 9 HIS 0.013 0.002 HIS o 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00747 / 0.39 (38419) covalent geometry : angle 0.73730 / 0.37 (57451) hydrogen bonds : bond 0.06487 / 3.83 ( 1305) hydrogen bonds : angle 3.69030 / 2.20 ( 2637) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7772.00 seconds wall clock time: 134 minutes 47.93 seconds (8087.93 seconds total)