Starting phenix.real_space_refine on Mon Oct 26 08:14:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/36pc_77732/10_2026/36pc_77732.cif Found real_map, /net/cci-nas-00/data/ceres_data/36pc_77732/10_2026/36pc_77732.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/36pc_77732/10_2026/36pc_77732.cif" } default_model = "/net/cci-nas-00/data/ceres_data/36pc_77732/10_2026/36pc_77732.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/36pc_77732/10_2026/36pc_77732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/36pc_77732/10_2026/36pc_77732.map" } resolution = 3.0 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= 0.025 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 135 5.49 5 S 143 5.16 5 C 12120 2.51 5 N 3383 2.21 5 O 4085 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 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: 19866 Number of models: 1 Model: "" Number of chains: 4 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: "A" Number of atoms: 1901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1901 Classifications: {'RNA': 88} Modifications used: {'rna2p_pur': 22, 'rna2p_pyr': 16, 'rna3p_pur': 31, 'rna3p_pyr': 19} Link IDs: {'rna2p': 37, 'rna3p': 50} Chain: "B" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 668 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "C" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 313 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Restraints were copied for chains: E, F, G, H, I, J, K, L, M, N Time building chain proxies: 3.35, per 1000 atoms: 0.17 Number of scatterers: 19866 At special positions: 0 Unit cell: (98.04, 100.32, 206.34, 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 143 16.00 P 135 15.00 O 4085 8.00 N 3383 7.00 C 12120 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: 1.78 Conformation dependent library (CDL) restraints added in 799.3 milliseconds 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4026 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 33 sheets defined 42.1% alpha, 36.9% beta 32 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'D' and resid 19 through 23 removed outlier: 3.550A 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 56 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 Processing helix chain 'D' and resid 111 through 116 Processing helix chain 'D' and resid 117 through 120 removed outlier: 6.452A 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 19 through 23 removed outlier: 3.549A pdb=" N ASP E 23 " --> pdb=" O THR E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 37 Processing helix chain 'E' and resid 42 through 56 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 86 through 93 Processing helix chain 'E' and resid 111 through 116 Processing helix chain 'E' and resid 117 through 120 removed outlier: 6.453A pdb=" N ASP E 120 " --> pdb=" O LYS E 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 117 through 120' Processing helix chain 'E' and resid 158 through 173 Processing helix chain 'F' and resid 19 through 23 removed outlier: 3.550A 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 56 Processing helix chain 'F' and resid 70 through 82 Processing helix chain 'F' and resid 83 through 85 No H-bonds generated for 'chain 'F' and resid 83 through 85' Processing helix chain 'F' and resid 86 through 93 Processing helix chain 'F' and resid 111 through 116 Processing helix chain 'F' and resid 117 through 120 removed outlier: 6.452A 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 Processing helix chain 'G' and resid 19 through 23 removed outlier: 3.549A 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 56 Processing helix chain 'G' and resid 70 through 82 Processing helix chain 'G' and resid 83 through 85 No H-bonds generated for 'chain 'G' and resid 83 through 85' Processing helix chain 'G' and resid 86 through 93 Processing helix chain 'G' and resid 111 through 116 Processing helix chain 'G' and resid 117 through 120 removed outlier: 6.452A 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 Processing helix chain 'H' and resid 19 through 23 removed outlier: 3.549A 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 56 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 Processing helix chain 'H' and resid 111 through 116 Processing helix chain 'H' and resid 117 through 120 removed outlier: 6.453A 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 Processing helix chain 'I' and resid 19 through 23 removed outlier: 3.549A pdb=" N ASP I 23 " --> pdb=" O THR I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 37 Processing helix chain 'I' and resid 42 through 56 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: 6.452A 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 Processing helix chain 'J' and resid 19 through 23 removed outlier: 3.549A pdb=" N ASP J 23 " --> pdb=" O THR J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 37 Processing helix chain 'J' and resid 42 through 56 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: 6.452A 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 removed outlier: 3.550A pdb=" N ASP K 23 " --> pdb=" O THR K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 37 Processing helix chain 'K' and resid 42 through 56 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 Processing helix chain 'K' and resid 111 through 116 Processing helix chain 'K' and resid 117 through 120 removed outlier: 6.453A 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: 3.549A 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 56 Processing helix chain 'L' and resid 70 through 82 Processing helix chain 'L' and resid 83 through 85 No H-bonds generated for 'chain 'L' and resid 83 through 85' Processing helix chain 'L' and resid 86 through 93 Processing helix chain 'L' and resid 111 through 116 Processing helix chain 'L' and resid 117 through 120 removed outlier: 6.452A pdb=" N ASP L 120 " --> pdb=" O LYS L 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 117 through 120' Processing helix chain 'L' and resid 158 through 173 Processing helix chain 'M' and resid 19 through 23 removed outlier: 3.549A pdb=" N ASP M 23 " --> pdb=" O THR M 20 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 37 Processing helix chain 'M' and resid 42 through 56 Processing helix chain 'M' and resid 70 through 82 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 Processing helix chain 'M' and resid 111 through 116 Processing helix chain 'M' and resid 117 through 120 removed outlier: 6.452A 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 helix chain 'N' and resid 19 through 23 removed outlier: 3.549A pdb=" N ASP N 23 " --> pdb=" O THR N 20 " (cutoff:3.500A) Processing helix chain 'N' and resid 26 through 37 Processing helix chain 'N' and resid 42 through 56 Processing helix chain 'N' and resid 70 through 82 Processing helix chain 'N' and resid 83 through 85 No H-bonds generated for 'chain 'N' and resid 83 through 85' Processing helix chain 'N' and resid 86 through 93 Processing helix chain 'N' and resid 111 through 116 Processing helix chain 'N' and resid 117 through 120 removed outlier: 6.453A pdb=" N ASP N 120 " --> pdb=" O LYS N 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 117 through 120' Processing helix chain 'N' and resid 158 through 173 Processing sheet with id=AA1, first strand: chain 'D' and resid 60 through 61 removed outlier: 5.313A pdb=" N PHE D 66 " --> pdb=" O MET D 103 " (cutoff:3.500A) removed outlier: 9.692A pdb=" N VAL D 100 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N GLY D 149 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 4.498A 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: 5.313A pdb=" N PHE D 66 " --> pdb=" O MET D 103 " (cutoff:3.500A) removed outlier: 9.692A pdb=" N VAL D 100 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N GLY D 149 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU D 147 " --> pdb=" O PRO D 102 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N TRP D 144 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU D 3 " --> pdb=" O GLU D 192 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLU D 192 " --> pdb=" O LEU D 3 " (cutoff:3.500A) removed outlier: 6.870A 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 Processing sheet with id=AA4, first strand: chain 'E' and resid 60 through 61 removed outlier: 5.313A pdb=" N PHE E 66 " --> pdb=" O MET E 103 " (cutoff:3.500A) removed outlier: 9.692A pdb=" N VAL E 100 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N GLY E 149 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 4.498A 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: 5.313A pdb=" N PHE E 66 " --> pdb=" O MET E 103 " (cutoff:3.500A) removed outlier: 9.692A pdb=" N VAL E 100 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N GLY E 149 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU E 147 " --> pdb=" O PRO E 102 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N TRP E 144 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU E 3 " --> pdb=" O GLU E 192 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLU E 192 " --> pdb=" O LEU E 3 " (cutoff:3.500A) removed outlier: 6.869A 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: 5.313A pdb=" N PHE F 66 " --> pdb=" O MET F 103 " (cutoff:3.500A) removed outlier: 9.692A pdb=" N VAL F 100 " --> pdb=" O GLY F 149 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N GLY F 149 " --> pdb=" O VAL F 100 " (cutoff:3.500A) removed outlier: 4.498A 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: 5.313A pdb=" N PHE F 66 " --> pdb=" O MET F 103 " (cutoff:3.500A) removed outlier: 9.692A pdb=" N VAL F 100 " --> pdb=" O GLY F 149 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N GLY F 149 " --> pdb=" O VAL F 100 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU F 147 " --> pdb=" O PRO F 102 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N TRP F 144 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU F 3 " --> pdb=" O GLU F 192 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLU F 192 " --> pdb=" O LEU F 3 " (cutoff:3.500A) removed outlier: 6.869A 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: 5.312A pdb=" N PHE G 66 " --> pdb=" O MET G 103 " (cutoff:3.500A) removed outlier: 9.693A pdb=" N VAL G 100 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N GLY G 149 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 4.499A 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: 5.312A pdb=" N PHE G 66 " --> pdb=" O MET G 103 " (cutoff:3.500A) removed outlier: 9.693A pdb=" N VAL G 100 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N GLY G 149 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU G 147 " --> pdb=" O PRO G 102 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N TRP G 144 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU G 3 " --> pdb=" O GLU G 192 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLU G 192 " --> pdb=" O LEU G 3 " (cutoff:3.500A) removed outlier: 6.869A 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: 5.313A pdb=" N PHE H 66 " --> pdb=" O MET H 103 " (cutoff:3.500A) removed outlier: 9.691A pdb=" N VAL H 100 " --> pdb=" O GLY H 149 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N GLY H 149 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 4.499A 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: 5.313A pdb=" N PHE H 66 " --> pdb=" O MET H 103 " (cutoff:3.500A) removed outlier: 9.691A pdb=" N VAL H 100 " --> pdb=" O GLY H 149 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N GLY H 149 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU H 147 " --> pdb=" O PRO H 102 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N TRP H 144 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU H 3 " --> pdb=" O GLU H 192 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLU H 192 " --> pdb=" O LEU H 3 " (cutoff:3.500A) removed outlier: 6.869A 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: 5.312A pdb=" N PHE I 66 " --> pdb=" O MET I 103 " (cutoff:3.500A) removed outlier: 9.692A pdb=" N VAL I 100 " --> pdb=" O GLY I 149 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N GLY I 149 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 4.499A 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: 5.312A pdb=" N PHE I 66 " --> pdb=" O MET I 103 " (cutoff:3.500A) removed outlier: 9.692A pdb=" N VAL I 100 " --> pdb=" O GLY I 149 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N GLY I 149 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU I 147 " --> pdb=" O PRO I 102 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N TRP I 144 " --> pdb=" O GLY I 10 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU I 3 " --> pdb=" O GLU I 192 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLU I 192 " --> pdb=" O LEU I 3 " (cutoff:3.500A) removed outlier: 6.869A 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: 5.312A pdb=" N PHE J 66 " --> pdb=" O MET J 103 " (cutoff:3.500A) removed outlier: 9.692A pdb=" N VAL J 100 " --> pdb=" O GLY J 149 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N GLY J 149 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 4.498A 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: 5.312A pdb=" N PHE J 66 " --> pdb=" O MET J 103 " (cutoff:3.500A) removed outlier: 9.692A pdb=" N VAL J 100 " --> pdb=" O GLY J 149 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N GLY J 149 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU J 147 " --> pdb=" O PRO J 102 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N TRP J 144 " --> pdb=" O GLY J 10 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU J 3 " --> pdb=" O GLU J 192 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLU J 192 " --> pdb=" O LEU J 3 " (cutoff:3.500A) removed outlier: 6.869A 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: 5.312A pdb=" N PHE K 66 " --> pdb=" O MET K 103 " (cutoff:3.500A) removed outlier: 9.691A pdb=" N VAL K 100 " --> pdb=" O GLY K 149 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N GLY K 149 " --> pdb=" O VAL K 100 " (cutoff:3.500A) removed outlier: 4.499A 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: 5.312A pdb=" N PHE K 66 " --> pdb=" O MET K 103 " (cutoff:3.500A) removed outlier: 9.691A pdb=" N VAL K 100 " --> pdb=" O GLY K 149 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N GLY K 149 " --> pdb=" O VAL K 100 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU K 147 " --> pdb=" O PRO K 102 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N TRP K 144 " --> pdb=" O GLY K 10 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU K 3 " --> pdb=" O GLU K 192 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLU K 192 " --> pdb=" O LEU K 3 " (cutoff:3.500A) removed outlier: 6.869A 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: 5.313A pdb=" N PHE L 66 " --> pdb=" O MET L 103 " (cutoff:3.500A) removed outlier: 9.692A pdb=" N VAL L 100 " --> pdb=" O GLY L 149 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N GLY L 149 " --> pdb=" O VAL L 100 " (cutoff:3.500A) removed outlier: 4.499A 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: 5.313A pdb=" N PHE L 66 " --> pdb=" O MET L 103 " (cutoff:3.500A) removed outlier: 9.692A pdb=" N VAL L 100 " --> pdb=" O GLY L 149 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N GLY L 149 " --> pdb=" O VAL L 100 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU L 147 " --> pdb=" O PRO L 102 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N TRP L 144 " --> pdb=" O GLY L 10 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU L 3 " --> pdb=" O GLU L 192 " (cutoff:3.500A) removed outlier: 4.674A 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: 5.312A pdb=" N PHE M 66 " --> pdb=" O MET M 103 " (cutoff:3.500A) removed outlier: 9.691A pdb=" N VAL M 100 " --> pdb=" O GLY M 149 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N GLY M 149 " --> pdb=" O VAL M 100 " (cutoff:3.500A) removed outlier: 4.498A 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: 5.312A pdb=" N PHE M 66 " --> pdb=" O MET M 103 " (cutoff:3.500A) removed outlier: 9.691A pdb=" N VAL M 100 " --> pdb=" O GLY M 149 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N GLY M 149 " --> pdb=" O VAL M 100 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU M 147 " --> pdb=" O PRO M 102 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N TRP M 144 " --> pdb=" O GLY M 10 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU M 3 " --> pdb=" O GLU M 192 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLU M 192 " --> pdb=" O LEU M 3 " (cutoff:3.500A) removed outlier: 6.869A 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 Processing sheet with id=AD4, first strand: chain 'N' and resid 60 through 61 removed outlier: 5.313A pdb=" N PHE N 66 " --> pdb=" O MET N 103 " (cutoff:3.500A) removed outlier: 9.692A pdb=" N VAL N 100 " --> pdb=" O GLY N 149 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N GLY N 149 " --> pdb=" O VAL N 100 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU N 147 " --> pdb=" O PRO N 102 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 60 through 61 removed outlier: 5.313A pdb=" N PHE N 66 " --> pdb=" O MET N 103 " (cutoff:3.500A) removed outlier: 9.692A pdb=" N VAL N 100 " --> pdb=" O GLY N 149 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N GLY N 149 " --> pdb=" O VAL N 100 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU N 147 " --> pdb=" O PRO N 102 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N TRP N 144 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU N 3 " --> pdb=" O GLU N 192 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLU N 192 " --> pdb=" O LEU N 3 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ASN N 5 " --> pdb=" O MET N 190 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 14 through 15 957 hydrogen bonds defined for protein. 2673 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 3.46 Time building geometry restraints manager: 2.50 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: 4442 1.33 - 1.45: 4613 1.45 - 1.57: 10959 1.57 - 1.69: 267 1.69 - 1.80: 242 Bond restraints: 20523 Sorted by residual: bond pdb=" C3' DT B 16 " pdb=" C2' DT B 16 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.31e+01 bond pdb=" C3' DT B 25 " pdb=" C2' DT B 25 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DC B 4 " pdb=" C2' DC B 4 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C1' DT B 16 " pdb=" N1 DT B 16 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.73e+00 bond pdb=" C3' DA B 30 " pdb=" O3' DA B 30 " ideal model delta sigma weight residual 1.435 1.472 -0.037 1.30e-02 5.92e+03 7.97e+00 ... (remaining 20518 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 27442 1.63 - 3.26: 740 3.26 - 4.88: 95 4.88 - 6.51: 26 6.51 - 8.14: 8 Bond angle restraints: 28311 Sorted by residual: angle pdb=" O5' U A 47 " pdb=" C5' U A 47 " pdb=" C4' U A 47 " ideal model delta sigma weight residual 109.40 113.74 -4.34 8.00e-01 1.56e+00 2.95e+01 angle pdb=" O4' DT C 24 " pdb=" C1' DT C 24 " pdb=" N1 DT C 24 " ideal model delta sigma weight residual 108.00 111.79 -3.79 7.00e-01 2.04e+00 2.93e+01 angle pdb=" O4' DG B 29 " pdb=" C4' DG B 29 " pdb=" C3' DG B 29 " ideal model delta sigma weight residual 106.00 103.02 2.98 6.00e-01 2.78e+00 2.47e+01 angle pdb=" O5' A A 22 " pdb=" C5' A A 22 " pdb=" C4' A A 22 " ideal model delta sigma weight residual 109.40 113.19 -3.79 8.00e-01 1.56e+00 2.24e+01 angle pdb=" C2' U A 52 " pdb=" C1' U A 52 " pdb=" N1 U A 52 " ideal model delta sigma weight residual 112.00 117.16 -5.16 1.10e+00 8.26e-01 2.20e+01 ... (remaining 28306 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.60: 12071 35.60 - 71.19: 434 71.19 - 106.79: 16 106.79 - 142.38: 0 142.38 - 177.98: 8 Dihedral angle restraints: 12529 sinusoidal: 6303 harmonic: 6226 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 63.09 168.91 1 1.70e+01 3.46e-03 6.58e+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 -77.08 -82.92 1 1.50e+01 4.44e-03 3.74e+01 dihedral pdb=" C4' DT C 16 " pdb=" C3' DT C 16 " pdb=" O3' DT C 16 " pdb=" P DG C 17 " ideal model delta sinusoidal sigma weight residual -140.00 37.98 -177.98 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 12526 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 3158 0.129 - 0.258: 62 0.258 - 0.386: 0 0.386 - 0.515: 6 0.515 - 0.644: 9 Chirality restraints: 3235 Sorted by residual: chirality pdb=" P DT C 16 " pdb=" OP1 DT C 16 " pdb=" OP2 DT C 16 " pdb=" O5' DT C 16 " both_signs ideal model delta sigma weight residual True 2.34 -2.98 -0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" P DG C 17 " pdb=" OP1 DG C 17 " pdb=" OP2 DG C 17 " pdb=" O5' DG C 17 " both_signs ideal model delta sigma weight residual True 2.34 -2.92 -0.58 2.00e-01 2.50e+01 8.41e+00 chirality pdb=" P DT C 24 " pdb=" OP1 DT C 24 " pdb=" OP2 DT C 24 " pdb=" O5' DT C 24 " both_signs ideal model delta sigma weight residual True 2.34 -2.91 -0.57 2.00e-01 2.50e+01 8.22e+00 ... (remaining 3232 not shown) Planarity restraints: 3105 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U A 52 " 0.033 2.00e-02 2.50e+03 1.77e-02 7.08e+00 pdb=" N1 U A 52 " -0.040 2.00e-02 2.50e+03 pdb=" C2 U A 52 " -0.001 2.00e-02 2.50e+03 pdb=" O2 U A 52 " -0.003 2.00e-02 2.50e+03 pdb=" N3 U A 52 " 0.003 2.00e-02 2.50e+03 pdb=" C4 U A 52 " 0.006 2.00e-02 2.50e+03 pdb=" O4 U A 52 " 0.008 2.00e-02 2.50e+03 pdb=" C5 U A 52 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U A 52 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 27 " 0.032 2.00e-02 2.50e+03 1.73e-02 6.72e+00 pdb=" N1 C A 27 " -0.039 2.00e-02 2.50e+03 pdb=" C2 C A 27 " -0.001 2.00e-02 2.50e+03 pdb=" O2 C A 27 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C A 27 " 0.004 2.00e-02 2.50e+03 pdb=" C4 C A 27 " 0.005 2.00e-02 2.50e+03 pdb=" N4 C A 27 " 0.008 2.00e-02 2.50e+03 pdb=" C5 C A 27 " 0.000 2.00e-02 2.50e+03 pdb=" C6 C A 27 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A 47 " -0.032 2.00e-02 2.50e+03 1.63e-02 5.96e+00 pdb=" N1 U A 47 " 0.033 2.00e-02 2.50e+03 pdb=" C2 U A 47 " 0.006 2.00e-02 2.50e+03 pdb=" O2 U A 47 " 0.003 2.00e-02 2.50e+03 pdb=" N3 U A 47 " -0.005 2.00e-02 2.50e+03 pdb=" C4 U A 47 " -0.003 2.00e-02 2.50e+03 pdb=" O4 U A 47 " -0.011 2.00e-02 2.50e+03 pdb=" C5 U A 47 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U A 47 " 0.006 2.00e-02 2.50e+03 ... (remaining 3102 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 8180 2.96 - 3.45: 17609 3.45 - 3.93: 32701 3.93 - 4.41: 38290 4.41 - 4.90: 63238 Nonbonded interactions: 160018 Sorted by model distance: nonbonded pdb=" N GLY J 87 " pdb=" OP1 DG C 20 " model vdw 2.475 3.120 nonbonded pdb=" O GLU G 154 " pdb=" OE1 GLU L 44 " model vdw 2.477 3.040 nonbonded pdb=" O GLU F 154 " pdb=" OE1 GLU K 44 " model vdw 2.509 3.040 nonbonded pdb=" O4' DT C 24 " pdb=" O2 DT C 24 " model vdw 2.510 3.040 nonbonded pdb=" O5' DG B 8 " pdb=" O4' DG B 8 " model vdw 2.532 2.432 ... (remaining 160013 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' selection = chain 'N' } 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: 3.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.740 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 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 0.041 20523 Z= 0.254 Angle : 0.634 8.139 28311 Z= 0.468 Chirality : 0.060 0.644 3235 Planarity : 0.004 0.031 3105 Dihedral : 16.669 177.979 8503 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % 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 (0.18), residues: 2123 helix: 1.43 (0.18), residues: 836 sheet: 0.98 (0.21), residues: 583 loop : -0.57 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M 179 TYR 0.007 0.001 TYR I 59 PHE 0.009 0.001 PHE D 152 TRP 0.003 0.001 TRP I 144 HIS 0.002 0.001 HIS D 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.25 (20523) covalent geometry : angle 0.63418 / 0.47 (28311) hydrogen bonds : bond 0.14087 / 9.45 ( 958) hydrogen bonds : angle 6.91448 / 6.67 ( 2827) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 439 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 33 LYS cc_start: 0.7863 (tptm) cc_final: 0.7600 (mtmt) REVERT: D 98 ASP cc_start: 0.8341 (t0) cc_final: 0.8056 (t0) REVERT: D 151 MET cc_start: 0.8418 (mtp) cc_final: 0.7924 (mtp) REVERT: D 155 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7129 (tp30) REVERT: E 188 GLU cc_start: 0.8778 (tt0) cc_final: 0.8538 (tt0) REVERT: E 190 MET cc_start: 0.8184 (mmm) cc_final: 0.7908 (mmm) REVERT: F 88 LYS cc_start: 0.8703 (mmmm) cc_final: 0.8415 (mptp) REVERT: F 119 GLN cc_start: 0.8342 (tp40) cc_final: 0.8068 (mm-40) REVERT: F 177 ASP cc_start: 0.8295 (t0) cc_final: 0.8083 (t0) REVERT: G 38 LYS cc_start: 0.7569 (ttmt) cc_final: 0.6927 (mttp) REVERT: G 62 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7158 (mp0) REVERT: G 88 LYS cc_start: 0.8567 (mmmm) cc_final: 0.8329 (mmtt) REVERT: G 99 VAL cc_start: 0.9071 (t) cc_final: 0.8862 (m) REVERT: G 106 LYS cc_start: 0.8272 (ttpt) cc_final: 0.8055 (ttpp) REVERT: G 135 MET cc_start: 0.9087 (tpt) cc_final: 0.8849 (mmt) REVERT: G 151 MET cc_start: 0.8552 (mtp) cc_final: 0.8268 (mtp) REVERT: G 190 MET cc_start: 0.8735 (mmm) cc_final: 0.8375 (mmm) REVERT: H 40 LYS cc_start: 0.7237 (mmtt) cc_final: 0.6781 (mttm) REVERT: H 156 GLN cc_start: 0.8432 (mt0) cc_final: 0.8121 (mt0) REVERT: I 2 LYS cc_start: 0.8348 (mmtm) cc_final: 0.7997 (mmtm) REVERT: I 19 ASP cc_start: 0.8123 (p0) cc_final: 0.7846 (p0) REVERT: I 23 ASP cc_start: 0.8352 (t0) cc_final: 0.8100 (t0) REVERT: I 33 LYS cc_start: 0.7548 (tptm) cc_final: 0.7264 (tmtt) REVERT: I 45 ASP cc_start: 0.7812 (m-30) cc_final: 0.7588 (m-30) REVERT: I 61 ASP cc_start: 0.8522 (t0) cc_final: 0.8295 (t0) REVERT: I 63 GLN cc_start: 0.7664 (mp10) cc_final: 0.7391 (mp10) REVERT: I 119 GLN cc_start: 0.9132 (tp40) cc_final: 0.8917 (tp40) REVERT: I 153 ASP cc_start: 0.8057 (t0) cc_final: 0.7807 (t0) REVERT: I 164 MET cc_start: 0.8415 (ttp) cc_final: 0.8207 (ttm) REVERT: J 98 ASP cc_start: 0.8933 (t0) cc_final: 0.8715 (t70) REVERT: J 113 GLN cc_start: 0.7967 (mp10) cc_final: 0.7761 (mm-40) REVERT: K 38 LYS cc_start: 0.7513 (ttmt) cc_final: 0.7241 (mtpt) REVERT: K 43 ASP cc_start: 0.7725 (m-30) cc_final: 0.7416 (m-30) REVERT: K 61 ASP cc_start: 0.8526 (t0) cc_final: 0.8090 (t70) REVERT: K 120 ASP cc_start: 0.8559 (m-30) cc_final: 0.8344 (m-30) REVERT: L 33 LYS cc_start: 0.6794 (tptm) cc_final: 0.6316 (mmtp) REVERT: L 135 MET cc_start: 0.8909 (tpt) cc_final: 0.8329 (tpt) REVERT: L 171 ASN cc_start: 0.8764 (m-40) cc_final: 0.8505 (m-40) REVERT: N 28 LEU cc_start: 0.7204 (mt) cc_final: 0.6974 (mt) REVERT: N 39 ARG cc_start: 0.6052 (ttm-80) cc_final: 0.5833 (ttp80) REVERT: N 44 GLU cc_start: 0.5663 (mp0) cc_final: 0.5433 (mt-10) REVERT: N 129 ILE cc_start: 0.7669 (mt) cc_final: 0.7468 (mt) outliers start: 0 outliers final: 0 residues processed: 439 average time/residue: 0.7704 time to fit residues: 372.1447 Evaluate side-chains 285 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: [216, 98, 194, 107, 10, 66, 130, 124, 103, 200, 212] chunk 216 optimal weight: 30.0000 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 84 ASN D 171 ASN E 17 HIS E 63 GLN G 5 ASN I 107 ASN J 17 HIS K 118 ASN L 17 HIS N 5 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.129498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.099207 restraints weight = 20914.322| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.00 r_work: 0.2859 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 20523 Z= 0.218 Angle : 0.644 7.543 28311 Z= 0.352 Chirality : 0.050 0.436 3235 Planarity : 0.005 0.045 3105 Dihedral : 20.441 172.259 4202 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 2.38 % Allowed : 10.57 % Favored : 87.05 % 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: 0.88 (0.18), residues: 2123 helix: 1.53 (0.18), residues: 836 sheet: 0.90 (0.23), residues: 473 loop : -0.56 (0.19), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 12 TYR 0.020 0.002 TYR J 59 PHE 0.016 0.002 PHE K 148 TRP 0.010 0.002 TRP E 178 HIS 0.006 0.002 HIS G 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.22 (20523) covalent geometry : angle 0.64366 / 0.35 (28311) hydrogen bonds : bond 0.04712 / 3.14 ( 958) hydrogen bonds : angle 5.25002 / 4.88 ( 2827) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 293 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 33 LYS cc_start: 0.7529 (tptm) cc_final: 0.7127 (mtmt) REVERT: D 91 ASP cc_start: 0.7925 (m-30) cc_final: 0.7711 (m-30) REVERT: D 98 ASP cc_start: 0.8455 (t0) cc_final: 0.8139 (t0) REVERT: D 151 MET cc_start: 0.8453 (mtp) cc_final: 0.8189 (mtp) REVERT: D 155 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7223 (tp30) REVERT: D 179 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.5898 (ppt170) REVERT: E 72 MET cc_start: 0.9230 (ttm) cc_final: 0.8939 (mtp) REVERT: F 19 ASP cc_start: 0.8186 (p0) cc_final: 0.7861 (p0) REVERT: F 88 LYS cc_start: 0.8581 (mmmm) cc_final: 0.8153 (mtmt) REVERT: F 98 ASP cc_start: 0.8566 (t0) cc_final: 0.8299 (t0) REVERT: G 62 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7414 (mp0) REVERT: G 88 LYS cc_start: 0.8517 (mmmm) cc_final: 0.8231 (mmtt) REVERT: G 99 VAL cc_start: 0.9340 (t) cc_final: 0.9078 (m) REVERT: G 151 MET cc_start: 0.8727 (mtp) cc_final: 0.8413 (mtp) REVERT: G 190 MET cc_start: 0.8756 (mmm) cc_final: 0.8415 (mmm) REVERT: H 40 LYS cc_start: 0.8368 (mmtt) cc_final: 0.8127 (mttm) REVERT: I 2 LYS cc_start: 0.8060 (mmtm) cc_final: 0.7603 (mmtp) REVERT: I 61 ASP cc_start: 0.8615 (t0) cc_final: 0.8406 (t0) REVERT: I 119 GLN cc_start: 0.9054 (tp40) cc_final: 0.8787 (tp40) REVERT: J 98 ASP cc_start: 0.8707 (t0) cc_final: 0.8451 (t70) REVERT: J 191 SER cc_start: 0.8249 (p) cc_final: 0.7718 (t) REVERT: K 61 ASP cc_start: 0.8581 (t0) cc_final: 0.8105 (t70) REVERT: K 163 LEU cc_start: 0.8392 (mp) cc_final: 0.8149 (mm) REVERT: K 167 GLU cc_start: 0.8102 (tt0) cc_final: 0.7893 (mp0) REVERT: K 179 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.8396 (pmt170) REVERT: L 135 MET cc_start: 0.9041 (tpt) cc_final: 0.8681 (tpt) REVERT: M 62 GLU cc_start: 0.7895 (tp30) cc_final: 0.7559 (tp30) REVERT: M 179 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.7728 (pmt170) REVERT: N 28 LEU cc_start: 0.7299 (mt) cc_final: 0.7083 (mt) REVERT: N 33 LYS cc_start: 0.7513 (tptm) cc_final: 0.7096 (tptt) REVERT: N 39 ARG cc_start: 0.7562 (ttm-80) cc_final: 0.7255 (ttm170) outliers start: 45 outliers final: 17 residues processed: 315 average time/residue: 0.6810 time to fit residues: 239.1755 Evaluate side-chains 292 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 272 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain G residue 192 GLU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 145 SER Chi-restraints excluded: chain K residue 164 MET Chi-restraints excluded: chain K residue 179 ARG Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 189 ILE Chi-restraints excluded: chain M residue 99 VAL Chi-restraints excluded: chain M residue 179 ARG Chi-restraints excluded: chain N residue 3 LEU Chi-restraints excluded: chain N residue 51 GLU Chi-restraints excluded: chain N residue 167 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: [26, 160, 7, 134, 135, 129, 114, 209, 11, 23, 2] chunk 26 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 209 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 63 GLN G 17 HIS H 171 ASN I 17 HIS K 118 ASN L 107 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.127390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.097260 restraints weight = 20975.574| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.03 r_work: 0.2830 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 20523 Z= 0.231 Angle : 0.631 7.536 28311 Z= 0.347 Chirality : 0.051 0.432 3235 Planarity : 0.005 0.044 3105 Dihedral : 20.496 173.143 4202 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 2.96 % Allowed : 11.79 % Favored : 85.25 % 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: 0.77 (0.18), residues: 2123 helix: 1.43 (0.18), residues: 836 sheet: 0.88 (0.24), residues: 473 loop : -0.65 (0.19), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 12 TYR 0.013 0.002 TYR E 59 PHE 0.015 0.002 PHE N 152 TRP 0.008 0.002 TRP M 144 HIS 0.005 0.002 HIS L 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.23 (20523) covalent geometry : angle 0.63078 / 0.35 (28311) hydrogen bonds : bond 0.04575 / 3.06 ( 958) hydrogen bonds : angle 5.11353 / 4.67 ( 2827) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 269 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 33 LYS cc_start: 0.7532 (tptm) cc_final: 0.6919 (mtmt) REVERT: D 98 ASP cc_start: 0.8501 (t0) cc_final: 0.8212 (t0) REVERT: D 151 MET cc_start: 0.8478 (mtp) cc_final: 0.8183 (mtp) REVERT: D 155 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7430 (tp30) REVERT: D 179 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.5689 (ppt170) REVERT: F 98 ASP cc_start: 0.8532 (t0) cc_final: 0.8291 (t0) REVERT: G 38 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.7769 (ttmt) REVERT: G 62 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7406 (mp0) REVERT: G 88 LYS cc_start: 0.8634 (mmmm) cc_final: 0.8314 (mmtt) REVERT: G 99 VAL cc_start: 0.9372 (t) cc_final: 0.9074 (m) REVERT: G 151 MET cc_start: 0.8783 (mtp) cc_final: 0.8512 (mtp) REVERT: G 154 GLU cc_start: 0.7820 (pm20) cc_final: 0.7530 (pm20) REVERT: G 190 MET cc_start: 0.8763 (mmm) cc_final: 0.8383 (mmm) REVERT: H 40 LYS cc_start: 0.8391 (mmtt) cc_final: 0.8141 (mttm) REVERT: H 156 GLN cc_start: 0.8671 (mt0) cc_final: 0.8042 (mt0) REVERT: I 1 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7607 (mmt) REVERT: I 2 LYS cc_start: 0.7918 (mmtm) cc_final: 0.7446 (mmtp) REVERT: I 33 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.7941 (mmtt) REVERT: I 40 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8445 (tttm) REVERT: I 63 GLN cc_start: 0.8189 (mp10) cc_final: 0.7952 (mp10) REVERT: J 98 ASP cc_start: 0.8741 (t0) cc_final: 0.8465 (t70) REVERT: J 191 SER cc_start: 0.8235 (p) cc_final: 0.7747 (t) REVERT: K 61 ASP cc_start: 0.8611 (t0) cc_final: 0.8155 (t70) REVERT: K 161 GLU cc_start: 0.7314 (mt-10) cc_final: 0.7097 (mt-10) REVERT: K 163 LEU cc_start: 0.8553 (mp) cc_final: 0.8275 (mm) REVERT: K 167 GLU cc_start: 0.8091 (tt0) cc_final: 0.7831 (mp0) REVERT: K 171 ASN cc_start: 0.8642 (m-40) cc_final: 0.8427 (m-40) REVERT: K 179 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8164 (pmt170) REVERT: L 113 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.7825 (mm-40) REVERT: M 62 GLU cc_start: 0.7941 (tp30) cc_final: 0.7634 (tp30) REVERT: M 164 MET cc_start: 0.7517 (OUTLIER) cc_final: 0.7287 (ttp) REVERT: M 167 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7268 (mm-30) REVERT: M 179 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.7588 (pmt170) REVERT: N 39 ARG cc_start: 0.7876 (ttm-80) cc_final: 0.7604 (ttm170) REVERT: N 95 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.7370 (mpp) outliers start: 56 outliers final: 25 residues processed: 305 average time/residue: 0.6841 time to fit residues: 231.9581 Evaluate side-chains 293 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 258 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain G residue 38 LYS Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain G residue 192 GLU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain I residue 40 LYS Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 145 SER Chi-restraints excluded: chain K residue 164 MET Chi-restraints excluded: chain K residue 179 ARG Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 113 GLN Chi-restraints excluded: chain M residue 99 VAL Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 164 MET Chi-restraints excluded: chain M residue 179 ARG Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 51 GLU Chi-restraints excluded: chain N residue 95 MET Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 167 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: [55, 87, 58, 48, 219, 59, 212, 147, 116, 4, 7] chunk 55 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 0.3980 chunk 219 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 212 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 63 GLN L 119 GLN L 171 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.127536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.098053 restraints weight = 20955.704| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 0.97 r_work: 0.2857 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 20523 Z= 0.171 Angle : 0.560 7.324 28311 Z= 0.312 Chirality : 0.047 0.367 3235 Planarity : 0.004 0.033 3105 Dihedral : 20.509 173.045 4202 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 2.70 % Allowed : 13.42 % Favored : 83.88 % 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: 0.93 (0.18), residues: 2123 helix: 1.61 (0.18), residues: 836 sheet: 0.87 (0.24), residues: 473 loop : -0.55 (0.19), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 39 TYR 0.011 0.002 TYR E 59 PHE 0.013 0.002 PHE K 148 TRP 0.006 0.001 TRP M 144 HIS 0.003 0.001 HIS E 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (20523) covalent geometry : angle 0.55950 / 0.31 (28311) hydrogen bonds : bond 0.03732 / 2.49 ( 958) hydrogen bonds : angle 4.92686 / 4.49 ( 2827) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 271 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 33 LYS cc_start: 0.7538 (tptm) cc_final: 0.6878 (mtmt) REVERT: D 98 ASP cc_start: 0.8501 (t0) cc_final: 0.8232 (t0) REVERT: D 151 MET cc_start: 0.8435 (mtp) cc_final: 0.8152 (mtp) REVERT: D 179 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.5701 (ppt170) REVERT: E 72 MET cc_start: 0.9207 (ttm) cc_final: 0.8949 (mtp) REVERT: E 190 MET cc_start: 0.8344 (mmm) cc_final: 0.8108 (mmm) REVERT: F 98 ASP cc_start: 0.8514 (t0) cc_final: 0.8276 (t0) REVERT: G 62 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7266 (mm-30) REVERT: G 88 LYS cc_start: 0.8604 (mmmm) cc_final: 0.8282 (mmtt) REVERT: G 99 VAL cc_start: 0.9330 (t) cc_final: 0.9024 (m) REVERT: G 154 GLU cc_start: 0.7800 (pm20) cc_final: 0.7535 (pm20) REVERT: G 167 GLU cc_start: 0.8094 (tt0) cc_final: 0.7648 (tp30) REVERT: G 190 MET cc_start: 0.8718 (mmm) cc_final: 0.8374 (mmm) REVERT: G 192 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8078 (mt-10) REVERT: H 40 LYS cc_start: 0.8346 (mmtt) cc_final: 0.8118 (mttm) REVERT: H 153 ASP cc_start: 0.8774 (t0) cc_final: 0.8559 (t0) REVERT: I 2 LYS cc_start: 0.7868 (mmtm) cc_final: 0.7378 (mmtp) REVERT: I 179 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.6761 (ptt-90) REVERT: J 98 ASP cc_start: 0.8727 (t0) cc_final: 0.8455 (t70) REVERT: K 61 ASP cc_start: 0.8575 (t0) cc_final: 0.8151 (t70) REVERT: K 161 GLU cc_start: 0.7311 (mt-10) cc_final: 0.7017 (mt-10) REVERT: K 163 LEU cc_start: 0.8570 (mp) cc_final: 0.8304 (mm) REVERT: K 167 GLU cc_start: 0.8070 (tt0) cc_final: 0.7816 (mp0) REVERT: L 2 LYS cc_start: 0.7756 (mtpt) cc_final: 0.7477 (mtpm) REVERT: L 113 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.7832 (mm-40) REVERT: M 164 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.7306 (ttp) REVERT: M 179 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.7668 (pmt170) REVERT: N 39 ARG cc_start: 0.7923 (ttm-80) cc_final: 0.7671 (ttm170) outliers start: 51 outliers final: 25 residues processed: 302 average time/residue: 0.6917 time to fit residues: 232.8507 Evaluate side-chains 290 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 259 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain G residue 192 GLU Chi-restraints excluded: chain H residue 95 MET Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 179 ARG Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 145 SER Chi-restraints excluded: chain K residue 164 MET Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain L residue 113 GLN Chi-restraints excluded: chain M residue 99 VAL Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 164 MET Chi-restraints excluded: chain M residue 179 ARG Chi-restraints excluded: chain N residue 3 LEU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 51 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: [95, 18, 14, 205, 187, 21, 86, 219, 155, 96, 183] chunk 95 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 0.0050 chunk 205 optimal weight: 5.9990 chunk 187 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 219 optimal weight: 10.0000 chunk 155 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 119 GLN E 63 GLN L 119 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.125932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.096063 restraints weight = 21006.204| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.01 r_work: 0.2823 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 20523 Z= 0.221 Angle : 0.611 7.611 28311 Z= 0.334 Chirality : 0.050 0.389 3235 Planarity : 0.005 0.043 3105 Dihedral : 20.487 174.171 4202 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 3.22 % Allowed : 13.64 % Favored : 83.14 % 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: 0.79 (0.18), residues: 2123 helix: 1.52 (0.18), residues: 836 sheet: 0.79 (0.24), residues: 473 loop : -0.66 (0.19), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 39 TYR 0.012 0.002 TYR E 59 PHE 0.016 0.002 PHE K 148 TRP 0.007 0.001 TRP M 144 HIS 0.004 0.002 HIS J 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.22 (20523) covalent geometry : angle 0.61090 / 0.33 (28311) hydrogen bonds : bond 0.04244 / 2.83 ( 958) hydrogen bonds : angle 4.97125 / 4.52 ( 2827) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 252 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 33 LYS cc_start: 0.7541 (tptm) cc_final: 0.6826 (mtmt) REVERT: D 88 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7774 (mttp) REVERT: D 98 ASP cc_start: 0.8595 (t0) cc_final: 0.8252 (t0) REVERT: D 151 MET cc_start: 0.8440 (mtp) cc_final: 0.8168 (mtp) REVERT: D 179 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.5710 (ppt170) REVERT: E 190 MET cc_start: 0.8356 (mmm) cc_final: 0.8086 (mmm) REVERT: F 98 ASP cc_start: 0.8529 (t0) cc_final: 0.8265 (t0) REVERT: G 62 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7319 (mm-30) REVERT: G 88 LYS cc_start: 0.8594 (mmmm) cc_final: 0.8253 (mmtt) REVERT: G 99 VAL cc_start: 0.9343 (t) cc_final: 0.9031 (m) REVERT: G 167 GLU cc_start: 0.8160 (tt0) cc_final: 0.7682 (tp30) REVERT: G 190 MET cc_start: 0.8667 (mmm) cc_final: 0.8306 (mmm) REVERT: G 192 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8166 (mt-10) REVERT: H 40 LYS cc_start: 0.8372 (mmtt) cc_final: 0.8142 (mttm) REVERT: H 153 ASP cc_start: 0.8775 (t0) cc_final: 0.8553 (t0) REVERT: I 2 LYS cc_start: 0.7840 (mmtm) cc_final: 0.7417 (mmtp) REVERT: I 33 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.7937 (mmtt) REVERT: I 179 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.6861 (ptt-90) REVERT: J 98 ASP cc_start: 0.8741 (t0) cc_final: 0.8465 (t70) REVERT: K 61 ASP cc_start: 0.8597 (t0) cc_final: 0.8177 (t70) REVERT: K 161 GLU cc_start: 0.7361 (mt-10) cc_final: 0.7081 (mt-10) REVERT: K 163 LEU cc_start: 0.8528 (mp) cc_final: 0.8255 (mm) REVERT: K 167 GLU cc_start: 0.8055 (tt0) cc_final: 0.7757 (mp0) REVERT: L 2 LYS cc_start: 0.7749 (mtpt) cc_final: 0.7496 (mtpm) REVERT: L 113 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.7900 (mm-40) REVERT: M 39 ARG cc_start: 0.8032 (ttt180) cc_final: 0.7689 (ttt180) REVERT: M 155 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.6446 (tp30) REVERT: M 164 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.7288 (ttp) REVERT: M 179 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.7633 (pmt170) REVERT: N 39 ARG cc_start: 0.7964 (ttm-80) cc_final: 0.7669 (ttm170) outliers start: 61 outliers final: 30 residues processed: 295 average time/residue: 0.6653 time to fit residues: 218.9871 Evaluate side-chains 286 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 247 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain G residue 192 GLU Chi-restraints excluded: chain H residue 95 MET Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 179 ARG Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 145 SER Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 189 ILE Chi-restraints excluded: chain L residue 113 GLN Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain M residue 99 VAL Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain M residue 164 MET Chi-restraints excluded: chain M residue 179 ARG Chi-restraints excluded: chain N residue 3 LEU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 51 GLU Chi-restraints excluded: chain N residue 100 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: [87, 8, 15, 114, 173, 214, 108, 20, 17, 91, 42] chunk 87 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 214 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 63 GLN L 119 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.127946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.099080 restraints weight = 20894.703| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 0.96 r_work: 0.2839 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20523 Z= 0.160 Angle : 0.550 8.585 28311 Z= 0.306 Chirality : 0.047 0.331 3235 Planarity : 0.004 0.032 3105 Dihedral : 20.465 174.168 4202 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.80 % Allowed : 14.53 % Favored : 82.66 % 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: 0.94 (0.18), residues: 2123 helix: 1.66 (0.18), residues: 836 sheet: 0.81 (0.24), residues: 473 loop : -0.54 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 39 TYR 0.012 0.001 TYR H 59 PHE 0.011 0.002 PHE K 148 TRP 0.006 0.001 TRP M 144 HIS 0.003 0.001 HIS K 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (20523) covalent geometry : angle 0.54963 / 0.31 (28311) hydrogen bonds : bond 0.03568 / 2.38 ( 958) hydrogen bonds : angle 4.83063 / 4.38 ( 2827) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 259 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 33 LYS cc_start: 0.7514 (tptm) cc_final: 0.6782 (mtmt) REVERT: D 88 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7845 (mmtm) REVERT: D 98 ASP cc_start: 0.8595 (t0) cc_final: 0.8255 (t0) REVERT: D 151 MET cc_start: 0.8357 (mtp) cc_final: 0.8101 (mtp) REVERT: D 179 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.5663 (ppt170) REVERT: E 190 MET cc_start: 0.8333 (mmm) cc_final: 0.8026 (mmm) REVERT: F 40 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.6915 (mptt) REVERT: F 88 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7938 (mtpt) REVERT: F 98 ASP cc_start: 0.8498 (t0) cc_final: 0.8271 (t0) REVERT: G 62 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7297 (mm-30) REVERT: G 88 LYS cc_start: 0.8562 (mmmm) cc_final: 0.8209 (mmtt) REVERT: G 99 VAL cc_start: 0.9303 (t) cc_final: 0.9007 (m) REVERT: G 167 GLU cc_start: 0.8115 (tt0) cc_final: 0.7621 (tp30) REVERT: G 190 MET cc_start: 0.8645 (mmm) cc_final: 0.8329 (mmm) REVERT: H 40 LYS cc_start: 0.8344 (mmtt) cc_final: 0.8134 (mttm) REVERT: I 2 LYS cc_start: 0.7791 (mmtm) cc_final: 0.7406 (mmtp) REVERT: I 33 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.7925 (mmtt) REVERT: I 179 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.6760 (ptt-90) REVERT: J 98 ASP cc_start: 0.8737 (t0) cc_final: 0.8455 (t70) REVERT: K 161 GLU cc_start: 0.7290 (mt-10) cc_final: 0.7020 (mt-10) REVERT: K 163 LEU cc_start: 0.8506 (mp) cc_final: 0.8252 (mm) REVERT: K 167 GLU cc_start: 0.8028 (tt0) cc_final: 0.7713 (mp0) REVERT: L 2 LYS cc_start: 0.7724 (mtpt) cc_final: 0.7473 (mtpm) REVERT: L 113 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.7851 (mm-40) REVERT: M 39 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7693 (ttt180) REVERT: M 151 MET cc_start: 0.7992 (mtt) cc_final: 0.7780 (mtt) REVERT: M 155 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.6451 (tp30) REVERT: M 164 MET cc_start: 0.7506 (OUTLIER) cc_final: 0.7251 (ttp) REVERT: M 179 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.7609 (pmt170) REVERT: N 39 ARG cc_start: 0.7987 (ttm-80) cc_final: 0.7725 (ttm170) outliers start: 53 outliers final: 28 residues processed: 294 average time/residue: 0.6579 time to fit residues: 216.2901 Evaluate side-chains 300 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 261 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain F residue 40 LYS Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain H residue 95 MET Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 179 ARG Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 145 SER Chi-restraints excluded: chain K residue 164 MET Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 189 ILE Chi-restraints excluded: chain L residue 113 GLN Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain M residue 39 ARG Chi-restraints excluded: chain M residue 99 VAL Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain M residue 164 MET Chi-restraints excluded: chain M residue 179 ARG Chi-restraints excluded: chain N residue 3 LEU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 51 GLU Chi-restraints excluded: chain N residue 135 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: [3, 172, 113, 205, 220, 134, 20, 63, 89, 102, 219] chunk 3 optimal weight: 7.9990 chunk 172 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 205 optimal weight: 7.9990 chunk 220 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 219 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 119 GLN E 63 GLN L 119 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.124089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.094649 restraints weight = 21173.228| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.03 r_work: 0.2787 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 20523 Z= 0.307 Angle : 0.697 8.224 28311 Z= 0.372 Chirality : 0.054 0.404 3235 Planarity : 0.005 0.051 3105 Dihedral : 20.526 175.977 4202 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.49 % Allowed : 14.22 % Favored : 82.29 % 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: 0.51 (0.18), residues: 2123 helix: 1.29 (0.18), residues: 836 sheet: 0.34 (0.23), residues: 517 loop : -0.63 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 12 TYR 0.014 0.002 TYR L 59 PHE 0.019 0.003 PHE K 148 TRP 0.007 0.002 TRP M 144 HIS 0.005 0.002 HIS N 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00750 / 0.31 (20523) covalent geometry : angle 0.69716 / 0.37 (28311) hydrogen bonds : bond 0.04942 / 3.30 ( 958) hydrogen bonds : angle 5.02316 / 4.51 ( 2827) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 264 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 33 LYS cc_start: 0.7643 (tptm) cc_final: 0.6963 (ttmt) REVERT: D 88 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7805 (mttp) REVERT: D 98 ASP cc_start: 0.8589 (t0) cc_final: 0.8264 (t0) REVERT: D 151 MET cc_start: 0.8408 (mtp) cc_final: 0.8189 (mtp) REVERT: D 179 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.5682 (ppt170) REVERT: D 184 ARG cc_start: 0.8992 (mtt180) cc_final: 0.8721 (mtt-85) REVERT: F 88 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8186 (mtpt) REVERT: F 98 ASP cc_start: 0.8546 (t0) cc_final: 0.8279 (t0) REVERT: G 62 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7346 (mm-30) REVERT: G 88 LYS cc_start: 0.8587 (mmmm) cc_final: 0.8240 (mmtt) REVERT: G 167 GLU cc_start: 0.8235 (tt0) cc_final: 0.7736 (tp30) REVERT: G 190 MET cc_start: 0.8673 (mmm) cc_final: 0.8349 (mmm) REVERT: H 40 LYS cc_start: 0.8458 (mmtt) cc_final: 0.8163 (mttm) REVERT: I 2 LYS cc_start: 0.7908 (mmtm) cc_final: 0.7513 (mmtp) REVERT: I 33 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.7990 (mmtt) REVERT: I 179 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.6953 (ptt-90) REVERT: J 98 ASP cc_start: 0.8842 (t0) cc_final: 0.8607 (t70) REVERT: J 191 SER cc_start: 0.8375 (p) cc_final: 0.7871 (t) REVERT: K 161 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7099 (mt-10) REVERT: K 163 LEU cc_start: 0.8559 (mp) cc_final: 0.8273 (mm) REVERT: K 167 GLU cc_start: 0.8067 (tt0) cc_final: 0.7756 (mp0) REVERT: L 2 LYS cc_start: 0.7804 (mtpt) cc_final: 0.7573 (mtpm) REVERT: L 113 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.7883 (mm-40) REVERT: M 39 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7746 (ttt180) REVERT: M 151 MET cc_start: 0.8043 (mtt) cc_final: 0.7771 (mtt) REVERT: M 155 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6662 (tp30) REVERT: M 164 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7350 (ttp) REVERT: M 179 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.7666 (pmt170) REVERT: N 103 MET cc_start: 0.8439 (ttm) cc_final: 0.7956 (ttm) outliers start: 66 outliers final: 41 residues processed: 310 average time/residue: 0.6663 time to fit residues: 230.6227 Evaluate side-chains 307 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 256 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain G residue 192 GLU Chi-restraints excluded: chain H residue 95 MET Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 179 ARG Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 145 SER Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain L residue 113 GLN Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 175 VAL Chi-restraints excluded: chain L residue 188 GLU Chi-restraints excluded: chain M residue 39 ARG Chi-restraints excluded: chain M residue 99 VAL Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain M residue 164 MET Chi-restraints excluded: chain M residue 179 ARG Chi-restraints excluded: chain N residue 3 LEU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 51 GLU Chi-restraints excluded: chain N residue 135 MET Chi-restraints excluded: chain N residue 167 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: [126, 155, 52, 150, 145, 75, 24, 103, 68, 29, 43] chunk 126 optimal weight: 0.2980 chunk 155 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 150 optimal weight: 0.9980 chunk 145 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 63 GLN K 53 GLN L 119 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.129075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.099550 restraints weight = 20918.925| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 0.98 r_work: 0.2877 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20523 Z= 0.113 Angle : 0.517 6.920 28311 Z= 0.293 Chirality : 0.045 0.316 3235 Planarity : 0.004 0.034 3105 Dihedral : 20.506 174.116 4202 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 1.90 % Allowed : 16.38 % Favored : 81.71 % 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: 1.01 (0.18), residues: 2123 helix: 1.71 (0.18), residues: 836 sheet: 0.49 (0.23), residues: 517 loop : -0.28 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 39 TYR 0.011 0.001 TYR H 59 PHE 0.008 0.001 PHE J 182 TRP 0.005 0.001 TRP M 144 HIS 0.002 0.001 HIS F 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (20523) covalent geometry : angle 0.51704 / 0.29 (28311) hydrogen bonds : bond 0.03105 / 2.06 ( 958) hydrogen bonds : angle 4.70725 / 4.21 ( 2827) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 264 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 33 LYS cc_start: 0.7564 (tptm) cc_final: 0.6848 (ttmt) REVERT: D 88 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7800 (mmtm) REVERT: D 98 ASP cc_start: 0.8675 (t0) cc_final: 0.8318 (t0) REVERT: D 151 MET cc_start: 0.8296 (mtp) cc_final: 0.8066 (mtp) REVERT: D 179 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.5729 (ppt170) REVERT: F 98 ASP cc_start: 0.8471 (t0) cc_final: 0.8246 (t0) REVERT: G 62 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7365 (mm-30) REVERT: G 72 MET cc_start: 0.8794 (ttp) cc_final: 0.8577 (ttm) REVERT: G 99 VAL cc_start: 0.9287 (t) cc_final: 0.9015 (m) REVERT: G 114 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7886 (mm-30) REVERT: G 167 GLU cc_start: 0.8035 (tt0) cc_final: 0.7586 (tp30) REVERT: G 190 MET cc_start: 0.8621 (mmm) cc_final: 0.8314 (mmm) REVERT: H 40 LYS cc_start: 0.8396 (mmtt) cc_final: 0.8100 (mttm) REVERT: I 2 LYS cc_start: 0.7787 (mmtm) cc_final: 0.7367 (mmtp) REVERT: I 33 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7919 (mmtt) REVERT: I 179 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.6597 (ptt-90) REVERT: J 98 ASP cc_start: 0.8818 (t0) cc_final: 0.8556 (t70) REVERT: K 161 GLU cc_start: 0.7288 (mt-10) cc_final: 0.6947 (mt-10) REVERT: K 163 LEU cc_start: 0.8506 (mp) cc_final: 0.8248 (mm) REVERT: K 167 GLU cc_start: 0.8008 (tt0) cc_final: 0.7729 (mp0) REVERT: L 2 LYS cc_start: 0.7806 (mtpt) cc_final: 0.7559 (mtpm) REVERT: M 39 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7687 (ttt180) REVERT: M 151 MET cc_start: 0.7991 (mtt) cc_final: 0.7734 (mtt) REVERT: M 155 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6692 (tp30) REVERT: M 164 MET cc_start: 0.7554 (ttm) cc_final: 0.7305 (ttp) REVERT: N 103 MET cc_start: 0.8330 (ttm) cc_final: 0.7898 (ttm) outliers start: 36 outliers final: 19 residues processed: 285 average time/residue: 0.6512 time to fit residues: 207.9677 Evaluate side-chains 282 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 257 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain H residue 95 MET Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain I residue 179 ARG Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 145 SER Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain L residue 175 VAL Chi-restraints excluded: chain M residue 39 ARG Chi-restraints excluded: chain M residue 99 VAL Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain N residue 3 LEU Chi-restraints excluded: chain N residue 135 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: [151, 207, 191, 109, 129, 51, 217, 143, 47, 115, 150] chunk 151 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 191 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 217 optimal weight: 9.9990 chunk 143 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 119 GLN E 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.133214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.102135 restraints weight = 20421.094| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.19 r_work: 0.2875 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20523 Z= 0.126 Angle : 0.523 6.925 28311 Z= 0.292 Chirality : 0.045 0.329 3235 Planarity : 0.004 0.033 3105 Dihedral : 20.481 175.246 4202 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.85 % Allowed : 16.60 % Favored : 81.55 % 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: 1.16 (0.18), residues: 2123 helix: 1.84 (0.18), residues: 836 sheet: 0.52 (0.23), residues: 517 loop : -0.17 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 39 TYR 0.013 0.001 TYR H 59 PHE 0.010 0.001 PHE K 148 TRP 0.005 0.001 TRP M 144 HIS 0.002 0.001 HIS K 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (20523) covalent geometry : angle 0.52263 / 0.29 (28311) hydrogen bonds : bond 0.03209 / 2.14 ( 958) hydrogen bonds : angle 4.64428 / 4.14 ( 2827) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 259 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 33 LYS cc_start: 0.7075 (tptm) cc_final: 0.6377 (ttmt) REVERT: D 88 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7417 (mmtm) REVERT: D 98 ASP cc_start: 0.8648 (t0) cc_final: 0.8286 (t0) REVERT: D 151 MET cc_start: 0.8227 (mtp) cc_final: 0.7983 (mtp) REVERT: D 179 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.5333 (ppt170) REVERT: E 79 SER cc_start: 0.8871 (OUTLIER) cc_final: 0.8309 (m) REVERT: F 88 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7646 (mmtm) REVERT: F 98 ASP cc_start: 0.8440 (t0) cc_final: 0.8234 (t0) REVERT: G 62 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7071 (mm-30) REVERT: G 99 VAL cc_start: 0.9103 (t) cc_final: 0.8729 (m) REVERT: G 114 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7572 (mm-30) REVERT: G 167 GLU cc_start: 0.7979 (tt0) cc_final: 0.7228 (tp30) REVERT: G 190 MET cc_start: 0.8517 (mmm) cc_final: 0.8175 (mmm) REVERT: H 40 LYS cc_start: 0.8298 (mmtt) cc_final: 0.7902 (mttm) REVERT: I 2 LYS cc_start: 0.7388 (mmtm) cc_final: 0.6921 (mmtp) REVERT: I 33 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7685 (mmtt) REVERT: I 179 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.6463 (ptt-90) REVERT: J 95 MET cc_start: 0.8638 (ptp) cc_final: 0.8420 (ptm) REVERT: J 98 ASP cc_start: 0.8809 (t0) cc_final: 0.8549 (t70) REVERT: K 161 GLU cc_start: 0.6955 (mt-10) cc_final: 0.6649 (mt-10) REVERT: K 163 LEU cc_start: 0.7918 (mp) cc_final: 0.7593 (mm) REVERT: K 167 GLU cc_start: 0.7778 (tt0) cc_final: 0.7184 (mp0) REVERT: L 2 LYS cc_start: 0.7364 (mtpt) cc_final: 0.7094 (mtpm) REVERT: M 39 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7634 (ttt180) REVERT: M 151 MET cc_start: 0.7689 (mtt) cc_final: 0.7373 (mtt) REVERT: M 155 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6579 (tp30) REVERT: M 164 MET cc_start: 0.7098 (ttm) cc_final: 0.6820 (ttp) REVERT: N 44 GLU cc_start: 0.7417 (tt0) cc_final: 0.7020 (tt0) outliers start: 35 outliers final: 22 residues processed: 283 average time/residue: 0.6283 time to fit residues: 199.6897 Evaluate side-chains 282 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 252 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain H residue 95 MET Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain I residue 179 ARG Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 145 SER Chi-restraints excluded: chain K residue 164 MET Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain L residue 175 VAL Chi-restraints excluded: chain M residue 39 ARG Chi-restraints excluded: chain M residue 99 VAL Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain N residue 3 LEU Chi-restraints excluded: chain N residue 51 GLU Chi-restraints excluded: chain N residue 135 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: [210, 121, 33, 78, 9, 188, 97, 64, 136, 82, 92] chunk 210 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 97 optimal weight: 0.0670 chunk 64 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 overall best weight: 1.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.131855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.100564 restraints weight = 20633.839| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.21 r_work: 0.2864 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20523 Z= 0.177 Angle : 0.567 7.210 28311 Z= 0.312 Chirality : 0.047 0.336 3235 Planarity : 0.004 0.035 3105 Dihedral : 20.488 176.551 4202 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 1.96 % Allowed : 16.65 % Favored : 81.40 % 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: 1.03 (0.18), residues: 2123 helix: 1.74 (0.18), residues: 836 sheet: 0.48 (0.23), residues: 517 loop : -0.27 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 39 TYR 0.012 0.002 TYR H 59 PHE 0.013 0.002 PHE K 148 TRP 0.006 0.001 TRP M 144 HIS 0.003 0.001 HIS N 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (20523) covalent geometry : angle 0.56670 / 0.31 (28311) hydrogen bonds : bond 0.03697 / 2.47 ( 958) hydrogen bonds : angle 4.71192 / 4.20 ( 2827) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 261 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 33 LYS cc_start: 0.7191 (tptm) cc_final: 0.6484 (ttmt) REVERT: D 88 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7511 (mmtm) REVERT: D 98 ASP cc_start: 0.8639 (t0) cc_final: 0.8299 (t0) REVERT: D 151 MET cc_start: 0.8287 (mtp) cc_final: 0.8051 (mtp) REVERT: D 179 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.5416 (ppt170) REVERT: E 79 SER cc_start: 0.8884 (OUTLIER) cc_final: 0.8360 (m) REVERT: F 88 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7694 (mmtm) REVERT: F 98 ASP cc_start: 0.8472 (t0) cc_final: 0.8259 (t0) REVERT: G 62 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7126 (mm-30) REVERT: G 88 LYS cc_start: 0.8341 (mmmm) cc_final: 0.7824 (mmtt) REVERT: G 99 VAL cc_start: 0.9123 (t) cc_final: 0.8751 (m) REVERT: G 114 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7659 (mm-30) REVERT: G 167 GLU cc_start: 0.8076 (tt0) cc_final: 0.7333 (tp30) REVERT: G 190 MET cc_start: 0.8546 (mmm) cc_final: 0.8200 (mmm) REVERT: H 40 LYS cc_start: 0.8359 (mmtt) cc_final: 0.8009 (mttm) REVERT: I 2 LYS cc_start: 0.7574 (mmtm) cc_final: 0.7101 (mmtp) REVERT: I 33 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7764 (mmtt) REVERT: I 179 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.6610 (ptt-90) REVERT: J 98 ASP cc_start: 0.8820 (t0) cc_final: 0.8556 (t70) REVERT: K 161 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6803 (mt-10) REVERT: K 163 LEU cc_start: 0.8015 (mp) cc_final: 0.7695 (mm) REVERT: K 167 GLU cc_start: 0.7828 (tt0) cc_final: 0.7279 (mp0) REVERT: K 177 ASP cc_start: 0.9055 (OUTLIER) cc_final: 0.8612 (t70) REVERT: L 2 LYS cc_start: 0.7455 (mtpt) cc_final: 0.7190 (mtpm) REVERT: M 39 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7671 (ttt180) REVERT: M 155 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6557 (tp30) REVERT: M 164 MET cc_start: 0.7201 (OUTLIER) cc_final: 0.6923 (ttp) REVERT: N 44 GLU cc_start: 0.7345 (tt0) cc_final: 0.6970 (tt0) outliers start: 37 outliers final: 22 residues processed: 284 average time/residue: 0.6593 time to fit residues: 209.6736 Evaluate side-chains 291 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 259 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain H residue 95 MET Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain I residue 179 ARG Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 145 SER Chi-restraints excluded: chain K residue 164 MET Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain K residue 177 ASP Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain L residue 175 VAL Chi-restraints excluded: chain M residue 39 ARG Chi-restraints excluded: chain M residue 99 VAL Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain M residue 164 MET Chi-restraints excluded: chain N residue 3 LEU Chi-restraints excluded: chain N residue 51 GLU Chi-restraints excluded: chain N residue 135 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: [193, 207, 31, 136, 65, 153, 130, 147, 70, 12, 133] chunk 193 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.129682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.098248 restraints weight = 20781.284| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 1.23 r_work: 0.2846 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 20523 Z= 0.214 Angle : 0.614 12.226 28311 Z= 0.332 Chirality : 0.050 0.339 3235 Planarity : 0.005 0.041 3105 Dihedral : 20.544 177.358 4202 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 2.01 % Allowed : 16.54 % Favored : 81.45 % 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: 0.86 (0.18), residues: 2123 helix: 1.60 (0.18), residues: 836 sheet: 0.41 (0.23), residues: 517 loop : -0.38 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 39 TYR 0.012 0.002 TYR H 59 PHE 0.016 0.002 PHE N 152 TRP 0.006 0.001 TRP M 144 HIS 0.004 0.001 HIS N 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.21 (20523) covalent geometry : angle 0.61395 / 0.33 (28311) hydrogen bonds : bond 0.04099 / 2.74 ( 958) hydrogen bonds : angle 4.80275 / 4.28 ( 2827) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6506.45 seconds wall clock time: 111 minutes 25.63 seconds (6685.63 seconds total)