Starting phenix.real_space_refine on Fri Mar 6 20:39:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bgd_12178/03_2026/7bgd_12178.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bgd_12178/03_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_12178/03_2026/7bgd_12178.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bgd_12178/03_2026/7bgd_12178.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bgd_12178/03_2026/7bgd_12178.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bgd_12178/03_2026/7bgd_12178.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 7.57, per 1000 atoms: 0.21 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: 2.78 Conformation dependent library (CDL) restraints added in 808.7 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: 5.69 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: 14.19 Time building geometry restraints manager: 3.94 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: 21510 35.22 - 70.43: 2698 70.43 - 105.65: 307 105.65 - 140.86: 6 140.86 - 176.08: 12 Dihedral angle restraints: 24533 sinusoidal: 20479 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 24530 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: 1.640 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: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 40.820 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 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 : 23.454 176.081 21917 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 covalent geometry : bond 0.00796 (38419) covalent geometry : angle 1.29991 (57451) hydrogen bonds : bond 0.12081 ( 1305) hydrogen bonds : angle 5.69283 ( 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 : 0.706 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: 0.2375 time to fit residues: 155.6170 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 : 0.672 ------------------------------------------------------------------------------- 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: 9.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 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... Flipped N/Q/H residues before XYZ refinement: 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 77 HIS l 5 ASN l 6 GLN ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 50 HIS p 46 ASN p 87 GLN t 42 ASN t 64 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.104768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.086500 restraints weight = 74441.239| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.71 r_work: 0.2818 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 38419 Z= 0.319 Angle : 0.701 12.162 57451 Z= 0.361 Chirality : 0.041 0.347 7345 Planarity : 0.006 0.074 3085 Dihedral : 23.761 177.509 19057 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % 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: -3.59 (0.19), residues: 1380 helix: -2.00 (0.19), residues: 484 sheet: -2.73 (0.30), residues: 241 loop : -2.46 (0.21), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG d 5 TYR 0.020 0.002 TYR p 40 PHE 0.031 0.002 PHE k 61 TRP 0.018 0.002 TRP k 44 HIS 0.013 0.002 HIS k 118 Details of bonding type rmsd covalent geometry : bond 0.00614 (38419) covalent geometry : angle 0.70119 (57451) hydrogen bonds : bond 0.06256 ( 1305) hydrogen bonds : angle 3.87821 ( 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 397 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 333 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 77 GLN cc_start: 0.7161 (pt0) cc_final: 0.6683 (pm20) REVERT: b 151 ILE cc_start: 0.6828 (OUTLIER) cc_final: 0.6553 (pp) REVERT: d 47 TYR cc_start: 0.9196 (t80) cc_final: 0.8939 (t80) REVERT: d 119 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8240 (pt) REVERT: d 149 ASN cc_start: 0.7248 (t0) cc_final: 0.6363 (t0) REVERT: f 5 GLU cc_start: 0.7768 (tt0) cc_final: 0.7465 (tt0) REVERT: f 60 TYR cc_start: 0.8645 (m-80) cc_final: 0.8425 (m-80) REVERT: f 79 LEU cc_start: 0.8360 (mm) cc_final: 0.7971 (mt) REVERT: h 22 HIS cc_start: 0.8834 (OUTLIER) cc_final: 0.8143 (m-70) REVERT: h 39 ILE cc_start: 0.9288 (mm) cc_final: 0.9073 (mt) REVERT: h 98 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8569 (mp) REVERT: k 24 ARG cc_start: 0.8158 (tpt-90) cc_final: 0.7803 (tpt-90) REVERT: k 65 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7682 (mmt) REVERT: k 125 LYS cc_start: 0.8205 (tmmt) cc_final: 0.7639 (tptm) REVERT: l 60 SER cc_start: 0.8277 (t) cc_final: 0.7808 (t) REVERT: o 64 ARG cc_start: 0.8213 (tpm170) cc_final: 0.7948 (tpm170) REVERT: p 21 VAL cc_start: 0.9406 (OUTLIER) cc_final: 0.9164 (m) REVERT: p 62 ASN cc_start: 0.8318 (m-40) cc_final: 0.7937 (m110) REVERT: q 28 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7609 (mm-30) REVERT: q 70 SER cc_start: 0.9236 (t) cc_final: 0.9010 (t) REVERT: r 27 ASP cc_start: 0.8414 (OUTLIER) cc_final: 0.7712 (t0) outliers start: 64 outliers final: 43 residues processed: 371 average time/residue: 0.2281 time to fit residues: 133.2847 Evaluate side-chains 374 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 324 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain o residue 45 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: 0.9990 chunk 216 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 154 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 208 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 67 GLN 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 37 ASN o 50 HIS p 87 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.104305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.087268 restraints weight = 74266.568| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.49 r_work: 0.2805 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 38419 Z= 0.298 Angle : 0.672 11.888 57451 Z= 0.345 Chirality : 0.040 0.298 7345 Planarity : 0.005 0.069 3085 Dihedral : 23.673 179.715 19057 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 6.72 % Allowed : 18.99 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.21), residues: 1380 helix: -1.07 (0.22), residues: 491 sheet: -2.64 (0.30), residues: 246 loop : -2.26 (0.23), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG h 72 TYR 0.017 0.002 TYR f 8 PHE 0.022 0.002 PHE k 61 TRP 0.014 0.002 TRP k 44 HIS 0.021 0.002 HIS h 22 Details of bonding type rmsd covalent geometry : bond 0.00574 (38419) covalent geometry : angle 0.67158 (57451) hydrogen bonds : bond 0.06097 ( 1305) hydrogen bonds : angle 3.68486 ( 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 412 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 331 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 73 LYS cc_start: 0.7439 (tptt) cc_final: 0.7195 (ttpt) REVERT: b 77 GLN cc_start: 0.7146 (pt0) cc_final: 0.6626 (pm20) REVERT: b 151 ILE cc_start: 0.6731 (OUTLIER) cc_final: 0.6466 (pp) REVERT: d 119 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8320 (pt) REVERT: e 14 ARG cc_start: 0.8426 (tpp-160) cc_final: 0.8217 (tpp80) REVERT: f 2 ARG cc_start: 0.8053 (mtt-85) cc_final: 0.7732 (mtt-85) REVERT: f 78 ARG cc_start: 0.8733 (tmm-80) cc_final: 0.8376 (tmm-80) REVERT: f 79 LEU cc_start: 0.8452 (mm) cc_final: 0.8116 (mt) REVERT: h 39 ILE cc_start: 0.9254 (mm) cc_final: 0.9022 (mt) REVERT: h 98 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8562 (mp) REVERT: k 24 ARG cc_start: 0.8149 (tpt-90) cc_final: 0.7814 (tpt-90) REVERT: k 65 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7707 (mmt) REVERT: k 125 LYS cc_start: 0.8279 (tmmt) cc_final: 0.7674 (tptm) REVERT: l 18 LYS cc_start: 0.7622 (ttpp) cc_final: 0.7295 (ttpp) REVERT: l 60 SER cc_start: 0.8193 (t) cc_final: 0.7765 (t) REVERT: p 50 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8613 (pt) REVERT: p 62 ASN cc_start: 0.8340 (m-40) cc_final: 0.7917 (m110) REVERT: q 28 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7677 (mm-30) REVERT: q 70 SER cc_start: 0.9232 (t) cc_final: 0.8968 (t) REVERT: r 27 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.7703 (t70) outliers start: 81 outliers final: 59 residues processed: 382 average time/residue: 0.2363 time to fit residues: 141.0301 Evaluate side-chains 381 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 316 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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 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 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: 0.0980 chunk 138 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 173 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 106 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3565 r_free = 0.3565 target = 0.104089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.085581 restraints weight = 74011.156| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.67 r_work: 0.2805 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 38419 Z= 0.301 Angle : 0.669 11.849 57451 Z= 0.343 Chirality : 0.040 0.268 7345 Planarity : 0.005 0.067 3085 Dihedral : 23.638 179.644 19057 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 7.30 % Allowed : 20.65 % Favored : 72.06 % 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: -2.57 (0.21), residues: 1380 helix: -0.69 (0.23), residues: 488 sheet: -2.44 (0.30), residues: 252 loop : -2.14 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG d 200 TYR 0.022 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 covalent geometry : bond 0.00580 (38419) covalent geometry : angle 0.66915 (57451) hydrogen bonds : bond 0.06023 ( 1305) hydrogen bonds : angle 3.61953 ( 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 407 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 319 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 73 LYS cc_start: 0.7436 (tptt) cc_final: 0.7166 (ttpt) REVERT: b 77 GLN cc_start: 0.7056 (pt0) cc_final: 0.6486 (pm20) REVERT: b 151 ILE cc_start: 0.6703 (OUTLIER) cc_final: 0.6451 (pp) REVERT: d 119 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8339 (pt) REVERT: e 14 ARG cc_start: 0.8483 (tpp-160) cc_final: 0.8277 (tpp80) REVERT: f 2 ARG cc_start: 0.8081 (mtt-85) cc_final: 0.7772 (mtt-85) REVERT: f 66 LYS cc_start: 0.8381 (tptp) cc_final: 0.8121 (tptt) REVERT: f 74 ASP cc_start: 0.8403 (p0) cc_final: 0.7877 (p0) REVERT: f 78 ARG cc_start: 0.8871 (tmm-80) cc_final: 0.8510 (tmm-80) REVERT: f 79 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8165 (mt) REVERT: h 39 ILE cc_start: 0.9252 (mm) cc_final: 0.9020 (mt) REVERT: h 61 ARG cc_start: 0.8451 (ttm110) cc_final: 0.8015 (ttm170) REVERT: h 98 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8568 (mp) REVERT: k 24 ARG cc_start: 0.8161 (tpt-90) cc_final: 0.7896 (tpt-90) REVERT: k 65 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7738 (mmt) REVERT: k 87 LYS cc_start: 0.8434 (ttmt) cc_final: 0.8208 (ttpt) REVERT: k 125 LYS cc_start: 0.8392 (tmmt) cc_final: 0.7724 (tptm) REVERT: l 60 SER cc_start: 0.8127 (t) cc_final: 0.7702 (t) REVERT: o 26 GLU cc_start: 0.8561 (mp0) cc_final: 0.8280 (mp0) REVERT: p 50 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8483 (pt) REVERT: q 4 ARG cc_start: 0.7059 (tpm170) cc_final: 0.6788 (tpm170) REVERT: q 28 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7671 (mm-30) REVERT: q 70 SER cc_start: 0.9248 (t) cc_final: 0.8970 (t) REVERT: r 27 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7551 (t70) REVERT: r 35 LYS cc_start: 0.8693 (mptt) cc_final: 0.8206 (mptt) outliers start: 88 outliers final: 64 residues processed: 372 average time/residue: 0.2298 time to fit residues: 134.4969 Evaluate side-chains 380 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 309 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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 190 ASN 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 61 LYS 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 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 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 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 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 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: 0.9990 chunk 228 optimal weight: 5.9990 chunk 166 optimal weight: 8.9990 chunk 176 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 192 optimal weight: 0.0030 chunk 77 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 246 optimal weight: 3.9990 chunk 149 optimal weight: 0.6980 chunk 208 optimal weight: 0.4980 overall best weight: 1.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 89 GLN ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 73 ASN p 87 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.107788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.082481 restraints weight = 74118.252| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 0.91 r_work: 0.2989 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 38419 Z= 0.151 Angle : 0.567 11.298 57451 Z= 0.292 Chirality : 0.034 0.252 7345 Planarity : 0.004 0.069 3085 Dihedral : 23.533 179.308 19057 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 5.56 % Allowed : 23.13 % 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: -2.09 (0.22), residues: 1380 helix: -0.16 (0.24), residues: 483 sheet: -2.43 (0.31), residues: 233 loop : -1.88 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG d 52 TYR 0.020 0.002 TYR f 60 PHE 0.018 0.001 PHE k 61 TRP 0.012 0.001 TRP k 44 HIS 0.019 0.002 HIS o 50 Details of bonding type rmsd covalent geometry : bond 0.00288 (38419) covalent geometry : angle 0.56670 (57451) hydrogen bonds : bond 0.05126 ( 1305) hydrogen bonds : angle 3.38801 ( 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 404 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 337 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 28 LYS cc_start: 0.8056 (ptmt) cc_final: 0.7590 (tptm) REVERT: b 77 GLN cc_start: 0.7067 (pt0) cc_final: 0.6763 (pm20) REVERT: b 151 ILE cc_start: 0.6865 (OUTLIER) cc_final: 0.6641 (pp) REVERT: d 47 TYR cc_start: 0.9192 (t80) cc_final: 0.8966 (t80) REVERT: d 198 TYR cc_start: 0.8905 (m-80) cc_final: 0.8664 (m-80) REVERT: f 2 ARG cc_start: 0.7940 (mtt-85) cc_final: 0.7738 (mtt-85) REVERT: f 74 ASP cc_start: 0.8401 (p0) cc_final: 0.7854 (p0) REVERT: f 78 ARG cc_start: 0.8635 (tmm-80) cc_final: 0.8399 (tmm-80) REVERT: f 79 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8119 (mt) REVERT: h 39 ILE cc_start: 0.9222 (mm) cc_final: 0.9010 (mt) REVERT: k 65 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7502 (mmt) REVERT: k 125 LYS cc_start: 0.8357 (tmmt) cc_final: 0.7738 (tptm) REVERT: o 26 GLU cc_start: 0.8547 (mp0) cc_final: 0.8339 (mp0) REVERT: p 50 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8422 (pt) REVERT: p 62 ASN cc_start: 0.8203 (m-40) cc_final: 0.7839 (m110) REVERT: p 88 LYS cc_start: 0.8312 (ttmm) cc_final: 0.7986 (ttpp) REVERT: q 4 ARG cc_start: 0.6816 (tpm170) cc_final: 0.6552 (tpm170) REVERT: q 28 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7630 (mm-30) REVERT: q 53 ASN cc_start: 0.8408 (m110) cc_final: 0.8137 (m-40) REVERT: q 70 SER cc_start: 0.9226 (t) cc_final: 0.8910 (t) REVERT: r 27 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7299 (t70) REVERT: r 73 LEU cc_start: 0.9171 (mt) cc_final: 0.8940 (mt) outliers start: 67 outliers final: 48 residues processed: 374 average time/residue: 0.2412 time to fit residues: 140.2023 Evaluate side-chains 367 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 314 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 d residue 19 LEU Chi-restraints excluded: chain d residue 64 THR 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 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 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 86 VAL 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 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 130 TYR 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 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 39 VAL Chi-restraints excluded: chain t residue 57 VAL 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: 9.9990 chunk 167 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 10 optimal weight: 30.0000 chunk 148 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 56 optimal weight: 8.9990 chunk 110 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 22 HIS h 122 ASN ** k 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 50 HIS p 73 ASN p 87 GLN t 77 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.100478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.083246 restraints weight = 74879.450| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.91 r_work: 0.2717 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.089 38419 Z= 0.582 Angle : 0.897 10.987 57451 Z= 0.446 Chirality : 0.051 0.351 7345 Planarity : 0.007 0.064 3085 Dihedral : 23.685 178.415 19057 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 8.04 % Allowed : 21.14 % 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: -2.46 (0.21), residues: 1380 helix: -0.62 (0.22), residues: 487 sheet: -2.27 (0.31), residues: 251 loop : -2.11 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG e 45 TYR 0.026 0.003 TYR r 75 PHE 0.019 0.003 PHE d 160 TRP 0.013 0.003 TRP h 132 HIS 0.013 0.002 HIS o 51 Details of bonding type rmsd covalent geometry : bond 0.01129 (38419) covalent geometry : angle 0.89675 (57451) hydrogen bonds : bond 0.07465 ( 1305) hydrogen bonds : angle 3.85026 ( 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 408 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 311 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 27 MET cc_start: 0.7953 (mmm) cc_final: 0.7332 (mmm) REVERT: b 28 LYS cc_start: 0.8010 (ptmt) cc_final: 0.7527 (tptm) REVERT: b 77 GLN cc_start: 0.7215 (pt0) cc_final: 0.6574 (pm20) REVERT: b 151 ILE cc_start: 0.6876 (OUTLIER) cc_final: 0.6622 (pp) REVERT: d 47 TYR cc_start: 0.9336 (t80) cc_final: 0.9053 (t80) REVERT: d 119 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8412 (pt) REVERT: d 198 TYR cc_start: 0.9089 (m-80) cc_final: 0.8859 (m-80) REVERT: f 74 ASP cc_start: 0.8563 (p0) cc_final: 0.7757 (p0) REVERT: f 79 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8119 (mt) REVERT: h 39 ILE cc_start: 0.9266 (mm) cc_final: 0.9041 (mt) REVERT: h 98 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8573 (mp) REVERT: k 65 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7746 (mmt) REVERT: k 125 LYS cc_start: 0.8473 (tmmt) cc_final: 0.7764 (tptm) REVERT: l 60 SER cc_start: 0.8413 (t) cc_final: 0.7991 (t) REVERT: l 75 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8190 (mp0) REVERT: o 26 GLU cc_start: 0.8713 (mp0) cc_final: 0.8498 (mp0) REVERT: q 16 SER cc_start: 0.9425 (t) cc_final: 0.9183 (m) REVERT: r 27 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.7645 (t70) REVERT: r 35 LYS cc_start: 0.8880 (mptt) cc_final: 0.8562 (mptt) outliers start: 97 outliers final: 74 residues processed: 370 average time/residue: 0.2356 time to fit residues: 137.6781 Evaluate side-chains 385 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 304 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 184 VAL 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 173 THR 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 61 ASN 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 103 ILE Chi-restraints excluded: chain h residue 105 LEU Chi-restraints excluded: chain h residue 108 THR 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 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 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 l residue 132 THR Chi-restraints excluded: chain o residue 12 ILE 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 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 25 HIS 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 57 VAL 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: 0.9990 chunk 120 optimal weight: 9.9990 chunk 165 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 chunk 123 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 chunk 133 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** k 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 73 ASN p 87 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.105684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.080667 restraints weight = 74187.640| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 0.89 r_work: 0.2942 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 38419 Z= 0.185 Angle : 0.606 10.948 57451 Z= 0.311 Chirality : 0.036 0.248 7345 Planarity : 0.005 0.070 3085 Dihedral : 23.573 179.218 19057 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 5.56 % Allowed : 24.21 % Favored : 70.23 % 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: -1.95 (0.22), residues: 1380 helix: -0.01 (0.23), residues: 479 sheet: -2.25 (0.32), residues: 234 loop : -1.87 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG e 45 TYR 0.019 0.002 TYR f 8 PHE 0.017 0.002 PHE d 79 TRP 0.008 0.002 TRP k 44 HIS 0.008 0.001 HIS o 50 Details of bonding type rmsd covalent geometry : bond 0.00355 (38419) covalent geometry : angle 0.60599 (57451) hydrogen bonds : bond 0.05443 ( 1305) hydrogen bonds : angle 3.48847 ( 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 382 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 315 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 28 LYS cc_start: 0.7976 (ptmt) cc_final: 0.7488 (tptm) REVERT: b 151 ILE cc_start: 0.6964 (OUTLIER) cc_final: 0.6752 (pp) REVERT: d 47 TYR cc_start: 0.9263 (t80) cc_final: 0.9012 (t80) REVERT: d 119 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8323 (pt) REVERT: d 120 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8529 (mt) REVERT: f 2 ARG cc_start: 0.8097 (mtt-85) cc_final: 0.7879 (mtt-85) REVERT: f 74 ASP cc_start: 0.8519 (p0) cc_final: 0.7808 (p0) REVERT: f 78 ARG cc_start: 0.8642 (tmm-80) cc_final: 0.8353 (tmm-80) REVERT: f 79 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8140 (mt) REVERT: h 39 ILE cc_start: 0.9249 (mm) cc_final: 0.9034 (mt) REVERT: h 61 ARG cc_start: 0.8539 (ttm110) cc_final: 0.8192 (ttm170) REVERT: h 98 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8645 (mp) REVERT: k 24 ARG cc_start: 0.8187 (tpt-90) cc_final: 0.7704 (tpt-90) REVERT: k 65 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7465 (mmt) REVERT: k 125 LYS cc_start: 0.8440 (tmmt) cc_final: 0.7760 (tptm) REVERT: l 60 SER cc_start: 0.7845 (t) cc_final: 0.7453 (t) REVERT: p 62 ASN cc_start: 0.8179 (m-40) cc_final: 0.7747 (m110) REVERT: q 16 SER cc_start: 0.9298 (t) cc_final: 0.9095 (m) REVERT: q 70 SER cc_start: 0.9233 (t) cc_final: 0.8964 (t) REVERT: r 27 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7507 (t70) outliers start: 67 outliers final: 50 residues processed: 357 average time/residue: 0.2336 time to fit residues: 131.5233 Evaluate side-chains 360 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 303 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 184 VAL Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain d residue 120 LEU 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 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 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 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 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 68 VAL 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 56 LEU 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 225 optimal weight: 9.9990 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: 2.9990 chunk 215 optimal weight: 3.9990 chunk 213 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 chunk 160 optimal weight: 4.9990 chunk 238 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 40 ASN ** k 77 HIS ** 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 = 0.3556 r_free = 0.3556 target = 0.103584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.079057 restraints weight = 74156.169| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 0.91 r_work: 0.2910 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 38419 Z= 0.310 Angle : 0.671 10.847 57451 Z= 0.342 Chirality : 0.040 0.262 7345 Planarity : 0.005 0.065 3085 Dihedral : 23.549 178.181 19057 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 6.14 % Allowed : 23.63 % Favored : 70.23 % 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: -2.01 (0.22), residues: 1380 helix: -0.04 (0.23), residues: 485 sheet: -2.24 (0.32), residues: 240 loop : -1.94 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG k 93 TYR 0.019 0.003 TYR f 8 PHE 0.016 0.002 PHE l 28 TRP 0.010 0.002 TRP d 9 HIS 0.012 0.002 HIS o 51 Details of bonding type rmsd covalent geometry : bond 0.00598 (38419) covalent geometry : angle 0.67122 (57451) hydrogen bonds : bond 0.06006 ( 1305) hydrogen bonds : angle 3.57660 ( 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 382 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 308 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 27 MET cc_start: 0.7972 (mmm) cc_final: 0.7338 (mmm) REVERT: b 28 LYS cc_start: 0.7941 (ptmt) cc_final: 0.7470 (tptm) REVERT: b 151 ILE cc_start: 0.6852 (OUTLIER) cc_final: 0.6598 (pp) REVERT: d 119 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8399 (pt) REVERT: d 120 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8560 (mt) REVERT: f 2 ARG cc_start: 0.8183 (mtt-85) cc_final: 0.7801 (mtt-85) REVERT: f 25 ARG cc_start: 0.8634 (ptm160) cc_final: 0.8429 (ptm160) REVERT: f 66 LYS cc_start: 0.8378 (tptt) cc_final: 0.8136 (tptt) REVERT: f 74 ASP cc_start: 0.8509 (p0) cc_final: 0.7929 (p0) REVERT: f 78 ARG cc_start: 0.8676 (tmm-80) cc_final: 0.8399 (tmm-80) REVERT: f 79 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8078 (mt) REVERT: h 39 ILE cc_start: 0.9266 (mm) cc_final: 0.9045 (mt) REVERT: h 98 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8536 (mp) REVERT: k 24 ARG cc_start: 0.8108 (tpt-90) cc_final: 0.7680 (tpt-90) REVERT: k 65 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7555 (mmt) REVERT: k 125 LYS cc_start: 0.8478 (tmmt) cc_final: 0.7774 (tptm) REVERT: l 60 SER cc_start: 0.7942 (t) cc_final: 0.7447 (t) REVERT: l 75 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8047 (mp0) REVERT: p 62 ASN cc_start: 0.8223 (m-40) cc_final: 0.7788 (m110) REVERT: r 27 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7404 (t70) REVERT: r 35 LYS cc_start: 0.8774 (mptt) cc_final: 0.8304 (mptt) outliers start: 74 outliers final: 61 residues processed: 357 average time/residue: 0.2338 time to fit residues: 131.5125 Evaluate side-chains 372 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 303 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 184 VAL 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 22 THR Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain d residue 120 LEU 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 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 79 LEU Chi-restraints excluded: chain f residue 86 ILE 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 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 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 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 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 39 THR 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 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 40 SER 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: 0.5980 chunk 119 optimal weight: 10.0000 chunk 231 optimal weight: 0.8980 chunk 139 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 163 optimal weight: 0.0170 chunk 146 optimal weight: 0.9980 chunk 237 optimal weight: 2.9990 chunk 186 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 89 GLN ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 146 GLN k 77 HIS ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 87 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.109124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.083877 restraints weight = 74351.555| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 0.90 r_work: 0.3033 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 38419 Z= 0.129 Angle : 0.561 10.490 57451 Z= 0.288 Chirality : 0.033 0.249 7345 Planarity : 0.004 0.069 3085 Dihedral : 23.431 177.985 19057 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 5.31 % Allowed : 24.96 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.22), residues: 1380 helix: 0.44 (0.24), residues: 480 sheet: -2.08 (0.34), residues: 214 loop : -1.74 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG d 3 TYR 0.019 0.002 TYR f 8 PHE 0.015 0.001 PHE k 61 TRP 0.011 0.001 TRP f 43 HIS 0.011 0.001 HIS o 50 Details of bonding type rmsd covalent geometry : bond 0.00247 (38419) covalent geometry : angle 0.56069 (57451) hydrogen bonds : bond 0.05121 ( 1305) hydrogen bonds : angle 3.33906 ( 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 378 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 314 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 27 MET cc_start: 0.7845 (mmm) cc_final: 0.7233 (mmm) REVERT: b 28 LYS cc_start: 0.7875 (ptmt) cc_final: 0.7373 (tptm) REVERT: b 151 ILE cc_start: 0.6799 (OUTLIER) cc_final: 0.6586 (pp) REVERT: f 2 ARG cc_start: 0.7871 (mtt-85) cc_final: 0.7482 (mtt-85) REVERT: f 66 LYS cc_start: 0.8239 (tptt) cc_final: 0.7956 (tptt) REVERT: f 74 ASP cc_start: 0.8365 (p0) cc_final: 0.7815 (p0) REVERT: f 78 ARG cc_start: 0.8558 (tmm-80) cc_final: 0.8337 (tmm-80) REVERT: f 79 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8126 (mt) REVERT: f 89 TYR cc_start: 0.8275 (p90) cc_final: 0.7989 (p90) REVERT: h 39 ILE cc_start: 0.9217 (mm) cc_final: 0.9012 (mt) REVERT: h 61 ARG cc_start: 0.8419 (ttm110) cc_final: 0.8165 (ttm110) REVERT: k 65 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7372 (mmt) REVERT: k 125 LYS cc_start: 0.8367 (tmmt) cc_final: 0.7728 (tptm) REVERT: l 60 SER cc_start: 0.7663 (t) cc_final: 0.7331 (t) REVERT: l 103 LEU cc_start: 0.9085 (mp) cc_final: 0.8858 (mp) REVERT: p 62 ASN cc_start: 0.8053 (m-40) cc_final: 0.7560 (m110) REVERT: q 70 SER cc_start: 0.9206 (t) cc_final: 0.8815 (t) REVERT: q 79 GLU cc_start: 0.8333 (pt0) cc_final: 0.8117 (pt0) REVERT: r 27 ASP cc_start: 0.7772 (OUTLIER) cc_final: 0.7229 (t70) REVERT: r 73 LEU cc_start: 0.9211 (mt) cc_final: 0.9005 (mt) outliers start: 64 outliers final: 49 residues processed: 353 average time/residue: 0.2372 time to fit residues: 131.4096 Evaluate side-chains 349 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 296 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 184 VAL Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 146 GLN 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 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 79 LEU Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 49 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 86 VAL Chi-restraints excluded: chain l residue 30 SER 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 12 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 88 optimal weight: 10.0000 chunk 242 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 170 optimal weight: 0.0570 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: 3.9990 chunk 151 optimal weight: 9.9990 overall best weight: 3.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** b 225 GLN d 146 GLN f 61 ASN ** k 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 87 GLN t 62 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.105148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.087963 restraints weight = 74172.727| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.41 r_work: 0.2828 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 38419 Z= 0.266 Angle : 0.631 10.648 57451 Z= 0.322 Chirality : 0.037 0.250 7345 Planarity : 0.005 0.064 3085 Dihedral : 23.409 179.346 19056 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 4.73 % Allowed : 26.12 % Favored : 69.15 % 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: -1.67 (0.22), residues: 1380 helix: 0.31 (0.24), residues: 480 sheet: -2.21 (0.31), residues: 241 loop : -1.72 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG r 47 TYR 0.022 0.002 TYR d 47 PHE 0.019 0.002 PHE d 79 TRP 0.010 0.002 TRP k 44 HIS 0.010 0.002 HIS o 51 Details of bonding type rmsd covalent geometry : bond 0.00516 (38419) covalent geometry : angle 0.63134 (57451) hydrogen bonds : bond 0.05631 ( 1305) hydrogen bonds : angle 3.47124 ( 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 351 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 294 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 27 MET cc_start: 0.7857 (mmm) cc_final: 0.7109 (mmm) REVERT: b 151 ILE cc_start: 0.6785 (OUTLIER) cc_final: 0.6513 (pp) REVERT: e 41 ASP cc_start: 0.8292 (p0) cc_final: 0.8004 (p0) REVERT: f 71 LYS cc_start: 0.8387 (mmtm) cc_final: 0.8184 (mmmt) REVERT: f 74 ASP cc_start: 0.8436 (p0) cc_final: 0.7723 (p0) REVERT: f 78 ARG cc_start: 0.8669 (tmm-80) cc_final: 0.8414 (tmm-80) REVERT: f 79 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8131 (mt) REVERT: h 39 ILE cc_start: 0.9267 (mm) cc_final: 0.9048 (mt) REVERT: h 61 ARG cc_start: 0.8551 (ttm110) cc_final: 0.8150 (ttm170) REVERT: k 24 ARG cc_start: 0.8115 (tpt-90) cc_final: 0.7729 (tpt90) REVERT: k 65 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7507 (mmt) REVERT: k 125 LYS cc_start: 0.8406 (tmmt) cc_final: 0.7785 (tptm) REVERT: l 60 SER cc_start: 0.7813 (t) cc_final: 0.7466 (t) REVERT: l 75 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8052 (mp0) REVERT: p 62 ASN cc_start: 0.8205 (m-40) cc_final: 0.7643 (m110) REVERT: p 78 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7672 (mm-30) REVERT: q 4 ARG cc_start: 0.6800 (tpm170) cc_final: 0.6581 (tpm170) REVERT: q 70 SER cc_start: 0.9254 (t) cc_final: 0.8950 (t) REVERT: r 27 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7079 (t70) outliers start: 57 outliers final: 48 residues processed: 332 average time/residue: 0.2289 time to fit residues: 120.1845 Evaluate side-chains 345 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 292 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 184 VAL Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 146 GLN 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 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 79 LEU Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 49 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 86 VAL Chi-restraints excluded: chain l residue 30 SER 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 12 SER 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 27 ASP 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: 5.9990 chunk 29 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 207 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 185 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 35 GLN ** d 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 61 ASN ** k 77 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.102677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.084879 restraints weight = 74387.211| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.73 r_work: 0.2778 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 38419 Z= 0.375 Angle : 0.733 11.153 57451 Z= 0.372 Chirality : 0.042 0.267 7345 Planarity : 0.006 0.068 3085 Dihedral : 23.525 178.852 19055 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.78 % Favored : 90.22 % Rotamer: Outliers : 4.73 % Allowed : 26.87 % Favored : 68.41 % 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: -1.95 (0.22), residues: 1380 helix: -0.05 (0.23), residues: 488 sheet: -2.23 (0.31), residues: 240 loop : -1.85 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG l 96 TYR 0.036 0.003 TYR d 47 PHE 0.018 0.002 PHE l 28 TRP 0.012 0.002 TRP d 9 HIS 0.012 0.002 HIS o 51 Details of bonding type rmsd covalent geometry : bond 0.00726 (38419) covalent geometry : angle 0.73282 (57451) hydrogen bonds : bond 0.06585 ( 1305) hydrogen bonds : angle 3.67973 ( 2637) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7766.54 seconds wall clock time: 134 minutes 9.13 seconds (8049.13 seconds total)