Starting phenix.real_space_refine on Mon Oct 26 00:08:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/36pk_77739/10_2026/36pk_77739.cif Found real_map, /net/cci-nas-00/data/ceres_data/36pk_77739/10_2026/36pk_77739.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/36pk_77739/10_2026/36pk_77739.cif" } default_model = "/net/cci-nas-00/data/ceres_data/36pk_77739/10_2026/36pk_77739.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/36pk_77739/10_2026/36pk_77739.map" default_real_map = "/net/cci-nas-00/data/ceres_data/36pk_77739/10_2026/36pk_77739.map" } resolution = 3.3 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= 0.000 sd= 0.013 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 144 5.49 5 S 130 5.16 5 C 11220 2.51 5 N 3156 2.21 5 O 3843 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18493 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1837 Classifications: {'RNA': 85} Modifications used: {'rna2p_pur': 22, 'rna2p_pyr': 16, 'rna3p_pur': 29, 'rna3p_pyr': 18} Link IDs: {'rna2p': 37, 'rna3p': 47} Chain: "B" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 670 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "C" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 546 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "D" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "E" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "F" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "G" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "H" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "I" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "J" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "K" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "L" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "M" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Time building chain proxies: 4.07, per 1000 atoms: 0.22 Number of scatterers: 18493 At special positions: 0 Unit cell: (100.32, 109.44, 194.94, 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 130 16.00 P 144 15.00 O 3843 8.00 N 3156 7.00 C 11220 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 668.3 milliseconds 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3660 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 30 sheets defined 42.2% alpha, 36.9% beta 28 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'D' and resid 19 through 23 removed outlier: 4.027A pdb=" N ASP D 23 " --> pdb=" O THR D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 37 Processing helix chain 'D' and resid 42 through 57 Processing helix chain 'D' and resid 70 through 82 Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 86 through 93 removed outlier: 3.728A pdb=" N ILE D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASP D 91 " --> pdb=" O GLY D 87 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ARG D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 116 Processing helix chain 'D' and resid 117 through 120 removed outlier: 6.564A pdb=" N ASP D 120 " --> pdb=" O LYS D 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 117 through 120' Processing helix chain 'D' and resid 158 through 173 Processing helix chain 'E' and resid 18 through 23 removed outlier: 4.630A pdb=" N LEU E 21 " --> pdb=" O ALA E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 37 removed outlier: 3.632A pdb=" N SER E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU E 35 " --> pdb=" O TYR E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 57 Processing helix chain 'E' and resid 70 through 82 Processing helix chain 'E' and resid 83 through 85 No H-bonds generated for 'chain 'E' and resid 83 through 85' Processing helix chain 'E' and resid 88 through 93 removed outlier: 4.397A pdb=" N ARG E 92 " --> pdb=" O LYS E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 116 Processing helix chain 'E' and resid 118 through 120 No H-bonds generated for 'chain 'E' and resid 118 through 120' Processing helix chain 'E' and resid 158 through 173 Processing helix chain 'F' and resid 18 through 23 removed outlier: 4.634A pdb=" N LEU F 21 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP F 23 " --> pdb=" O THR F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 37 Processing helix chain 'F' and resid 42 through 57 Processing helix chain 'F' and resid 70 through 84 removed outlier: 4.171A pdb=" N LEU F 83 " --> pdb=" O SER F 79 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASN F 84 " --> pdb=" O GLY F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 93 removed outlier: 3.846A pdb=" N ARG F 92 " --> pdb=" O LYS F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 116 Processing helix chain 'F' and resid 117 through 120 removed outlier: 6.620A pdb=" N ASP F 120 " --> pdb=" O LYS F 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 117 through 120' Processing helix chain 'F' and resid 158 through 173 removed outlier: 3.793A pdb=" N MET F 164 " --> pdb=" O GLU F 160 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU F 167 " --> pdb=" O LEU F 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 23 removed outlier: 3.633A pdb=" N ASP G 23 " --> pdb=" O THR G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 42 through 57 Processing helix chain 'G' and resid 70 through 82 Processing helix chain 'G' and resid 86 through 94 removed outlier: 3.775A pdb=" N ILE G 94 " --> pdb=" O ILE G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 116 Processing helix chain 'G' and resid 117 through 120 removed outlier: 6.738A pdb=" N ASP G 120 " --> pdb=" O LYS G 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 117 through 120' Processing helix chain 'G' and resid 158 through 173 removed outlier: 3.576A pdb=" N MET G 164 " --> pdb=" O GLU G 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 23 removed outlier: 3.926A pdb=" N ASP H 23 " --> pdb=" O THR H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 37 Processing helix chain 'H' and resid 42 through 57 Processing helix chain 'H' and resid 70 through 82 Processing helix chain 'H' and resid 83 through 85 No H-bonds generated for 'chain 'H' and resid 83 through 85' Processing helix chain 'H' and resid 86 through 93 removed outlier: 3.587A pdb=" N ASP H 91 " --> pdb=" O GLY H 87 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG H 92 " --> pdb=" O LYS H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 116 Processing helix chain 'H' and resid 117 through 120 removed outlier: 6.122A pdb=" N ASP H 120 " --> pdb=" O LYS H 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 117 through 120' Processing helix chain 'H' and resid 158 through 173 removed outlier: 3.721A pdb=" N MET H 164 " --> pdb=" O GLU H 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 23 Processing helix chain 'I' and resid 26 through 37 removed outlier: 3.525A pdb=" N SER I 34 " --> pdb=" O LYS I 30 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU I 35 " --> pdb=" O TYR I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 57 Processing helix chain 'I' and resid 70 through 82 Processing helix chain 'I' and resid 83 through 85 No H-bonds generated for 'chain 'I' and resid 83 through 85' Processing helix chain 'I' and resid 86 through 93 Processing helix chain 'I' and resid 111 through 116 Processing helix chain 'I' and resid 117 through 120 removed outlier: 6.221A pdb=" N ASP I 120 " --> pdb=" O LYS I 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 117 through 120' Processing helix chain 'I' and resid 158 through 173 removed outlier: 3.685A pdb=" N MET I 164 " --> pdb=" O GLU I 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 23 Processing helix chain 'J' and resid 26 through 37 removed outlier: 3.686A pdb=" N LEU J 35 " --> pdb=" O TYR J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 58 removed outlier: 3.923A pdb=" N CYS J 58 " --> pdb=" O LEU J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 82 Processing helix chain 'J' and resid 83 through 85 No H-bonds generated for 'chain 'J' and resid 83 through 85' Processing helix chain 'J' and resid 86 through 93 Processing helix chain 'J' and resid 111 through 116 Processing helix chain 'J' and resid 117 through 120 removed outlier: 6.536A pdb=" N ASP J 120 " --> pdb=" O LYS J 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 117 through 120' Processing helix chain 'J' and resid 158 through 173 Processing helix chain 'K' and resid 19 through 23 Processing helix chain 'K' and resid 26 through 37 Processing helix chain 'K' and resid 42 through 58 removed outlier: 3.958A pdb=" N CYS K 58 " --> pdb=" O LEU K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 82 Processing helix chain 'K' and resid 83 through 85 No H-bonds generated for 'chain 'K' and resid 83 through 85' Processing helix chain 'K' and resid 86 through 93 removed outlier: 3.737A pdb=" N ARG K 92 " --> pdb=" O LYS K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 116 Processing helix chain 'K' and resid 117 through 120 removed outlier: 6.701A pdb=" N ASP K 120 " --> pdb=" O LYS K 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 117 through 120' Processing helix chain 'K' and resid 158 through 173 Processing helix chain 'L' and resid 19 through 23 removed outlier: 3.831A pdb=" N ASP L 23 " --> pdb=" O THR L 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 37 Processing helix chain 'L' and resid 42 through 57 Processing helix chain 'L' and resid 70 through 83 removed outlier: 4.136A pdb=" N LEU L 83 " --> pdb=" O SER L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 93 removed outlier: 4.297A pdb=" N ARG L 92 " --> pdb=" O LYS L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 116 Processing helix chain 'L' and resid 158 through 173 Processing helix chain 'M' and resid 18 through 23 removed outlier: 4.404A pdb=" N LEU M 21 " --> pdb=" O ALA M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 37 Processing helix chain 'M' and resid 42 through 57 Processing helix chain 'M' and resid 70 through 82 removed outlier: 3.664A pdb=" N LYS M 82 " --> pdb=" O LYS M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 85 No H-bonds generated for 'chain 'M' and resid 83 through 85' Processing helix chain 'M' and resid 86 through 93 removed outlier: 4.426A pdb=" N ARG M 92 " --> pdb=" O LYS M 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 116 Processing helix chain 'M' and resid 117 through 120 removed outlier: 6.591A pdb=" N ASP M 120 " --> pdb=" O LYS M 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 117 through 120' Processing helix chain 'M' and resid 158 through 173 Processing sheet with id=AA1, first strand: chain 'D' and resid 60 through 61 removed outlier: 5.147A pdb=" N PHE D 66 " --> pdb=" O MET D 103 " (cutoff:3.500A) removed outlier: 9.228A pdb=" N VAL D 100 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N GLY D 149 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU D 147 " --> pdb=" O PRO D 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 60 through 61 removed outlier: 5.147A pdb=" N PHE D 66 " --> pdb=" O MET D 103 " (cutoff:3.500A) removed outlier: 9.228A pdb=" N VAL D 100 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N GLY D 149 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU D 147 " --> pdb=" O PRO D 102 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TRP D 144 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU D 3 " --> pdb=" O GLU D 192 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU D 192 " --> pdb=" O LEU D 3 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ASN D 5 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 14 through 15 removed outlier: 3.548A pdb=" N ALA D 132 " --> pdb=" O ILE D 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 60 through 61 removed outlier: 5.232A pdb=" N PHE E 66 " --> pdb=" O MET E 103 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N VAL E 100 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N GLY E 149 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU E 147 " --> pdb=" O PRO E 102 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 60 through 61 removed outlier: 5.232A pdb=" N PHE E 66 " --> pdb=" O MET E 103 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N VAL E 100 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N GLY E 149 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU E 147 " --> pdb=" O PRO E 102 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N TRP E 144 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU E 3 " --> pdb=" O GLU E 192 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU E 192 " --> pdb=" O LEU E 3 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASN E 5 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 14 through 15 Processing sheet with id=AA7, first strand: chain 'F' and resid 60 through 61 removed outlier: 5.427A pdb=" N PHE F 66 " --> pdb=" O MET F 103 " (cutoff:3.500A) removed outlier: 9.621A pdb=" N VAL F 100 " --> pdb=" O GLY F 149 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N GLY F 149 " --> pdb=" O VAL F 100 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLU F 147 " --> pdb=" O PRO F 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 60 through 61 removed outlier: 5.427A pdb=" N PHE F 66 " --> pdb=" O MET F 103 " (cutoff:3.500A) removed outlier: 9.621A pdb=" N VAL F 100 " --> pdb=" O GLY F 149 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N GLY F 149 " --> pdb=" O VAL F 100 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLU F 147 " --> pdb=" O PRO F 102 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N TRP F 144 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU F 3 " --> pdb=" O GLU F 192 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLU F 192 " --> pdb=" O LEU F 3 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASN F 5 " --> pdb=" O MET F 190 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 14 through 15 Processing sheet with id=AB1, first strand: chain 'G' and resid 60 through 61 removed outlier: 5.329A pdb=" N PHE G 66 " --> pdb=" O MET G 103 " (cutoff:3.500A) removed outlier: 9.781A pdb=" N VAL G 100 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N GLY G 149 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLU G 147 " --> pdb=" O PRO G 102 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 60 through 61 removed outlier: 5.329A pdb=" N PHE G 66 " --> pdb=" O MET G 103 " (cutoff:3.500A) removed outlier: 9.781A pdb=" N VAL G 100 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N GLY G 149 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLU G 147 " --> pdb=" O PRO G 102 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N TRP G 144 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU G 3 " --> pdb=" O GLU G 192 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLU G 192 " --> pdb=" O LEU G 3 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASN G 5 " --> pdb=" O MET G 190 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 14 through 15 Processing sheet with id=AB4, first strand: chain 'H' and resid 60 through 61 removed outlier: 5.281A pdb=" N PHE H 66 " --> pdb=" O MET H 103 " (cutoff:3.500A) removed outlier: 9.560A pdb=" N VAL H 100 " --> pdb=" O GLY H 149 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N GLY H 149 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU H 147 " --> pdb=" O PRO H 102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 60 through 61 removed outlier: 5.281A pdb=" N PHE H 66 " --> pdb=" O MET H 103 " (cutoff:3.500A) removed outlier: 9.560A pdb=" N VAL H 100 " --> pdb=" O GLY H 149 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N GLY H 149 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU H 147 " --> pdb=" O PRO H 102 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N TRP H 144 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU H 3 " --> pdb=" O GLU H 192 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLU H 192 " --> pdb=" O LEU H 3 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASN H 5 " --> pdb=" O MET H 190 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 14 through 15 Processing sheet with id=AB7, first strand: chain 'I' and resid 60 through 61 removed outlier: 5.205A pdb=" N PHE I 66 " --> pdb=" O MET I 103 " (cutoff:3.500A) removed outlier: 9.546A pdb=" N VAL I 100 " --> pdb=" O GLY I 149 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N GLY I 149 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLU I 147 " --> pdb=" O PRO I 102 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 60 through 61 removed outlier: 5.205A pdb=" N PHE I 66 " --> pdb=" O MET I 103 " (cutoff:3.500A) removed outlier: 9.546A pdb=" N VAL I 100 " --> pdb=" O GLY I 149 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N GLY I 149 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLU I 147 " --> pdb=" O PRO I 102 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N TRP I 144 " --> pdb=" O GLY I 10 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU I 3 " --> pdb=" O GLU I 192 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLU I 192 " --> pdb=" O LEU I 3 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASN I 5 " --> pdb=" O MET I 190 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 14 through 15 Processing sheet with id=AC1, first strand: chain 'J' and resid 60 through 61 removed outlier: 5.308A pdb=" N PHE J 66 " --> pdb=" O MET J 103 " (cutoff:3.500A) removed outlier: 9.643A pdb=" N VAL J 100 " --> pdb=" O GLY J 149 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N GLY J 149 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLU J 147 " --> pdb=" O PRO J 102 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 60 through 61 removed outlier: 5.308A pdb=" N PHE J 66 " --> pdb=" O MET J 103 " (cutoff:3.500A) removed outlier: 9.643A pdb=" N VAL J 100 " --> pdb=" O GLY J 149 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N GLY J 149 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLU J 147 " --> pdb=" O PRO J 102 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N TRP J 144 " --> pdb=" O GLY J 10 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU J 3 " --> pdb=" O GLU J 192 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU J 192 " --> pdb=" O LEU J 3 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASN J 5 " --> pdb=" O MET J 190 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 14 through 15 Processing sheet with id=AC4, first strand: chain 'K' and resid 60 through 61 removed outlier: 5.240A pdb=" N PHE K 66 " --> pdb=" O MET K 103 " (cutoff:3.500A) removed outlier: 9.408A pdb=" N VAL K 100 " --> pdb=" O GLY K 149 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N GLY K 149 " --> pdb=" O VAL K 100 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLU K 147 " --> pdb=" O PRO K 102 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 60 through 61 removed outlier: 5.240A pdb=" N PHE K 66 " --> pdb=" O MET K 103 " (cutoff:3.500A) removed outlier: 9.408A pdb=" N VAL K 100 " --> pdb=" O GLY K 149 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N GLY K 149 " --> pdb=" O VAL K 100 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLU K 147 " --> pdb=" O PRO K 102 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N TRP K 144 " --> pdb=" O GLY K 10 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU K 3 " --> pdb=" O GLU K 192 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLU K 192 " --> pdb=" O LEU K 3 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASN K 5 " --> pdb=" O MET K 190 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 14 through 15 Processing sheet with id=AC7, first strand: chain 'L' and resid 60 through 61 removed outlier: 5.303A pdb=" N PHE L 66 " --> pdb=" O MET L 103 " (cutoff:3.500A) removed outlier: 8.883A pdb=" N VAL L 100 " --> pdb=" O GLY L 149 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N GLY L 149 " --> pdb=" O VAL L 100 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLU L 147 " --> pdb=" O PRO L 102 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 60 through 61 removed outlier: 5.303A pdb=" N PHE L 66 " --> pdb=" O MET L 103 " (cutoff:3.500A) removed outlier: 8.883A pdb=" N VAL L 100 " --> pdb=" O GLY L 149 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N GLY L 149 " --> pdb=" O VAL L 100 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLU L 147 " --> pdb=" O PRO L 102 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N TRP L 144 " --> pdb=" O GLY L 10 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU L 3 " --> pdb=" O GLU L 192 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLU L 192 " --> pdb=" O LEU L 3 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASN L 5 " --> pdb=" O MET L 190 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 14 through 15 Processing sheet with id=AD1, first strand: chain 'M' and resid 60 through 61 removed outlier: 5.090A pdb=" N PHE M 66 " --> pdb=" O MET M 103 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N VAL M 100 " --> pdb=" O GLY M 149 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N GLY M 149 " --> pdb=" O VAL M 100 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLU M 147 " --> pdb=" O PRO M 102 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 60 through 61 removed outlier: 5.090A pdb=" N PHE M 66 " --> pdb=" O MET M 103 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N VAL M 100 " --> pdb=" O GLY M 149 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N GLY M 149 " --> pdb=" O VAL M 100 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLU M 147 " --> pdb=" O PRO M 102 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N TRP M 144 " --> pdb=" O GLY M 10 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU M 3 " --> pdb=" O GLU M 192 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLU M 192 " --> pdb=" O LEU M 3 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASN M 5 " --> pdb=" O MET M 190 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 14 through 15 861 hydrogen bonds defined for protein. 2388 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 69 hydrogen bonds 128 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 3.21 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3824 1.33 - 1.45: 4724 1.45 - 1.57: 10089 1.57 - 1.69: 285 1.69 - 1.81: 220 Bond restraints: 19142 Sorted by residual: bond pdb=" C1' DC C 13 " pdb=" N1 DC C 13 " ideal model delta sigma weight residual 1.468 1.545 -0.077 1.40e-02 5.10e+03 3.04e+01 bond pdb=" C3' DC C 24 " pdb=" O3' DC C 24 " ideal model delta sigma weight residual 1.435 1.476 -0.041 1.30e-02 5.92e+03 1.01e+01 bond pdb=" C3' DT B 29 " pdb=" C2' DT B 29 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.00e+01 bond pdb=" C3' DA B 23 " pdb=" C2' DA B 23 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.99e+00 bond pdb=" C3' DA B 22 " pdb=" O3' DA B 22 " ideal model delta sigma weight residual 1.435 1.475 -0.040 1.30e-02 5.92e+03 9.34e+00 ... (remaining 19137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 25601 1.63 - 3.25: 760 3.25 - 4.88: 104 4.88 - 6.51: 17 6.51 - 8.13: 2 Bond angle restraints: 26484 Sorted by residual: angle pdb=" O4' DG B 40 " pdb=" C4' DG B 40 " pdb=" C3' DG B 40 " ideal model delta sigma weight residual 106.00 102.19 3.81 6.00e-01 2.78e+00 4.02e+01 angle pdb=" O4' DC C 13 " pdb=" C1' DC C 13 " pdb=" N1 DC C 13 " ideal model delta sigma weight residual 108.00 112.20 -4.20 7.00e-01 2.04e+00 3.60e+01 angle pdb=" O4' DC C 24 " pdb=" C4' DC C 24 " pdb=" C3' DC C 24 " ideal model delta sigma weight residual 106.00 102.49 3.51 6.00e-01 2.78e+00 3.42e+01 angle pdb=" O4' DC C 24 " pdb=" C1' DC C 24 " pdb=" N1 DC C 24 " ideal model delta sigma weight residual 108.00 111.94 -3.94 7.00e-01 2.04e+00 3.16e+01 angle pdb=" C3' G A 78 " pdb=" O3' G A 78 " pdb=" P U A 79 " ideal model delta sigma weight residual 119.70 126.32 -6.62 1.20e+00 6.94e-01 3.04e+01 ... (remaining 26479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.27: 11128 34.27 - 68.54: 503 68.54 - 102.81: 19 102.81 - 137.08: 1 137.08 - 171.35: 12 Dihedral angle restraints: 11663 sinusoidal: 6003 harmonic: 5660 Sorted by residual: dihedral pdb=" O4' U A 30 " pdb=" C1' U A 30 " pdb=" N1 U A 30 " pdb=" C2 U A 30 " ideal model delta sinusoidal sigma weight residual 232.00 65.78 166.22 1 1.70e+01 3.46e-03 6.55e+01 dihedral pdb=" O4' U A 80 " pdb=" C1' U A 80 " pdb=" N1 U A 80 " pdb=" C2 U A 80 " ideal model delta sinusoidal sigma weight residual -160.00 -66.26 -93.74 1 1.50e+01 4.44e-03 4.54e+01 dihedral pdb=" C5' C A 17 " pdb=" C4' C A 17 " pdb=" C3' C A 17 " pdb=" O3' C A 17 " ideal model delta sinusoidal sigma weight residual 147.00 104.32 42.68 1 8.00e+00 1.56e-02 3.97e+01 ... (remaining 11660 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2449 0.062 - 0.123: 490 0.123 - 0.185: 82 0.185 - 0.247: 7 0.247 - 0.308: 3 Chirality restraints: 3031 Sorted by residual: chirality pdb=" C1' G A 56 " pdb=" O4' G A 56 " pdb=" C2' G A 56 " pdb=" N9 G A 56 " both_signs ideal model delta sigma weight residual False 2.47 2.16 0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" C3' C A 17 " pdb=" C4' C A 17 " pdb=" O3' C A 17 " pdb=" C2' C A 17 " both_signs ideal model delta sigma weight residual False -2.74 -2.44 -0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" C3' G A 60 " pdb=" C4' G A 60 " pdb=" O3' G A 60 " pdb=" C2' G A 60 " both_signs ideal model delta sigma weight residual False -2.48 -2.20 -0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 3028 not shown) Planarity restraints: 2844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC C 24 " 0.030 2.00e-02 2.50e+03 1.64e-02 6.07e+00 pdb=" N1 DC C 24 " -0.038 2.00e-02 2.50e+03 pdb=" C2 DC C 24 " -0.002 2.00e-02 2.50e+03 pdb=" O2 DC C 24 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DC C 24 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DC C 24 " 0.003 2.00e-02 2.50e+03 pdb=" N4 DC C 24 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DC C 24 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DC C 24 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 56 " -0.032 2.00e-02 2.50e+03 1.38e-02 5.74e+00 pdb=" N9 G A 56 " 0.033 2.00e-02 2.50e+03 pdb=" C8 G A 56 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G A 56 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G A 56 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G A 56 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G A 56 " -0.010 2.00e-02 2.50e+03 pdb=" N1 G A 56 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G A 56 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G A 56 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G A 56 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G A 56 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A 52 " 0.028 2.00e-02 2.50e+03 1.48e-02 4.93e+00 pdb=" N1 U A 52 " -0.032 2.00e-02 2.50e+03 pdb=" C2 U A 52 " -0.002 2.00e-02 2.50e+03 pdb=" O2 U A 52 " -0.003 2.00e-02 2.50e+03 pdb=" N3 U A 52 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U A 52 " 0.003 2.00e-02 2.50e+03 pdb=" O4 U A 52 " 0.010 2.00e-02 2.50e+03 pdb=" C5 U A 52 " -0.003 2.00e-02 2.50e+03 pdb=" C6 U A 52 " -0.003 2.00e-02 2.50e+03 ... (remaining 2841 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 5905 2.87 - 3.38: 15998 3.38 - 3.89: 29779 3.89 - 4.39: 34314 4.39 - 4.90: 58278 Nonbonded interactions: 144274 Sorted by model distance: nonbonded pdb=" OG SER M 126 " pdb=" NH1 ARG M 133 " model vdw 2.367 3.120 nonbonded pdb=" OG1 THR F 42 " pdb=" OE2 GLU F 44 " model vdw 2.467 3.040 nonbonded pdb=" O2' C A 17 " pdb=" O4' G A 18 " model vdw 2.480 3.040 nonbonded pdb=" O4' DC C 13 " pdb=" O2 DC C 13 " model vdw 2.516 3.040 nonbonded pdb=" O5' G A 70 " pdb=" O4' G A 70 " model vdw 2.553 2.432 ... (remaining 144269 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 18.290 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 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 : 0.004 0.077 19142 Z= 0.267 Angle : 0.651 8.134 26484 Z= 0.526 Chirality : 0.051 0.308 3031 Planarity : 0.004 0.041 2844 Dihedral : 17.386 171.347 8003 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.90 (0.19), residues: 1930 helix: 0.61 (0.19), residues: 750 sheet: 1.13 (0.24), residues: 450 loop : 0.46 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 181 TYR 0.011 0.001 TYR E 59 PHE 0.013 0.001 PHE G 14 TRP 0.006 0.001 TRP E 178 HIS 0.002 0.001 HIS G 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.27 (19142) covalent geometry : angle 0.65103 / 0.53 (26484) hydrogen bonds : bond 0.16817 / 18.61 ( 860) hydrogen bonds : angle 8.07347 / 10.55 ( 2516) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 492 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.3492 (mtm) cc_final: 0.2132 (ttm) REVERT: D 2 LYS cc_start: 0.6282 (mmtp) cc_final: 0.5942 (pttt) REVERT: D 95 MET cc_start: 0.3984 (ptm) cc_final: 0.3679 (ptm) REVERT: D 103 MET cc_start: 0.2674 (ttt) cc_final: 0.2086 (ttp) REVERT: D 117 LYS cc_start: 0.6663 (mtmm) cc_final: 0.6219 (mmmt) REVERT: D 138 ARG cc_start: 0.6043 (mtm180) cc_final: 0.5037 (mtm-85) REVERT: D 164 MET cc_start: 0.5807 (ttp) cc_final: 0.5451 (tmm) REVERT: E 95 MET cc_start: 0.5162 (ptm) cc_final: 0.4763 (ptm) REVERT: E 101 PHE cc_start: 0.7085 (m-80) cc_final: 0.6638 (m-80) REVERT: E 114 GLU cc_start: 0.7398 (tp30) cc_final: 0.6187 (mt-10) REVERT: E 153 ASP cc_start: 0.5760 (t0) cc_final: 0.5287 (m-30) REVERT: E 179 ARG cc_start: 0.7145 (ptt90) cc_final: 0.6160 (ptt-90) REVERT: F 23 ASP cc_start: 0.8397 (t0) cc_final: 0.8184 (t0) REVERT: F 33 LYS cc_start: 0.7916 (mmmt) cc_final: 0.7673 (mttt) REVERT: F 153 ASP cc_start: 0.7609 (t0) cc_final: 0.6901 (t0) REVERT: F 190 MET cc_start: 0.5106 (mmp) cc_final: 0.4852 (ttm) REVERT: G 9 THR cc_start: 0.8948 (m) cc_final: 0.8496 (p) REVERT: G 38 LYS cc_start: 0.8080 (mmmm) cc_final: 0.7834 (mmtp) REVERT: G 107 ASN cc_start: 0.8429 (m110) cc_final: 0.7970 (t0) REVERT: H 2 LYS cc_start: 0.8609 (mmtp) cc_final: 0.8283 (mttt) REVERT: H 39 ARG cc_start: 0.8085 (ttm170) cc_final: 0.7834 (tpm170) REVERT: H 91 ASP cc_start: 0.8922 (m-30) cc_final: 0.8657 (m-30) REVERT: H 95 MET cc_start: 0.8681 (ptm) cc_final: 0.8447 (ptp) REVERT: H 114 GLU cc_start: 0.8611 (tp30) cc_final: 0.8383 (tt0) REVERT: I 1 MET cc_start: 0.8569 (mtm) cc_final: 0.8191 (mtp) REVERT: I 2 LYS cc_start: 0.8479 (mmtp) cc_final: 0.7893 (tttp) REVERT: I 114 GLU cc_start: 0.8030 (tp30) cc_final: 0.7776 (tt0) REVERT: I 188 GLU cc_start: 0.8243 (tt0) cc_final: 0.7854 (mt-10) REVERT: J 1 MET cc_start: 0.7765 (mtm) cc_final: 0.7447 (mtt) REVERT: J 2 LYS cc_start: 0.7930 (mmtp) cc_final: 0.7313 (mtpp) REVERT: J 114 GLU cc_start: 0.8132 (tp30) cc_final: 0.7457 (tm-30) REVERT: J 117 LYS cc_start: 0.8525 (mtmm) cc_final: 0.7992 (mmtt) REVERT: J 151 MET cc_start: 0.8564 (mtm) cc_final: 0.8344 (mtm) REVERT: J 161 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7604 (mt-10) REVERT: K 19 ASP cc_start: 0.7481 (p0) cc_final: 0.7183 (p0) REVERT: K 151 MET cc_start: 0.8472 (mtm) cc_final: 0.7818 (mtt) REVERT: K 171 ASN cc_start: 0.7976 (m-40) cc_final: 0.7358 (m110) REVERT: K 188 GLU cc_start: 0.7274 (tt0) cc_final: 0.6593 (pt0) REVERT: L 6 ILE cc_start: 0.7199 (mt) cc_final: 0.6876 (mp) REVERT: L 147 GLU cc_start: 0.7307 (tt0) cc_final: 0.6919 (pm20) REVERT: L 190 MET cc_start: 0.4346 (mmp) cc_final: 0.3756 (mtm) REVERT: M 6 ILE cc_start: 0.6668 (mt) cc_final: 0.6381 (mm) REVERT: M 68 MET cc_start: 0.5792 (ttm) cc_final: 0.5013 (mpp) outliers start: 0 outliers final: 0 residues processed: 492 average time/residue: 0.1428 time to fit residues: 105.5212 Evaluate side-chains 308 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: [98, 194, 107, 10, 66, 130, 124, 103, 200, 77, 122] chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 0.0970 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 107 ASN K 118 ASN L 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.208072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.145488 restraints weight = 23194.449| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 3.18 r_work: 0.3187 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19142 Z= 0.142 Angle : 0.605 9.313 26484 Z= 0.343 Chirality : 0.049 0.483 3031 Planarity : 0.004 0.063 2844 Dihedral : 21.426 171.898 4093 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 2.03 % Allowed : 9.53 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.46 (0.19), residues: 1930 helix: 1.35 (0.20), residues: 690 sheet: 1.13 (0.24), residues: 450 loop : 0.71 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 39 TYR 0.022 0.001 TYR M 123 PHE 0.020 0.001 PHE D 148 TRP 0.005 0.001 TRP L 144 HIS 0.002 0.001 HIS J 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 (19142) covalent geometry : angle 0.60463 / 0.34 (26484) hydrogen bonds : bond 0.04810 / 5.39 ( 860) hydrogen bonds : angle 6.15470 / 8.01 ( 2516) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 325 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.3378 (mtm) cc_final: 0.2270 (ttm) REVERT: D 2 LYS cc_start: 0.6089 (mmtp) cc_final: 0.5630 (pttt) REVERT: D 33 LYS cc_start: 0.8058 (mmmt) cc_final: 0.7485 (tttp) REVERT: D 40 LYS cc_start: 0.5151 (ttmm) cc_final: 0.4914 (mppt) REVERT: D 77 ILE cc_start: 0.7601 (tt) cc_final: 0.7298 (mt) REVERT: D 95 MET cc_start: 0.3610 (ptm) cc_final: 0.3389 (ptm) REVERT: D 117 LYS cc_start: 0.6721 (mtmm) cc_final: 0.6392 (mmmt) REVERT: D 138 ARG cc_start: 0.5873 (mtm180) cc_final: 0.4979 (mtm-85) REVERT: D 164 MET cc_start: 0.5793 (ttp) cc_final: 0.5476 (tmm) REVERT: E 7 LYS cc_start: 0.8170 (tttt) cc_final: 0.7931 (tttm) REVERT: E 95 MET cc_start: 0.5279 (ptm) cc_final: 0.4779 (ptm) REVERT: E 101 PHE cc_start: 0.7059 (m-80) cc_final: 0.6574 (m-80) REVERT: E 179 ARG cc_start: 0.7082 (ptt90) cc_final: 0.6153 (ptt-90) REVERT: F 113 GLN cc_start: 0.7901 (mp10) cc_final: 0.7628 (mp10) REVERT: F 114 GLU cc_start: 0.8104 (tp30) cc_final: 0.7734 (tm-30) REVERT: F 143 ASP cc_start: 0.6981 (t70) cc_final: 0.6769 (t70) REVERT: F 153 ASP cc_start: 0.7682 (t0) cc_final: 0.6918 (t0) REVERT: F 190 MET cc_start: 0.5030 (mmp) cc_final: 0.4628 (ttm) REVERT: G 9 THR cc_start: 0.9037 (m) cc_final: 0.8618 (p) REVERT: G 107 ASN cc_start: 0.8409 (m110) cc_final: 0.7951 (t0) REVERT: H 95 MET cc_start: 0.8768 (ptm) cc_final: 0.8511 (ptp) REVERT: H 114 GLU cc_start: 0.8626 (tp30) cc_final: 0.8399 (tt0) REVERT: I 1 MET cc_start: 0.8476 (mtm) cc_final: 0.8165 (mtp) REVERT: I 188 GLU cc_start: 0.8225 (tt0) cc_final: 0.7718 (mt-10) REVERT: J 2 LYS cc_start: 0.7115 (mmtp) cc_final: 0.6543 (mtpp) REVERT: J 114 GLU cc_start: 0.7950 (tp30) cc_final: 0.7403 (tm-30) REVERT: J 117 LYS cc_start: 0.8517 (mtmm) cc_final: 0.7993 (mmtt) REVERT: K 19 ASP cc_start: 0.7561 (p0) cc_final: 0.7258 (p0) REVERT: K 111 ASN cc_start: 0.8559 (p0) cc_final: 0.8201 (p0) REVERT: K 151 MET cc_start: 0.8501 (mtm) cc_final: 0.8099 (mtt) REVERT: K 171 ASN cc_start: 0.7927 (m-40) cc_final: 0.7330 (m110) REVERT: L 2 LYS cc_start: 0.7695 (mmtp) cc_final: 0.7374 (mttm) REVERT: L 6 ILE cc_start: 0.7011 (mt) cc_final: 0.6709 (mp) REVERT: L 45 ASP cc_start: 0.6302 (m-30) cc_final: 0.6098 (m-30) REVERT: L 147 GLU cc_start: 0.7388 (tt0) cc_final: 0.7047 (pm20) REVERT: L 190 MET cc_start: 0.4565 (mmp) cc_final: 0.3970 (mtm) REVERT: M 17 HIS cc_start: 0.4490 (t70) cc_final: 0.3662 (t-90) REVERT: M 143 ASP cc_start: 0.5070 (t0) cc_final: 0.4353 (m-30) REVERT: M 147 GLU cc_start: 0.7034 (tt0) cc_final: 0.6661 (pm20) outliers start: 35 outliers final: 18 residues processed: 346 average time/residue: 0.1296 time to fit residues: 68.4018 Evaluate side-chains 294 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 276 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain E residue 19 ASP Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain I residue 68 MET Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain L residue 186 SER Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 191 SER Chi-restraints excluded: chain M residue 140 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: [13, 6, 76, 141, 35, 20, 110, 165, 143, 106, 84] chunk 13 optimal weight: 10.0000 chunk 6 optimal weight: 50.0000 chunk 76 optimal weight: 4.9990 chunk 141 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 165 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 17 HIS I 194 ASN J 107 ASN L 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.204657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.141107 restraints weight = 23421.528| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 3.17 r_work: 0.3120 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 19142 Z= 0.228 Angle : 0.654 9.770 26484 Z= 0.361 Chirality : 0.051 0.384 3031 Planarity : 0.005 0.049 2844 Dihedral : 21.495 170.392 4093 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 3.37 % Allowed : 10.23 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.08 (0.19), residues: 1930 helix: 1.58 (0.21), residues: 630 sheet: 0.88 (0.26), residues: 400 loop : 0.11 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 181 TYR 0.014 0.002 TYR E 31 PHE 0.021 0.002 PHE L 152 TRP 0.008 0.001 TRP J 144 HIS 0.007 0.001 HIS E 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.23 (19142) covalent geometry : angle 0.65418 / 0.36 (26484) hydrogen bonds : bond 0.04752 / 5.31 ( 860) hydrogen bonds : angle 5.62360 / 7.33 ( 2516) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 290 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.3376 (mtm) cc_final: 0.2575 (ttm) REVERT: D 2 LYS cc_start: 0.6154 (mmtp) cc_final: 0.5664 (pttt) REVERT: D 33 LYS cc_start: 0.7943 (mmmt) cc_final: 0.7411 (tttp) REVERT: D 77 ILE cc_start: 0.7801 (tt) cc_final: 0.7558 (mt) REVERT: D 98 ASP cc_start: 0.3675 (t0) cc_final: 0.3437 (t70) REVERT: D 117 LYS cc_start: 0.6665 (mtmm) cc_final: 0.6409 (mmmt) REVERT: D 138 ARG cc_start: 0.5746 (mtm180) cc_final: 0.4884 (mtm-85) REVERT: D 164 MET cc_start: 0.5695 (ttp) cc_final: 0.5376 (tmm) REVERT: E 2 LYS cc_start: 0.6115 (mmtp) cc_final: 0.5665 (ttpt) REVERT: E 85 LYS cc_start: 0.7827 (mttt) cc_final: 0.6984 (tptm) REVERT: E 101 PHE cc_start: 0.7170 (m-80) cc_final: 0.6615 (m-80) REVERT: E 179 ARG cc_start: 0.6966 (ptt90) cc_final: 0.6024 (ptt-90) REVERT: F 153 ASP cc_start: 0.7779 (t0) cc_final: 0.6908 (t0) REVERT: F 190 MET cc_start: 0.5058 (mmp) cc_final: 0.4595 (ttm) REVERT: G 9 THR cc_start: 0.9115 (m) cc_final: 0.8685 (p) REVERT: G 107 ASN cc_start: 0.8414 (m110) cc_final: 0.7933 (t0) REVERT: G 154 GLU cc_start: 0.7266 (pm20) cc_final: 0.6920 (pm20) REVERT: H 95 MET cc_start: 0.8829 (ptm) cc_final: 0.8604 (ptp) REVERT: I 1 MET cc_start: 0.8497 (mtm) cc_final: 0.8203 (mtp) REVERT: I 188 GLU cc_start: 0.8183 (tt0) cc_final: 0.7613 (mt-10) REVERT: J 2 LYS cc_start: 0.7061 (mmtp) cc_final: 0.6543 (mtpp) REVERT: J 114 GLU cc_start: 0.8067 (tp30) cc_final: 0.7421 (tm-30) REVERT: J 117 LYS cc_start: 0.8549 (mtmm) cc_final: 0.7998 (mmtt) REVERT: K 151 MET cc_start: 0.8250 (mtm) cc_final: 0.7769 (mtt) REVERT: L 2 LYS cc_start: 0.7748 (mmtp) cc_final: 0.7390 (mttm) REVERT: L 6 ILE cc_start: 0.7105 (mt) cc_final: 0.6804 (mp) REVERT: L 45 ASP cc_start: 0.6398 (m-30) cc_final: 0.6150 (m-30) REVERT: L 147 GLU cc_start: 0.7382 (tt0) cc_final: 0.7082 (pm20) REVERT: L 190 MET cc_start: 0.4527 (mmp) cc_final: 0.3975 (mtm) REVERT: M 17 HIS cc_start: 0.4381 (t70) cc_final: 0.3601 (t70) REVERT: M 143 ASP cc_start: 0.5086 (t0) cc_final: 0.4328 (m-30) REVERT: M 157 ILE cc_start: 0.5362 (OUTLIER) cc_final: 0.5130 (tt) REVERT: M 164 MET cc_start: 0.7062 (OUTLIER) cc_final: 0.6807 (ptt) outliers start: 58 outliers final: 41 residues processed: 324 average time/residue: 0.1364 time to fit residues: 68.3115 Evaluate side-chains 315 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 272 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain E residue 19 ASP Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 84 ASN Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 133 ARG Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 163 LEU Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain I residue 68 MET Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 151 MET Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 191 SER Chi-restraints excluded: chain M residue 77 ILE Chi-restraints excluded: chain M residue 151 MET Chi-restraints excluded: chain M residue 157 ILE Chi-restraints excluded: chain M residue 164 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: [19, 158, 64, 129, 16, 118, 119, 139, 18, 46, 175] chunk 19 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 118 optimal weight: 0.5980 chunk 119 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 175 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 113 GLN F 17 HIS F 84 ASN J 107 ASN L 26 ASN L 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.205624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.142619 restraints weight = 23489.112| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 3.01 r_work: 0.3188 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19142 Z= 0.150 Angle : 0.583 11.016 26484 Z= 0.324 Chirality : 0.048 0.386 3031 Planarity : 0.004 0.052 2844 Dihedral : 21.467 171.133 4093 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 2.44 % Allowed : 11.98 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.07 (0.19), residues: 1930 helix: 1.26 (0.21), residues: 690 sheet: 0.76 (0.25), residues: 450 loop : 0.34 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 184 TYR 0.014 0.001 TYR E 31 PHE 0.019 0.002 PHE E 148 TRP 0.006 0.001 TRP L 144 HIS 0.002 0.001 HIS I 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (19142) covalent geometry : angle 0.58278 / 0.32 (26484) hydrogen bonds : bond 0.04047 / 4.54 ( 860) hydrogen bonds : angle 5.33664 / 6.93 ( 2516) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 288 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.3494 (mtm) cc_final: 0.2628 (ttm) REVERT: D 2 LYS cc_start: 0.6148 (mmtp) cc_final: 0.5664 (pttt) REVERT: D 33 LYS cc_start: 0.7889 (mmmt) cc_final: 0.7300 (tttp) REVERT: D 35 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7234 (tp) REVERT: D 77 ILE cc_start: 0.7792 (tt) cc_final: 0.7564 (mt) REVERT: D 98 ASP cc_start: 0.3690 (t0) cc_final: 0.3413 (t70) REVERT: D 138 ARG cc_start: 0.5826 (mtm180) cc_final: 0.4885 (mtm-85) REVERT: D 164 MET cc_start: 0.5724 (ttp) cc_final: 0.5411 (tmm) REVERT: E 2 LYS cc_start: 0.6241 (mmtp) cc_final: 0.5753 (ttpt) REVERT: E 7 LYS cc_start: 0.8351 (tttt) cc_final: 0.8144 (tttm) REVERT: E 85 LYS cc_start: 0.7748 (mttt) cc_final: 0.6959 (tptm) REVERT: E 101 PHE cc_start: 0.7215 (m-80) cc_final: 0.6675 (m-80) REVERT: E 118 ASN cc_start: 0.6799 (t0) cc_final: 0.6251 (p0) REVERT: E 179 ARG cc_start: 0.6878 (ptt90) cc_final: 0.5967 (ptt-90) REVERT: F 153 ASP cc_start: 0.7833 (t0) cc_final: 0.7198 (t0) REVERT: F 190 MET cc_start: 0.5028 (mmp) cc_final: 0.4669 (ttm) REVERT: G 9 THR cc_start: 0.9099 (m) cc_final: 0.8742 (p) REVERT: G 107 ASN cc_start: 0.8325 (m110) cc_final: 0.7907 (t0) REVERT: G 154 GLU cc_start: 0.7333 (pm20) cc_final: 0.7125 (pm20) REVERT: H 95 MET cc_start: 0.8726 (ptm) cc_final: 0.8515 (ptp) REVERT: I 1 MET cc_start: 0.8484 (mtm) cc_final: 0.8201 (mtt) REVERT: I 188 GLU cc_start: 0.8176 (tt0) cc_final: 0.7713 (mt-10) REVERT: J 2 LYS cc_start: 0.7109 (mmtp) cc_final: 0.6688 (mtpp) REVERT: J 114 GLU cc_start: 0.8044 (tp30) cc_final: 0.7438 (tm-30) REVERT: J 117 LYS cc_start: 0.8453 (mtmm) cc_final: 0.7957 (mmtt) REVERT: K 151 MET cc_start: 0.8343 (mtm) cc_final: 0.7909 (mtt) REVERT: L 1 MET cc_start: 0.6660 (tpp) cc_final: 0.6432 (tpp) REVERT: L 2 LYS cc_start: 0.7768 (mmtp) cc_final: 0.7431 (mttp) REVERT: L 6 ILE cc_start: 0.7223 (mt) cc_final: 0.6843 (mp) REVERT: L 45 ASP cc_start: 0.6390 (m-30) cc_final: 0.6177 (m-30) REVERT: L 147 GLU cc_start: 0.7360 (tt0) cc_final: 0.7055 (pm20) REVERT: L 190 MET cc_start: 0.4666 (mmp) cc_final: 0.4122 (ptp) REVERT: M 14 PHE cc_start: 0.4789 (t80) cc_final: 0.4573 (t80) REVERT: M 17 HIS cc_start: 0.4342 (t70) cc_final: 0.3583 (t70) REVERT: M 150 LEU cc_start: 0.7487 (tp) cc_final: 0.7195 (pp) REVERT: M 157 ILE cc_start: 0.5478 (OUTLIER) cc_final: 0.5212 (tt) REVERT: M 164 MET cc_start: 0.6869 (OUTLIER) cc_final: 0.6604 (ptt) REVERT: M 166 LEU cc_start: 0.7788 (mm) cc_final: 0.7421 (pp) outliers start: 42 outliers final: 26 residues processed: 309 average time/residue: 0.1268 time to fit residues: 60.9045 Evaluate side-chains 304 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 275 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain E residue 19 ASP Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain I residue 68 MET Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 191 SER Chi-restraints excluded: chain M residue 77 ILE Chi-restraints excluded: chain M residue 157 ILE Chi-restraints excluded: chain M residue 164 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: [122, 139, 3, 20, 143, 183, 71, 90, 95, 39, 127] chunk 122 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 143 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 113 GLN J 107 ASN L 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.205886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.144005 restraints weight = 23213.883| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 3.07 r_work: 0.3190 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19142 Z= 0.139 Angle : 0.574 10.208 26484 Z= 0.317 Chirality : 0.047 0.387 3031 Planarity : 0.004 0.053 2844 Dihedral : 21.462 172.152 4093 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.79 % Allowed : 12.38 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.95 (0.19), residues: 1930 helix: 1.36 (0.21), residues: 690 sheet: 0.45 (0.24), residues: 470 loop : 0.23 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 184 TYR 0.015 0.001 TYR E 31 PHE 0.018 0.001 PHE E 148 TRP 0.005 0.001 TRP L 144 HIS 0.003 0.001 HIS E 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (19142) covalent geometry : angle 0.57355 / 0.32 (26484) hydrogen bonds : bond 0.03816 / 4.30 ( 860) hydrogen bonds : angle 5.13479 / 6.66 ( 2516) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 285 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.3450 (mtm) cc_final: 0.2530 (ttm) REVERT: D 2 LYS cc_start: 0.6145 (mmtp) cc_final: 0.5671 (pttt) REVERT: D 33 LYS cc_start: 0.7894 (mmmt) cc_final: 0.7310 (tttp) REVERT: D 35 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7312 (tp) REVERT: D 98 ASP cc_start: 0.3649 (t0) cc_final: 0.3414 (t70) REVERT: D 138 ARG cc_start: 0.5834 (mtm180) cc_final: 0.4949 (mtm-85) REVERT: D 164 MET cc_start: 0.5813 (ttp) cc_final: 0.5544 (tmm) REVERT: E 2 LYS cc_start: 0.6228 (mmtp) cc_final: 0.5750 (ttpt) REVERT: E 85 LYS cc_start: 0.7744 (mttt) cc_final: 0.6954 (tptm) REVERT: E 101 PHE cc_start: 0.7180 (m-80) cc_final: 0.6629 (m-80) REVERT: E 118 ASN cc_start: 0.6557 (t0) cc_final: 0.6110 (p0) REVERT: E 135 MET cc_start: 0.7193 (tpt) cc_final: 0.6652 (tpp) REVERT: E 179 ARG cc_start: 0.6825 (ptt90) cc_final: 0.5899 (ptt-90) REVERT: F 153 ASP cc_start: 0.7877 (t0) cc_final: 0.7256 (t0) REVERT: F 190 MET cc_start: 0.5016 (mmp) cc_final: 0.4607 (ttm) REVERT: G 9 THR cc_start: 0.9115 (m) cc_final: 0.8775 (p) REVERT: G 107 ASN cc_start: 0.8339 (m110) cc_final: 0.7914 (t0) REVERT: H 95 MET cc_start: 0.8745 (ptm) cc_final: 0.8540 (ptp) REVERT: I 1 MET cc_start: 0.8496 (mtm) cc_final: 0.8208 (mtt) REVERT: I 188 GLU cc_start: 0.8182 (tt0) cc_final: 0.7716 (mt-10) REVERT: J 2 LYS cc_start: 0.7102 (mmtp) cc_final: 0.6691 (mtpp) REVERT: J 114 GLU cc_start: 0.8074 (tp30) cc_final: 0.7454 (tm-30) REVERT: J 117 LYS cc_start: 0.8459 (mtmm) cc_final: 0.7940 (mmtt) REVERT: K 151 MET cc_start: 0.8203 (mtm) cc_final: 0.7794 (mtt) REVERT: L 2 LYS cc_start: 0.7771 (mmtp) cc_final: 0.7449 (mttp) REVERT: L 6 ILE cc_start: 0.7210 (mt) cc_final: 0.6947 (mp) REVERT: L 45 ASP cc_start: 0.6392 (m-30) cc_final: 0.6187 (m-30) REVERT: L 68 MET cc_start: 0.6473 (OUTLIER) cc_final: 0.6052 (ttm) REVERT: L 147 GLU cc_start: 0.7399 (tt0) cc_final: 0.7047 (pm20) REVERT: L 190 MET cc_start: 0.4694 (mmp) cc_final: 0.4036 (ptp) REVERT: M 17 HIS cc_start: 0.4307 (t70) cc_final: 0.3554 (t70) REVERT: M 83 LEU cc_start: 0.5354 (mp) cc_final: 0.5121 (pp) REVERT: M 150 LEU cc_start: 0.7548 (tp) cc_final: 0.7337 (pp) REVERT: M 157 ILE cc_start: 0.5481 (OUTLIER) cc_final: 0.5212 (tt) REVERT: M 164 MET cc_start: 0.6847 (OUTLIER) cc_final: 0.6582 (ptt) outliers start: 48 outliers final: 32 residues processed: 312 average time/residue: 0.1259 time to fit residues: 61.3284 Evaluate side-chains 308 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 272 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain E residue 19 ASP Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 133 ARG Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 163 LEU Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain L residue 68 MET Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 191 SER Chi-restraints excluded: chain M residue 77 ILE Chi-restraints excluded: chain M residue 151 MET Chi-restraints excluded: chain M residue 157 ILE Chi-restraints excluded: chain M residue 164 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: [51, 186, 77, 36, 139, 26, 67, 32, 63, 145, 163] chunk 51 optimal weight: 2.9990 chunk 186 optimal weight: 20.0000 chunk 77 optimal weight: 0.6980 chunk 36 optimal weight: 0.1980 chunk 139 optimal weight: 0.9980 chunk 26 optimal weight: 20.0000 chunk 67 optimal weight: 0.9990 chunk 32 optimal weight: 0.0570 chunk 63 optimal weight: 0.7980 chunk 145 optimal weight: 0.5980 chunk 163 optimal weight: 4.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 113 GLN L 84 ASN L 171 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.207416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.147087 restraints weight = 23283.016| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.90 r_work: 0.3237 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19142 Z= 0.113 Angle : 0.554 10.716 26484 Z= 0.307 Chirality : 0.046 0.387 3031 Planarity : 0.004 0.054 2844 Dihedral : 21.449 173.092 4093 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.33 % Allowed : 13.78 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.09 (0.19), residues: 1930 helix: 1.45 (0.21), residues: 690 sheet: 0.51 (0.25), residues: 470 loop : 0.35 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 179 TYR 0.016 0.001 TYR E 31 PHE 0.016 0.001 PHE E 148 TRP 0.005 0.001 TRP L 144 HIS 0.007 0.001 HIS J 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.11 (19142) covalent geometry : angle 0.55357 / 0.31 (26484) hydrogen bonds : bond 0.03567 / 4.03 ( 860) hydrogen bonds : angle 4.96608 / 6.47 ( 2516) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 289 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.3457 (mtm) cc_final: 0.2527 (ttm) REVERT: D 2 LYS cc_start: 0.6194 (mmtp) cc_final: 0.5717 (pttt) REVERT: D 33 LYS cc_start: 0.7783 (mmmt) cc_final: 0.7130 (tttp) REVERT: D 35 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7280 (tp) REVERT: D 91 ASP cc_start: 0.3827 (t0) cc_final: 0.3517 (t0) REVERT: D 98 ASP cc_start: 0.3809 (t0) cc_final: 0.3568 (t70) REVERT: D 127 VAL cc_start: 0.1341 (OUTLIER) cc_final: 0.1127 (t) REVERT: D 138 ARG cc_start: 0.5578 (mtm180) cc_final: 0.4782 (mtm-85) REVERT: D 164 MET cc_start: 0.5844 (ttp) cc_final: 0.5596 (tmm) REVERT: E 2 LYS cc_start: 0.6243 (mmtp) cc_final: 0.5765 (ttpt) REVERT: E 85 LYS cc_start: 0.7764 (mttt) cc_final: 0.6940 (tptm) REVERT: E 101 PHE cc_start: 0.7213 (m-80) cc_final: 0.6679 (m-80) REVERT: E 118 ASN cc_start: 0.6591 (t0) cc_final: 0.6062 (p0) REVERT: E 179 ARG cc_start: 0.6893 (ptt90) cc_final: 0.6021 (ptt-90) REVERT: E 190 MET cc_start: 0.5625 (mmt) cc_final: 0.5399 (mmt) REVERT: F 153 ASP cc_start: 0.7856 (t0) cc_final: 0.7225 (t0) REVERT: F 190 MET cc_start: 0.4927 (mmp) cc_final: 0.4483 (ttm) REVERT: G 9 THR cc_start: 0.9100 (m) cc_final: 0.8751 (p) REVERT: G 107 ASN cc_start: 0.8303 (m110) cc_final: 0.7885 (t0) REVERT: G 114 GLU cc_start: 0.8046 (tp30) cc_final: 0.7582 (tt0) REVERT: G 155 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7634 (mm-30) REVERT: H 44 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7148 (mm-30) REVERT: H 95 MET cc_start: 0.8748 (ptm) cc_final: 0.8532 (ptp) REVERT: H 129 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8363 (mp) REVERT: I 1 MET cc_start: 0.8473 (mtm) cc_final: 0.8185 (mtt) REVERT: I 188 GLU cc_start: 0.8117 (tt0) cc_final: 0.7683 (mt-10) REVERT: J 2 LYS cc_start: 0.6949 (mmtp) cc_final: 0.6516 (mtpp) REVERT: J 90 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8543 (mm) REVERT: J 114 GLU cc_start: 0.8001 (tp30) cc_final: 0.7383 (tm-30) REVERT: J 117 LYS cc_start: 0.8419 (mtmm) cc_final: 0.7916 (mmtt) REVERT: K 151 MET cc_start: 0.8149 (mtm) cc_final: 0.7708 (mtt) REVERT: L 2 LYS cc_start: 0.7808 (mmtp) cc_final: 0.7478 (mttm) REVERT: L 45 ASP cc_start: 0.6429 (m-30) cc_final: 0.6228 (m-30) REVERT: L 68 MET cc_start: 0.6131 (ttm) cc_final: 0.5396 (tmm) REVERT: L 147 GLU cc_start: 0.7351 (tt0) cc_final: 0.7109 (pm20) REVERT: L 190 MET cc_start: 0.5026 (mmp) cc_final: 0.4186 (mtp) REVERT: M 17 HIS cc_start: 0.4256 (t70) cc_final: 0.3550 (t70) REVERT: M 28 LEU cc_start: 0.3652 (mp) cc_final: 0.3392 (mt) REVERT: M 83 LEU cc_start: 0.5353 (mp) cc_final: 0.5063 (pp) REVERT: M 150 LEU cc_start: 0.7868 (tp) cc_final: 0.7440 (pp) REVERT: M 157 ILE cc_start: 0.5549 (OUTLIER) cc_final: 0.5278 (tt) REVERT: M 164 MET cc_start: 0.6844 (OUTLIER) cc_final: 0.6568 (ptt) outliers start: 40 outliers final: 24 residues processed: 310 average time/residue: 0.1282 time to fit residues: 62.1530 Evaluate side-chains 303 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 272 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain H residue 133 ARG Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 90 ILE Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 162 LEU Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain M residue 77 ILE Chi-restraints excluded: chain M residue 151 MET Chi-restraints excluded: chain M residue 157 ILE Chi-restraints excluded: chain M residue 164 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: [67, 124, 105, 193, 160, 174, 148, 71, 79, 10, 163] chunk 67 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 193 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 10 optimal weight: 30.0000 chunk 163 optimal weight: 3.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 168 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.207204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.145566 restraints weight = 23416.718| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 3.12 r_work: 0.3179 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19142 Z= 0.173 Angle : 0.586 10.278 26484 Z= 0.322 Chirality : 0.048 0.388 3031 Planarity : 0.004 0.051 2844 Dihedral : 21.476 174.280 4093 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.73 % Allowed : 13.78 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.91 (0.19), residues: 1930 helix: 1.36 (0.21), residues: 690 sheet: 0.35 (0.24), residues: 470 loop : 0.23 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 179 TYR 0.014 0.001 TYR E 31 PHE 0.014 0.002 PHE K 14 TRP 0.005 0.001 TRP H 144 HIS 0.005 0.001 HIS J 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (19142) covalent geometry : angle 0.58592 / 0.32 (26484) hydrogen bonds : bond 0.03868 / 4.34 ( 860) hydrogen bonds : angle 5.00390 / 6.52 ( 2516) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 274 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.3539 (mtm) cc_final: 0.2581 (ttm) REVERT: D 2 LYS cc_start: 0.6210 (mmtp) cc_final: 0.5724 (pttt) REVERT: D 33 LYS cc_start: 0.7798 (mmmt) cc_final: 0.7150 (tttp) REVERT: D 35 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7301 (tp) REVERT: D 91 ASP cc_start: 0.4074 (t0) cc_final: 0.3797 (t70) REVERT: D 98 ASP cc_start: 0.3809 (t0) cc_final: 0.3560 (t70) REVERT: D 127 VAL cc_start: 0.1244 (OUTLIER) cc_final: 0.0998 (t) REVERT: D 138 ARG cc_start: 0.5684 (mtm180) cc_final: 0.4827 (mtm-85) REVERT: D 164 MET cc_start: 0.5858 (ttp) cc_final: 0.5633 (tmm) REVERT: E 2 LYS cc_start: 0.6238 (mmtp) cc_final: 0.5732 (ttpt) REVERT: E 85 LYS cc_start: 0.7779 (mttt) cc_final: 0.6930 (tptm) REVERT: E 101 PHE cc_start: 0.7142 (m-80) cc_final: 0.6602 (m-80) REVERT: E 118 ASN cc_start: 0.6611 (t0) cc_final: 0.6089 (p0) REVERT: E 135 MET cc_start: 0.7447 (tpt) cc_final: 0.6883 (tpp) REVERT: E 179 ARG cc_start: 0.6918 (ptt90) cc_final: 0.5986 (ptt-90) REVERT: F 153 ASP cc_start: 0.7939 (t0) cc_final: 0.7350 (t0) REVERT: F 190 MET cc_start: 0.4988 (mmp) cc_final: 0.4499 (ttm) REVERT: G 9 THR cc_start: 0.9122 (m) cc_final: 0.8768 (p) REVERT: G 107 ASN cc_start: 0.8345 (m110) cc_final: 0.7884 (t0) REVERT: G 114 GLU cc_start: 0.8098 (tp30) cc_final: 0.7628 (tt0) REVERT: G 155 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7679 (mm-30) REVERT: H 44 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7208 (mm-30) REVERT: H 129 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8497 (mp) REVERT: I 1 MET cc_start: 0.8453 (mtm) cc_final: 0.8146 (mtt) REVERT: I 188 GLU cc_start: 0.8174 (tt0) cc_final: 0.7700 (mt-10) REVERT: J 2 LYS cc_start: 0.7086 (mmtp) cc_final: 0.6689 (mtpp) REVERT: J 114 GLU cc_start: 0.8064 (tp30) cc_final: 0.7415 (tm-30) REVERT: J 117 LYS cc_start: 0.8443 (mtmm) cc_final: 0.7928 (mmtt) REVERT: K 151 MET cc_start: 0.8222 (mtm) cc_final: 0.7799 (mtt) REVERT: L 1 MET cc_start: 0.6389 (tpp) cc_final: 0.6070 (tpp) REVERT: L 2 LYS cc_start: 0.7715 (mmtp) cc_final: 0.7368 (mttm) REVERT: L 68 MET cc_start: 0.5950 (OUTLIER) cc_final: 0.5322 (tmm) REVERT: L 147 GLU cc_start: 0.7345 (tt0) cc_final: 0.7050 (pm20) REVERT: L 190 MET cc_start: 0.5013 (mmp) cc_final: 0.4121 (ptp) REVERT: M 28 LEU cc_start: 0.3659 (mp) cc_final: 0.3403 (mt) REVERT: M 68 MET cc_start: 0.4916 (ttm) cc_final: 0.4609 (mtt) REVERT: M 83 LEU cc_start: 0.5350 (mp) cc_final: 0.5070 (pp) REVERT: M 157 ILE cc_start: 0.5541 (OUTLIER) cc_final: 0.5269 (tt) REVERT: M 164 MET cc_start: 0.6925 (OUTLIER) cc_final: 0.6638 (ptt) outliers start: 47 outliers final: 33 residues processed: 304 average time/residue: 0.1340 time to fit residues: 63.4219 Evaluate side-chains 307 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 267 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain E residue 19 ASP Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain H residue 133 ARG Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain L residue 68 MET Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 151 MET Chi-restraints excluded: chain L residue 162 LEU Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 191 SER Chi-restraints excluded: chain M residue 77 ILE Chi-restraints excluded: chain M residue 157 ILE Chi-restraints excluded: chain M residue 164 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: [161, 20, 34, 133, 164, 110, 1, 28, 69, 186, 58] chunk 161 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 chunk 164 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 69 optimal weight: 0.7980 chunk 186 optimal weight: 20.0000 chunk 58 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 113 GLN ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.207125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.145823 restraints weight = 23237.685| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 3.16 r_work: 0.3176 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19142 Z= 0.162 Angle : 0.580 10.273 26484 Z= 0.320 Chirality : 0.047 0.389 3031 Planarity : 0.004 0.050 2844 Dihedral : 21.493 175.744 4093 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.20 % Allowed : 14.01 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.11 (0.19), residues: 1930 helix: 1.85 (0.21), residues: 630 sheet: 0.21 (0.23), residues: 510 loop : 0.34 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 179 TYR 0.016 0.001 TYR E 31 PHE 0.013 0.002 PHE G 14 TRP 0.005 0.001 TRP L 178 HIS 0.003 0.001 HIS E 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (19142) covalent geometry : angle 0.58029 / 0.32 (26484) hydrogen bonds : bond 0.03766 / 4.22 ( 860) hydrogen bonds : angle 4.97834 / 6.50 ( 2516) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 274 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.3579 (mtm) cc_final: 0.2612 (ttm) REVERT: D 2 LYS cc_start: 0.6180 (mmtp) cc_final: 0.5691 (pttt) REVERT: D 33 LYS cc_start: 0.7785 (mmmt) cc_final: 0.7117 (tttp) REVERT: D 35 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7286 (tp) REVERT: D 91 ASP cc_start: 0.4080 (t0) cc_final: 0.3857 (t70) REVERT: D 98 ASP cc_start: 0.3831 (t0) cc_final: 0.3573 (t70) REVERT: D 138 ARG cc_start: 0.5773 (mtm180) cc_final: 0.4988 (mtm-85) REVERT: D 164 MET cc_start: 0.5832 (ttp) cc_final: 0.5586 (tmm) REVERT: D 190 MET cc_start: 0.5535 (mpp) cc_final: 0.5041 (mtm) REVERT: E 2 LYS cc_start: 0.6299 (mmtp) cc_final: 0.5764 (ttpt) REVERT: E 85 LYS cc_start: 0.7656 (mttt) cc_final: 0.6860 (tptm) REVERT: E 101 PHE cc_start: 0.7084 (m-80) cc_final: 0.6498 (m-80) REVERT: E 118 ASN cc_start: 0.6575 (t0) cc_final: 0.6131 (p0) REVERT: E 179 ARG cc_start: 0.6946 (ptt90) cc_final: 0.6042 (ptt-90) REVERT: F 153 ASP cc_start: 0.7958 (t0) cc_final: 0.7358 (t0) REVERT: F 190 MET cc_start: 0.4959 (mmp) cc_final: 0.4503 (ttm) REVERT: G 9 THR cc_start: 0.9128 (m) cc_final: 0.8760 (p) REVERT: G 107 ASN cc_start: 0.8338 (m110) cc_final: 0.7955 (t0) REVERT: G 114 GLU cc_start: 0.8092 (tp30) cc_final: 0.7616 (tt0) REVERT: G 154 GLU cc_start: 0.7435 (pm20) cc_final: 0.7123 (pm20) REVERT: G 155 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7834 (mm-30) REVERT: H 44 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7194 (mm-30) REVERT: H 129 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8476 (mp) REVERT: I 1 MET cc_start: 0.8471 (mtm) cc_final: 0.8173 (mtt) REVERT: I 188 GLU cc_start: 0.8163 (tt0) cc_final: 0.7677 (mt-10) REVERT: J 2 LYS cc_start: 0.7048 (mmtp) cc_final: 0.6645 (mtpp) REVERT: J 90 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8587 (mm) REVERT: J 114 GLU cc_start: 0.8094 (tp30) cc_final: 0.7383 (tm-30) REVERT: J 117 LYS cc_start: 0.8428 (mtmm) cc_final: 0.7890 (mmtt) REVERT: K 151 MET cc_start: 0.8216 (mtm) cc_final: 0.7777 (mtt) REVERT: K 153 ASP cc_start: 0.7929 (t0) cc_final: 0.7543 (t0) REVERT: L 1 MET cc_start: 0.6358 (tpp) cc_final: 0.6038 (tpp) REVERT: L 2 LYS cc_start: 0.7758 (mmtp) cc_final: 0.7423 (mttm) REVERT: L 45 ASP cc_start: 0.5488 (m-30) cc_final: 0.5237 (m-30) REVERT: L 68 MET cc_start: 0.5801 (OUTLIER) cc_final: 0.4804 (tmm) REVERT: L 147 GLU cc_start: 0.7357 (tt0) cc_final: 0.7095 (pm20) REVERT: L 190 MET cc_start: 0.4992 (mmp) cc_final: 0.4103 (ptp) REVERT: M 83 LEU cc_start: 0.5361 (mp) cc_final: 0.5077 (pp) REVERT: M 103 MET cc_start: 0.7243 (mmt) cc_final: 0.6949 (mmt) REVERT: M 157 ILE cc_start: 0.5545 (OUTLIER) cc_final: 0.5272 (tt) REVERT: M 164 MET cc_start: 0.6925 (OUTLIER) cc_final: 0.6632 (ptt) outliers start: 55 outliers final: 38 residues processed: 307 average time/residue: 0.1223 time to fit residues: 58.6270 Evaluate side-chains 313 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 268 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain H residue 133 ARG Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 163 LEU Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 90 ILE Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 122 ILE Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain L residue 68 MET Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 151 MET Chi-restraints excluded: chain L residue 162 LEU Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain M residue 77 ILE Chi-restraints excluded: chain M residue 157 ILE Chi-restraints excluded: chain M residue 164 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: [74, 100, 112, 174, 37, 69, 18, 16, 85, 26, 124] chunk 74 optimal weight: 1.9990 chunk 100 optimal weight: 0.4980 chunk 112 optimal weight: 0.7980 chunk 174 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 17 HIS E 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.208421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.149467 restraints weight = 23317.887| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.85 r_work: 0.3210 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19142 Z= 0.125 Angle : 0.561 10.443 26484 Z= 0.310 Chirality : 0.046 0.388 3031 Planarity : 0.004 0.050 2844 Dihedral : 21.489 176.953 4093 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.50 % Allowed : 14.71 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.20 (0.19), residues: 1930 helix: 1.41 (0.21), residues: 690 sheet: 0.49 (0.24), residues: 490 loop : 0.64 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 179 TYR 0.016 0.001 TYR E 31 PHE 0.015 0.001 PHE E 148 TRP 0.005 0.001 TRP K 144 HIS 0.003 0.001 HIS J 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (19142) covalent geometry : angle 0.56123 / 0.31 (26484) hydrogen bonds : bond 0.03520 / 3.95 ( 860) hydrogen bonds : angle 4.90430 / 6.40 ( 2516) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 274 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.3806 (mtm) cc_final: 0.2681 (ttm) REVERT: D 2 LYS cc_start: 0.6188 (mmtp) cc_final: 0.5728 (pttt) REVERT: D 33 LYS cc_start: 0.7757 (mmmt) cc_final: 0.7052 (tttp) REVERT: D 35 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7155 (tp) REVERT: D 98 ASP cc_start: 0.3876 (t0) cc_final: 0.3586 (t70) REVERT: D 138 ARG cc_start: 0.5945 (mtm180) cc_final: 0.5074 (mtm-85) REVERT: D 164 MET cc_start: 0.5969 (ttp) cc_final: 0.5696 (tmm) REVERT: D 190 MET cc_start: 0.5654 (mpp) cc_final: 0.5427 (mtt) REVERT: E 2 LYS cc_start: 0.6445 (mmtp) cc_final: 0.5863 (ttpt) REVERT: E 85 LYS cc_start: 0.7662 (mttt) cc_final: 0.6875 (tptm) REVERT: E 101 PHE cc_start: 0.7218 (m-80) cc_final: 0.6648 (m-80) REVERT: E 118 ASN cc_start: 0.6691 (t0) cc_final: 0.6302 (p0) REVERT: E 135 MET cc_start: 0.7422 (tpt) cc_final: 0.6960 (tpp) REVERT: E 179 ARG cc_start: 0.6988 (ptt90) cc_final: 0.6185 (ptt-90) REVERT: F 153 ASP cc_start: 0.8101 (t0) cc_final: 0.7598 (t0) REVERT: F 190 MET cc_start: 0.4804 (mmp) cc_final: 0.4585 (ttm) REVERT: G 9 THR cc_start: 0.9062 (m) cc_final: 0.8779 (p) REVERT: G 107 ASN cc_start: 0.8292 (m110) cc_final: 0.7867 (t0) REVERT: G 114 GLU cc_start: 0.8183 (tp30) cc_final: 0.7833 (tt0) REVERT: G 154 GLU cc_start: 0.7424 (pm20) cc_final: 0.7096 (pm20) REVERT: G 155 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7819 (mm-30) REVERT: H 44 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7343 (mm-30) REVERT: H 129 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8623 (mp) REVERT: I 1 MET cc_start: 0.8479 (mtm) cc_final: 0.8228 (mtt) REVERT: J 2 LYS cc_start: 0.7269 (mmtp) cc_final: 0.6961 (mtpp) REVERT: J 90 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8690 (mm) REVERT: J 114 GLU cc_start: 0.8039 (tp30) cc_final: 0.7686 (tm-30) REVERT: J 117 LYS cc_start: 0.8314 (mtmm) cc_final: 0.7913 (mmtt) REVERT: K 43 ASP cc_start: 0.6611 (m-30) cc_final: 0.6386 (m-30) REVERT: K 151 MET cc_start: 0.8338 (mtm) cc_final: 0.7930 (mtt) REVERT: K 153 ASP cc_start: 0.8071 (t0) cc_final: 0.7843 (t0) REVERT: L 1 MET cc_start: 0.6389 (tpp) cc_final: 0.6023 (tpp) REVERT: L 2 LYS cc_start: 0.7809 (mmtp) cc_final: 0.7450 (mttm) REVERT: L 68 MET cc_start: 0.5912 (OUTLIER) cc_final: 0.5626 (ttm) REVERT: L 190 MET cc_start: 0.5039 (mmp) cc_final: 0.4262 (mtp) REVERT: M 157 ILE cc_start: 0.5570 (OUTLIER) cc_final: 0.5301 (tt) REVERT: M 164 MET cc_start: 0.6823 (OUTLIER) cc_final: 0.6495 (ptt) outliers start: 43 outliers final: 31 residues processed: 298 average time/residue: 0.1228 time to fit residues: 56.3869 Evaluate side-chains 301 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 263 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain F residue 108 CYS Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain H residue 133 ARG Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 163 LEU Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 90 ILE Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain L residue 68 MET Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 151 MET Chi-restraints excluded: chain L residue 162 LEU Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain M residue 77 ILE Chi-restraints excluded: chain M residue 157 ILE Chi-restraints excluded: chain M residue 164 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: [170, 12, 197, 9, 84, 111, 20, 148, 41, 32, 11] chunk 170 optimal weight: 2.9990 chunk 12 optimal weight: 20.0000 chunk 197 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 84 optimal weight: 0.0020 chunk 111 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 11 optimal weight: 30.0000 overall best weight: 3.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 113 GLN ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 168 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.202558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.139459 restraints weight = 23221.899| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.87 r_work: 0.3123 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.064 19142 Z= 0.365 Angle : 0.759 10.440 26484 Z= 0.407 Chirality : 0.056 0.393 3031 Planarity : 0.006 0.061 2844 Dihedral : 21.639 177.757 4093 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.79 % Allowed : 14.42 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.35 (0.19), residues: 1930 helix: 1.22 (0.21), residues: 630 sheet: -0.14 (0.23), residues: 510 loop : -0.18 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 133 TYR 0.018 0.002 TYR F 123 PHE 0.032 0.003 PHE K 14 TRP 0.014 0.002 TRP L 178 HIS 0.009 0.002 HIS E 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00870 / 0.37 (19142) covalent geometry : angle 0.75878 / 0.41 (26484) hydrogen bonds : bond 0.05103 / 5.63 ( 860) hydrogen bonds : angle 5.34348 / 6.96 ( 2516) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 270 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.3849 (mtm) cc_final: 0.2766 (ttp) REVERT: D 2 LYS cc_start: 0.6168 (mmtp) cc_final: 0.5645 (pttt) REVERT: D 33 LYS cc_start: 0.7773 (mmmt) cc_final: 0.7135 (tttp) REVERT: D 35 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7292 (tp) REVERT: D 98 ASP cc_start: 0.3847 (t0) cc_final: 0.3549 (t70) REVERT: D 138 ARG cc_start: 0.5914 (mtm180) cc_final: 0.5050 (mtm-85) REVERT: D 164 MET cc_start: 0.5957 (ttp) cc_final: 0.5664 (tmm) REVERT: E 2 LYS cc_start: 0.6378 (mmtp) cc_final: 0.5857 (ttpt) REVERT: E 19 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.7970 (p0) REVERT: E 85 LYS cc_start: 0.7799 (mttt) cc_final: 0.6940 (tptm) REVERT: E 101 PHE cc_start: 0.7143 (m-80) cc_final: 0.6571 (m-80) REVERT: E 115 LEU cc_start: 0.7217 (tp) cc_final: 0.6961 (tp) REVERT: E 135 MET cc_start: 0.7693 (tpt) cc_final: 0.7137 (tpp) REVERT: E 179 ARG cc_start: 0.6908 (ptt90) cc_final: 0.6456 (ptm-80) REVERT: F 17 HIS cc_start: 0.8967 (OUTLIER) cc_final: 0.8317 (t-90) REVERT: F 153 ASP cc_start: 0.8138 (t0) cc_final: 0.7543 (t0) REVERT: F 190 MET cc_start: 0.5062 (mmp) cc_final: 0.4575 (ttm) REVERT: G 9 THR cc_start: 0.9154 (m) cc_final: 0.8754 (p) REVERT: G 107 ASN cc_start: 0.8408 (m110) cc_final: 0.7939 (t0) REVERT: G 114 GLU cc_start: 0.8122 (tp30) cc_final: 0.7733 (tt0) REVERT: G 154 GLU cc_start: 0.7280 (pm20) cc_final: 0.6940 (pm20) REVERT: G 155 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7701 (mm-30) REVERT: H 2 LYS cc_start: 0.8331 (mmtp) cc_final: 0.8002 (mttt) REVERT: H 44 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7306 (mm-30) REVERT: H 129 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8603 (mp) REVERT: I 1 MET cc_start: 0.8544 (mtm) cc_final: 0.8246 (mtt) REVERT: I 188 GLU cc_start: 0.8132 (tt0) cc_final: 0.7682 (mt-10) REVERT: J 2 LYS cc_start: 0.7193 (mmtp) cc_final: 0.6834 (mtpp) REVERT: J 114 GLU cc_start: 0.8124 (tp30) cc_final: 0.7524 (tm-30) REVERT: J 117 LYS cc_start: 0.8444 (mtmm) cc_final: 0.7890 (mmtt) REVERT: K 151 MET cc_start: 0.8190 (mtm) cc_final: 0.7753 (mtt) REVERT: K 153 ASP cc_start: 0.8052 (t0) cc_final: 0.7691 (t0) REVERT: L 1 MET cc_start: 0.6371 (tpp) cc_final: 0.6015 (tpp) REVERT: L 2 LYS cc_start: 0.7799 (mmtp) cc_final: 0.7500 (mttm) REVERT: L 68 MET cc_start: 0.5236 (OUTLIER) cc_final: 0.4826 (ttm) REVERT: L 190 MET cc_start: 0.4790 (mmp) cc_final: 0.4094 (ptp) REVERT: M 103 MET cc_start: 0.7141 (mmt) cc_final: 0.6771 (mmt) outliers start: 48 outliers final: 35 residues processed: 296 average time/residue: 0.1193 time to fit residues: 55.0351 Evaluate side-chains 304 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 263 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain E residue 19 ASP Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain F residue 17 HIS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 108 CYS Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 60 TYR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 122 ILE Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain L residue 68 MET Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 151 MET Chi-restraints excluded: chain L residue 162 LEU Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 191 SER Chi-restraints excluded: chain M residue 77 ILE Chi-restraints excluded: chain M residue 164 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: [111, 122, 69, 73, 21, 53, 164, 158, 167, 32, 118] chunk 111 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 21 optimal weight: 0.0770 chunk 53 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 158 optimal weight: 0.5980 chunk 167 optimal weight: 0.5980 chunk 32 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 113 GLN L 171 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.207136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.145840 restraints weight = 23346.470| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 3.28 r_work: 0.3181 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19142 Z= 0.126 Angle : 0.592 10.479 26484 Z= 0.323 Chirality : 0.047 0.389 3031 Planarity : 0.004 0.049 2844 Dihedral : 21.569 179.369 4093 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.63 % Allowed : 15.87 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.83 (0.19), residues: 1930 helix: 1.67 (0.21), residues: 630 sheet: -0.00 (0.23), residues: 510 loop : 0.17 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 179 TYR 0.018 0.001 TYR G 31 PHE 0.014 0.001 PHE E 148 TRP 0.007 0.001 TRP K 178 HIS 0.003 0.001 HIS J 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (19142) covalent geometry : angle 0.59181 / 0.32 (26484) hydrogen bonds : bond 0.03515 / 3.91 ( 860) hydrogen bonds : angle 4.96427 / 6.46 ( 2516) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4566.95 seconds wall clock time: 78 minutes 49.88 seconds (4729.88 seconds total)