Starting phenix.real_space_refine on Sun Oct 25 22:02:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/36pb_77731/10_2026/36pb_77731.cif Found real_map, /net/cci-nas-00/data/ceres_data/36pb_77731/10_2026/36pb_77731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/36pb_77731/10_2026/36pb_77731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/36pb_77731/10_2026/36pb_77731.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/36pb_77731/10_2026/36pb_77731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/36pb_77731/10_2026/36pb_77731.map" } resolution = 3.1 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= 0.022 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 133 5.49 5 S 130 5.16 5 C 11118 2.51 5 N 3117 2.21 5 O 3782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 18280 Number of models: 1 Model: "" Number of chains: 13 Chain: "D" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "E" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "F" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "G" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "H" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "I" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "J" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "K" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "L" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "M" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "A" Number of atoms: 1859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1859 Classifications: {'RNA': 86} Modifications used: {'rna2p_pur': 21, 'rna2p_pyr': 15, 'rna3p_pur': 31, 'rna3p_pyr': 19} Link IDs: {'rna2p': 35, '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} Time building chain proxies: 4.05, per 1000 atoms: 0.22 Number of scatterers: 18280 At special positions: 0 Unit cell: (98.04, 102.6, 191.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 130 16.00 P 133 15.00 O 3782 8.00 N 3117 7.00 C 11118 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: 1.60 Conformation dependent library (CDL) restraints added in 654.6 milliseconds 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3660 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 31 sheets defined 42.1% alpha, 35.8% beta 30 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'D' and resid 19 through 23 removed outlier: 3.521A 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 118 through 120 No H-bonds generated for 'chain 'D' and resid 118 through 120' Processing helix chain 'D' and resid 158 through 173 Processing helix chain 'E' and resid 19 through 23 Processing helix chain 'E' and resid 26 through 37 Processing helix chain 'E' and resid 42 through 57 removed outlier: 3.579A pdb=" N SER E 57 " --> pdb=" O GLN E 53 " (cutoff:3.500A) 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: 6.627A 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: 3.570A 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 58 removed outlier: 3.666A pdb=" N SER F 57 " --> pdb=" O GLN F 53 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N CYS F 58 " --> pdb=" O LEU F 54 " (cutoff:3.500A) 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: 6.224A 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 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 118 through 120 No H-bonds generated for 'chain 'G' and resid 118 through 120' Processing helix chain 'G' and resid 158 through 173 Processing helix chain 'H' and resid 19 through 23 removed outlier: 3.514A pdb=" N SER H 22 " --> pdb=" O ASP H 19 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP H 23 " --> pdb=" O THR H 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 19 through 23' Processing helix chain 'H' and resid 26 through 37 Processing helix chain 'H' and resid 42 through 58 removed outlier: 4.017A pdb=" N CYS H 58 " --> pdb=" O LEU H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 82 Processing helix chain 'H' and resid 83 through 85 No H-bonds generated for 'chain 'H' and resid 83 through 85' Processing helix chain 'H' and resid 86 through 93 removed outlier: 3.615A pdb=" N ARG H 92 " --> pdb=" O LYS H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 116 Processing helix chain 'H' and resid 118 through 122 removed outlier: 3.616A pdb=" N PHE H 121 " --> pdb=" O ASN H 118 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE H 122 " --> pdb=" O GLN H 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 118 through 122' Processing helix chain 'H' and resid 158 through 173 Processing helix chain 'I' and resid 19 through 23 removed outlier: 3.527A 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 57 Processing helix chain 'I' and resid 70 through 82 Processing helix chain 'I' and resid 86 through 93 Processing helix chain 'I' and resid 111 through 116 Processing helix chain 'I' and resid 118 through 120 No H-bonds generated for 'chain 'I' and resid 118 through 120' Processing helix chain 'I' and resid 158 through 173 Processing helix chain 'J' and resid 19 through 23 Processing helix chain 'J' and resid 26 through 37 Processing helix chain 'J' and resid 42 through 57 removed outlier: 3.576A pdb=" N SER J 57 " --> pdb=" O GLN J 53 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 82 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: 6.265A pdb=" N ASP J 120 " --> pdb=" O LYS J 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 117 through 120' Processing helix chain 'J' and resid 158 through 173 Processing helix chain 'K' and resid 19 through 23 Processing helix chain 'K' and resid 26 through 37 Processing helix chain 'K' and resid 42 through 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 94 Processing helix chain 'K' and resid 111 through 116 Processing helix chain 'K' and resid 117 through 120 removed outlier: 6.383A 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 Processing helix chain 'L' and resid 26 through 37 Processing helix chain 'L' and resid 42 through 57 removed outlier: 3.611A pdb=" N SER L 57 " --> pdb=" O GLN L 53 " (cutoff:3.500A) 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 94 removed outlier: 3.609A pdb=" N ILE L 94 " --> pdb=" O ILE L 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 116 Processing helix chain 'L' and resid 117 through 120 removed outlier: 6.282A 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: 3.678A 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 92 Processing helix chain 'M' and resid 111 through 116 Processing helix chain 'M' and resid 118 through 120 No H-bonds generated for 'chain 'M' and resid 118 through 120' Processing helix chain 'M' and resid 158 through 173 Processing sheet with id=AA1, first strand: chain 'D' and resid 60 through 61 removed outlier: 5.520A pdb=" N PHE D 66 " --> pdb=" O MET D 103 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N VAL D 100 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N GLY D 149 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 4.653A 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: 5.520A pdb=" N PHE D 66 " --> pdb=" O MET D 103 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N VAL D 100 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N GLY D 149 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLU D 147 " --> pdb=" O PRO D 102 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N TRP D 144 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU D 3 " --> pdb=" O GLU D 192 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLU D 192 " --> pdb=" O LEU D 3 " (cutoff:3.500A) removed outlier: 7.009A 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: 5.307A pdb=" N PHE E 66 " --> pdb=" O MET E 103 " (cutoff:3.500A) removed outlier: 9.613A pdb=" N VAL E 100 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N GLY E 149 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 4.432A 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: 5.307A pdb=" N PHE E 66 " --> pdb=" O MET E 103 " (cutoff:3.500A) removed outlier: 9.613A pdb=" N VAL E 100 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N GLY E 149 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLU E 147 " --> pdb=" O PRO E 102 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N TRP E 144 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE E 152 " --> pdb=" O LYS E 2 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU E 3 " --> pdb=" O GLU E 192 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N GLU E 192 " --> pdb=" O LEU E 3 " (cutoff:3.500A) removed outlier: 6.934A 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: 5.223A pdb=" N PHE F 66 " --> pdb=" O MET F 103 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N VAL F 100 " --> pdb=" O GLY F 149 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N GLY F 149 " --> pdb=" O VAL F 100 " (cutoff:3.500A) removed outlier: 4.478A 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: 5.223A pdb=" N PHE F 66 " --> pdb=" O MET F 103 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N VAL F 100 " --> pdb=" O GLY F 149 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N GLY F 149 " --> pdb=" O VAL F 100 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLU F 147 " --> pdb=" O PRO F 102 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N TRP F 144 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU F 3 " --> pdb=" O GLU F 192 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLU F 192 " --> pdb=" O LEU F 3 " (cutoff:3.500A) removed outlier: 6.920A 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: 5.315A pdb=" N PHE G 66 " --> pdb=" O MET G 103 " (cutoff:3.500A) removed outlier: 9.626A pdb=" N VAL G 100 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N GLY G 149 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 4.570A 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: 5.315A pdb=" N PHE G 66 " --> pdb=" O MET G 103 " (cutoff:3.500A) removed outlier: 9.626A pdb=" N VAL G 100 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N GLY G 149 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU G 147 " --> pdb=" O PRO G 102 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N TRP G 144 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU G 3 " --> pdb=" O GLU G 192 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLU G 192 " --> pdb=" O LEU G 3 " (cutoff:3.500A) removed outlier: 6.896A 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: 5.250A pdb=" N PHE H 66 " --> pdb=" O MET H 103 " (cutoff:3.500A) removed outlier: 9.843A pdb=" N VAL H 100 " --> pdb=" O GLY H 149 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N GLY H 149 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 4.569A 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: 5.250A pdb=" N PHE H 66 " --> pdb=" O MET H 103 " (cutoff:3.500A) removed outlier: 9.843A pdb=" N VAL H 100 " --> pdb=" O GLY H 149 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N GLY H 149 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLU H 147 " --> pdb=" O PRO H 102 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N TRP H 144 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE H 152 " --> pdb=" O LYS H 2 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU H 3 " --> pdb=" O GLU H 192 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLU H 192 " --> pdb=" O LEU H 3 " (cutoff:3.500A) removed outlier: 6.941A 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 'H' and resid 123 through 129 Processing sheet with id=AB8, first strand: chain 'I' and resid 60 through 61 removed outlier: 5.326A pdb=" N PHE I 66 " --> pdb=" O MET I 103 " (cutoff:3.500A) removed outlier: 9.641A pdb=" N VAL I 100 " --> pdb=" O GLY I 149 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N GLY I 149 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLU I 147 " --> pdb=" O PRO I 102 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 60 through 61 removed outlier: 5.326A pdb=" N PHE I 66 " --> pdb=" O MET I 103 " (cutoff:3.500A) removed outlier: 9.641A pdb=" N VAL I 100 " --> pdb=" O GLY I 149 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N GLY I 149 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLU I 147 " --> pdb=" O PRO I 102 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N TRP I 144 " --> pdb=" O GLY I 10 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE I 152 " --> pdb=" O LYS I 2 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU I 3 " --> pdb=" O GLU I 192 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N GLU I 192 " --> pdb=" O LEU I 3 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN I 5 " --> pdb=" O MET I 190 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 14 through 15 Processing sheet with id=AC2, first strand: chain 'J' and resid 60 through 61 removed outlier: 5.360A pdb=" N PHE J 66 " --> pdb=" O MET J 103 " (cutoff:3.500A) removed outlier: 9.704A pdb=" N VAL J 100 " --> pdb=" O GLY J 149 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N GLY J 149 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU J 147 " --> pdb=" O PRO J 102 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 60 through 61 removed outlier: 5.360A pdb=" N PHE J 66 " --> pdb=" O MET J 103 " (cutoff:3.500A) removed outlier: 9.704A pdb=" N VAL J 100 " --> pdb=" O GLY J 149 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N GLY J 149 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU J 147 " --> pdb=" O PRO J 102 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N TRP J 144 " --> pdb=" O GLY J 10 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU J 3 " --> pdb=" O GLU J 192 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLU J 192 " --> pdb=" O LEU J 3 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ASN J 5 " --> pdb=" O MET J 190 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 14 through 15 Processing sheet with id=AC5, first strand: chain 'K' and resid 60 through 61 removed outlier: 5.379A pdb=" N PHE K 66 " --> pdb=" O MET K 103 " (cutoff:3.500A) removed outlier: 9.754A pdb=" N VAL K 100 " --> pdb=" O GLY K 149 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N GLY K 149 " --> pdb=" O VAL K 100 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU K 147 " --> pdb=" O PRO K 102 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 60 through 61 removed outlier: 5.379A pdb=" N PHE K 66 " --> pdb=" O MET K 103 " (cutoff:3.500A) removed outlier: 9.754A pdb=" N VAL K 100 " --> pdb=" O GLY K 149 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N GLY K 149 " --> pdb=" O VAL K 100 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU K 147 " --> pdb=" O PRO K 102 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N TRP K 144 " --> pdb=" O GLY K 10 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU K 3 " --> pdb=" O GLU K 192 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLU K 192 " --> pdb=" O LEU K 3 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASN K 5 " --> pdb=" O MET K 190 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 14 through 15 Processing sheet with id=AC8, first strand: chain 'L' and resid 60 through 61 removed outlier: 5.385A pdb=" N PHE L 66 " --> pdb=" O MET L 103 " (cutoff:3.500A) removed outlier: 9.708A pdb=" N VAL L 100 " --> pdb=" O GLY L 149 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N GLY L 149 " --> pdb=" O VAL L 100 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU L 147 " --> pdb=" O PRO L 102 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N TRP L 144 " --> pdb=" O GLY L 10 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 95 through 96 removed outlier: 5.229A pdb=" N TRP L 144 " --> pdb=" O GLY L 10 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER L 191 " --> pdb=" O ASN L 5 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LYS L 7 " --> pdb=" O ILE L 189 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ILE L 189 " --> pdb=" O LYS L 7 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 14 through 15 Processing sheet with id=AD2, first strand: chain 'M' and resid 60 through 61 removed outlier: 5.389A pdb=" N PHE M 66 " --> pdb=" O MET M 103 " (cutoff:3.500A) removed outlier: 9.737A pdb=" N VAL M 100 " --> pdb=" O GLY M 149 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N GLY M 149 " --> pdb=" O VAL M 100 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU M 147 " --> pdb=" O PRO M 102 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 60 through 61 removed outlier: 5.389A pdb=" N PHE M 66 " --> pdb=" O MET M 103 " (cutoff:3.500A) removed outlier: 9.737A pdb=" N VAL M 100 " --> pdb=" O GLY M 149 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N GLY M 149 " --> pdb=" O VAL M 100 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU M 147 " --> pdb=" O PRO M 102 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N TRP M 144 " --> pdb=" O GLY M 10 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER M 191 " --> pdb=" O ASN M 5 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LYS M 7 " --> pdb=" O ILE M 189 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ILE M 189 " --> pdb=" O LYS M 7 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N THR M 9 " --> pdb=" O VAL M 187 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VAL M 187 " --> pdb=" O THR M 9 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 14 through 15 866 hydrogen bonds defined for protein. 2397 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 74 hydrogen bonds 146 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 3.00 Time building geometry restraints manager: 2.00 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: 4582 1.33 - 1.45: 3931 1.45 - 1.57: 9908 1.57 - 1.69: 263 1.69 - 1.81: 220 Bond restraints: 18904 Sorted by residual: bond pdb=" C3' DG B 8 " pdb=" C2' DG B 8 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.00e+01 bond pdb=" C3' DA B 9 " pdb=" C2' DA B 9 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.68e+00 bond pdb=" C3' DT B 16 " pdb=" C2' DT B 16 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.78e+00 bond pdb=" C3' DA B 30 " pdb=" C2' DA B 30 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.68e+00 bond pdb=" C3' DT B 25 " pdb=" C2' DT B 25 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.20e+00 ... (remaining 18899 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 25400 1.67 - 3.35: 626 3.35 - 5.02: 69 5.02 - 6.70: 20 6.70 - 8.37: 6 Bond angle restraints: 26121 Sorted by residual: angle pdb=" O4' DT C 24 " pdb=" C1' DT C 24 " pdb=" N1 DT C 24 " ideal model delta sigma weight residual 108.00 111.54 -3.54 7.00e-01 2.04e+00 2.56e+01 angle pdb=" C4' DT C 24 " pdb=" O4' DT C 24 " pdb=" C1' DT C 24 " ideal model delta sigma weight residual 110.10 105.48 4.62 1.00e+00 1.00e+00 2.13e+01 angle pdb=" C2' U A 52 " pdb=" C1' U A 52 " pdb=" N1 U A 52 " ideal model delta sigma weight residual 112.00 116.79 -4.79 1.10e+00 8.26e-01 1.90e+01 angle pdb=" N3 DT B 16 " pdb=" C4 DT B 16 " pdb=" O4 DT B 16 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" O4' DG C 26 " pdb=" C1' DG C 26 " pdb=" N9 DG C 26 " ideal model delta sigma weight residual 108.00 111.02 -3.02 7.00e-01 2.04e+00 1.87e+01 ... (remaining 26116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 11051 35.84 - 71.68: 459 71.68 - 107.51: 16 107.51 - 143.35: 2 143.35 - 179.19: 7 Dihedral angle restraints: 11535 sinusoidal: 5875 harmonic: 5660 Sorted by residual: dihedral pdb=" O4' U A 30 " pdb=" C1' U A 30 " pdb=" N1 U A 30 " pdb=" C2 U A 30 " ideal model delta sinusoidal sigma weight residual 232.00 63.23 168.77 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 -82.95 -77.05 1 1.50e+01 4.44e-03 3.31e+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 39.19 -179.19 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 11532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 2921 0.130 - 0.261: 52 0.261 - 0.391: 0 0.391 - 0.522: 7 0.522 - 0.652: 8 Chirality restraints: 2988 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 -2.99 -0.65 2.00e-01 2.50e+01 1.06e+01 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 -2.93 -0.59 2.00e-01 2.50e+01 8.76e+00 chirality pdb=" P DG C 27 " pdb=" OP1 DG C 27 " pdb=" OP2 DG C 27 " pdb=" O5' DG C 27 " both_signs ideal model delta sigma weight residual True 2.34 -2.91 -0.58 2.00e-01 2.50e+01 8.30e+00 ... (remaining 2985 not shown) Planarity restraints: 2833 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U A 52 " 0.033 2.00e-02 2.50e+03 1.74e-02 6.81e+00 pdb=" N1 U A 52 " -0.038 2.00e-02 2.50e+03 pdb=" C2 U A 52 " -0.002 2.00e-02 2.50e+03 pdb=" O2 U A 52 " -0.003 2.00e-02 2.50e+03 pdb=" N3 U A 52 " 0.003 2.00e-02 2.50e+03 pdb=" C4 U A 52 " 0.005 2.00e-02 2.50e+03 pdb=" O4 U A 52 " 0.009 2.00e-02 2.50e+03 pdb=" C5 U A 52 " -0.001 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' U A 12 " 0.032 2.00e-02 2.50e+03 1.63e-02 5.96e+00 pdb=" N1 U A 12 " -0.033 2.00e-02 2.50e+03 pdb=" C2 U A 12 " -0.003 2.00e-02 2.50e+03 pdb=" O2 U A 12 " -0.004 2.00e-02 2.50e+03 pdb=" N3 U A 12 " 0.003 2.00e-02 2.50e+03 pdb=" C4 U A 12 " 0.004 2.00e-02 2.50e+03 pdb=" O4 U A 12 " 0.013 2.00e-02 2.50e+03 pdb=" C5 U A 12 " -0.008 2.00e-02 2.50e+03 pdb=" C6 U A 12 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 27 " 0.028 2.00e-02 2.50e+03 1.53e-02 5.24e+00 pdb=" N1 C A 27 " -0.035 2.00e-02 2.50e+03 pdb=" C2 C A 27 " -0.001 2.00e-02 2.50e+03 pdb=" O2 C A 27 " -0.001 2.00e-02 2.50e+03 pdb=" N3 C A 27 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C A 27 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C A 27 " 0.008 2.00e-02 2.50e+03 pdb=" C5 C A 27 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C A 27 " -0.005 2.00e-02 2.50e+03 ... (remaining 2830 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 8022 2.98 - 3.46: 16033 3.46 - 3.94: 30122 3.94 - 4.42: 35178 4.42 - 4.90: 57221 Nonbonded interactions: 146576 Sorted by model distance: nonbonded pdb=" O5' A A 81 " pdb=" O4' A A 81 " model vdw 2.498 2.432 nonbonded pdb=" O4' DT C 24 " pdb=" O2 DT C 24 " model vdw 2.518 3.040 nonbonded pdb=" O5' G A 60 " pdb=" O4' G A 60 " model vdw 2.530 2.432 nonbonded pdb=" N GLY J 87 " pdb=" OP1 DG C 20 " model vdw 2.536 3.120 nonbonded pdb=" O THR F 131 " pdb=" CG2 THR F 131 " model vdw 2.546 3.460 ... (remaining 146571 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.560 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 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 : 0.003 0.037 18904 Z= 0.233 Angle : 0.605 8.372 26121 Z= 0.437 Chirality : 0.061 0.652 2988 Planarity : 0.004 0.037 2833 Dihedral : 17.088 179.189 7875 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: 0.82 (0.19), residues: 1930 helix: 1.36 (0.20), residues: 760 sheet: 0.81 (0.24), residues: 490 loop : -0.53 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 179 TYR 0.010 0.001 TYR F 59 PHE 0.010 0.001 PHE E 148 TRP 0.005 0.001 TRP H 144 HIS 0.002 0.001 HIS K 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.23 (18904) covalent geometry : angle 0.60483 / 0.44 (26121) hydrogen bonds : bond 0.15858 / 10.38 ( 868) hydrogen bonds : angle 6.98372 / 4.96 ( 2543) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 98 ASP cc_start: 0.8281 (t0) cc_final: 0.8038 (t0) REVERT: E 91 ASP cc_start: 0.8364 (m-30) cc_final: 0.8153 (m-30) REVERT: E 106 LYS cc_start: 0.8656 (ttpt) cc_final: 0.7939 (mmtt) REVERT: E 135 MET cc_start: 0.8966 (mmt) cc_final: 0.8491 (mmt) REVERT: G 19 ASP cc_start: 0.8683 (p0) cc_final: 0.8471 (p0) REVERT: G 40 LYS cc_start: 0.8343 (mttt) cc_final: 0.8021 (mttp) REVERT: G 135 MET cc_start: 0.9132 (mmm) cc_final: 0.8585 (mmt) REVERT: G 142 ARG cc_start: 0.8763 (mtt90) cc_final: 0.8440 (mtt-85) REVERT: H 2 LYS cc_start: 0.8549 (mmtm) cc_final: 0.8195 (mttt) REVERT: I 190 MET cc_start: 0.8593 (mmm) cc_final: 0.8373 (mmp) REVERT: J 2 LYS cc_start: 0.8192 (mtmm) cc_final: 0.7531 (mtpt) REVERT: J 106 LYS cc_start: 0.8368 (ttpt) cc_final: 0.8128 (tttm) REVERT: L 2 LYS cc_start: 0.8455 (mttt) cc_final: 0.8015 (ttmt) REVERT: L 151 MET cc_start: 0.8524 (mtm) cc_final: 0.8162 (mtp) REVERT: L 167 GLU cc_start: 0.8134 (tt0) cc_final: 0.7830 (mm-30) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.1402 time to fit residues: 60.6033 Evaluate side-chains 221 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [98, 194, 107, 10, 66, 130, 124, 103, 200, 77, 122] chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 84 ASN D 171 ASN E 156 GLN F 119 GLN F 171 ASN H 156 GLN J 171 ASN K 107 ASN L 84 ASN L 107 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.130869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.097917 restraints weight = 20377.813| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.26 r_work: 0.2878 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.0796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18904 Z= 0.124 Angle : 0.514 6.191 26121 Z= 0.295 Chirality : 0.045 0.295 2988 Planarity : 0.004 0.036 2833 Dihedral : 20.684 174.175 3965 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 0.64 % Allowed : 4.36 % Favored : 95.00 % 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: 1.15 (0.19), residues: 1930 helix: 1.72 (0.20), residues: 760 sheet: 1.03 (0.24), residues: 490 loop : -0.49 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 142 TYR 0.011 0.001 TYR H 59 PHE 0.011 0.001 PHE K 148 TRP 0.003 0.001 TRP K 178 HIS 0.002 0.001 HIS L 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (18904) covalent geometry : angle 0.51400 / 0.30 (26121) hydrogen bonds : bond 0.03919 / 2.51 ( 868) hydrogen bonds : angle 5.42389 / 3.87 ( 2543) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 239 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 106 LYS cc_start: 0.8556 (ttpt) cc_final: 0.7568 (mmtt) REVERT: F 79 SER cc_start: 0.9101 (t) cc_final: 0.8867 (m) REVERT: G 40 LYS cc_start: 0.8512 (mttt) cc_final: 0.8133 (mttp) REVERT: G 135 MET cc_start: 0.9151 (mmm) cc_final: 0.8598 (mmt) REVERT: G 142 ARG cc_start: 0.8760 (mtt90) cc_final: 0.8498 (mtt-85) REVERT: I 153 ASP cc_start: 0.8519 (t0) cc_final: 0.8299 (t0) REVERT: I 190 MET cc_start: 0.8574 (mmm) cc_final: 0.8234 (mmp) REVERT: J 106 LYS cc_start: 0.8380 (ttpt) cc_final: 0.7984 (tttm) REVERT: K 19 ASP cc_start: 0.9002 (p0) cc_final: 0.8781 (p0) REVERT: K 153 ASP cc_start: 0.8767 (t70) cc_final: 0.8289 (t0) REVERT: L 59 TYR cc_start: 0.8610 (m-80) cc_final: 0.7908 (m-80) REVERT: L 147 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7838 (mt-10) REVERT: L 151 MET cc_start: 0.8662 (mtm) cc_final: 0.8328 (mtp) outliers start: 11 outliers final: 10 residues processed: 244 average time/residue: 0.1202 time to fit residues: 45.7785 Evaluate side-chains 232 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 222 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain M residue 145 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [130, 66, 33, 176, 151, 48, 189, 18, 10, 160, 9] chunk 130 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 189 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 160 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 84 ASN E 107 ASN H 156 GLN J 171 ASN K 107 ASN L 84 ASN L 107 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.127904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.094758 restraints weight = 20395.496| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.26 r_work: 0.2858 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18904 Z= 0.181 Angle : 0.558 6.298 26121 Z= 0.312 Chirality : 0.048 0.317 2988 Planarity : 0.004 0.035 2833 Dihedral : 20.722 174.946 3965 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.28 % Allowed : 5.35 % Favored : 93.37 % 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: 0.92 (0.19), residues: 1930 helix: 1.66 (0.20), residues: 760 sheet: 0.77 (0.23), residues: 510 loop : -0.72 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 181 TYR 0.014 0.001 TYR H 59 PHE 0.013 0.002 PHE K 148 TRP 0.005 0.001 TRP L 144 HIS 0.006 0.001 HIS L 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (18904) covalent geometry : angle 0.55825 / 0.31 (26121) hydrogen bonds : bond 0.04112 / 2.67 ( 868) hydrogen bonds : angle 5.06419 / 3.61 ( 2543) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 238 time to evaluate : 0.708 Fit side-chains revert: symmetry clash REVERT: E 106 LYS cc_start: 0.8608 (ttpt) cc_final: 0.7628 (mmtt) REVERT: E 135 MET cc_start: 0.9054 (mmt) cc_final: 0.8527 (mmt) REVERT: F 79 SER cc_start: 0.9156 (t) cc_final: 0.8926 (m) REVERT: G 40 LYS cc_start: 0.8470 (mttt) cc_final: 0.8099 (mttp) REVERT: G 135 MET cc_start: 0.9156 (mmm) cc_final: 0.8655 (mmt) REVERT: G 142 ARG cc_start: 0.8766 (mtt90) cc_final: 0.8501 (mtt-85) REVERT: H 98 ASP cc_start: 0.8445 (t0) cc_final: 0.8130 (t0) REVERT: I 190 MET cc_start: 0.8688 (mmm) cc_final: 0.8319 (mmp) REVERT: J 106 LYS cc_start: 0.8394 (ttpt) cc_final: 0.7960 (tttm) REVERT: K 19 ASP cc_start: 0.9020 (p0) cc_final: 0.8803 (p0) REVERT: K 45 ASP cc_start: 0.7860 (m-30) cc_final: 0.7648 (m-30) REVERT: K 161 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7238 (mt-10) REVERT: L 2 LYS cc_start: 0.7488 (mttt) cc_final: 0.7192 (ttmt) outliers start: 22 outliers final: 18 residues processed: 246 average time/residue: 0.1327 time to fit residues: 50.8408 Evaluate side-chains 247 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 229 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain M residue 145 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [49, 176, 138, 143, 10, 161, 27, 81, 118, 34, 62] chunk 49 optimal weight: 0.7980 chunk 176 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 10 optimal weight: 0.0770 chunk 161 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 84 ASN E 53 GLN E 107 ASN F 171 ASN K 107 ASN L 84 ASN L 107 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.126025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.094494 restraints weight = 20372.131| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.08 r_work: 0.2813 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 18904 Z= 0.126 Angle : 0.496 6.183 26121 Z= 0.283 Chirality : 0.045 0.311 2988 Planarity : 0.004 0.034 2833 Dihedral : 20.641 174.466 3965 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.10 % Allowed : 6.86 % Favored : 92.03 % 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: 1.05 (0.20), residues: 1930 helix: 1.76 (0.20), residues: 760 sheet: 0.80 (0.23), residues: 510 loop : -0.61 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 39 TYR 0.012 0.001 TYR F 59 PHE 0.009 0.001 PHE I 14 TRP 0.005 0.001 TRP H 178 HIS 0.003 0.001 HIS L 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (18904) covalent geometry : angle 0.49574 / 0.28 (26121) hydrogen bonds : bond 0.03295 / 2.13 ( 868) hydrogen bonds : angle 4.83284 / 3.45 ( 2543) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 242 time to evaluate : 0.663 Fit side-chains revert: symmetry clash REVERT: E 106 LYS cc_start: 0.8624 (ttpt) cc_final: 0.7736 (mmtt) REVERT: E 135 MET cc_start: 0.9028 (mmt) cc_final: 0.8547 (mmt) REVERT: G 135 MET cc_start: 0.9052 (mmm) cc_final: 0.8550 (mmt) REVERT: G 142 ARG cc_start: 0.8702 (mtt90) cc_final: 0.8433 (mtt-85) REVERT: H 98 ASP cc_start: 0.8360 (t0) cc_final: 0.8048 (t0) REVERT: H 147 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8525 (mt-10) REVERT: I 103 MET cc_start: 0.9111 (ttt) cc_final: 0.8821 (ttp) REVERT: J 106 LYS cc_start: 0.8409 (ttpt) cc_final: 0.7991 (tttm) REVERT: K 19 ASP cc_start: 0.8945 (p0) cc_final: 0.8711 (p0) REVERT: K 45 ASP cc_start: 0.7784 (m-30) cc_final: 0.7572 (m-30) REVERT: K 153 ASP cc_start: 0.8534 (t0) cc_final: 0.7806 (t0) REVERT: L 2 LYS cc_start: 0.7398 (mttt) cc_final: 0.7118 (ttpt) REVERT: L 147 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7739 (mt-10) outliers start: 19 outliers final: 16 residues processed: 249 average time/residue: 0.1385 time to fit residues: 52.7116 Evaluate side-chains 245 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 229 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 145 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [5, 195, 79, 119, 141, 93, 4, 22, 179, 12, 59] chunk 5 optimal weight: 3.9990 chunk 195 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 179 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 84 ASN E 107 ASN F 171 ASN ** H 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 5 ASN K 107 ASN L 84 ASN L 107 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.121249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.089993 restraints weight = 20441.529| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 1.04 r_work: 0.2753 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 18904 Z= 0.282 Angle : 0.645 7.576 26121 Z= 0.352 Chirality : 0.052 0.316 2988 Planarity : 0.005 0.042 2833 Dihedral : 20.673 176.783 3965 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.57 % Allowed : 7.44 % Favored : 90.99 % 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: 0.62 (0.19), residues: 1930 helix: 1.41 (0.19), residues: 760 sheet: 0.64 (0.23), residues: 510 loop : -0.90 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 179 TYR 0.017 0.002 TYR H 59 PHE 0.017 0.003 PHE I 182 TRP 0.009 0.002 TRP H 144 HIS 0.007 0.002 HIS J 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00678 / 0.28 (18904) covalent geometry : angle 0.64533 / 0.35 (26121) hydrogen bonds : bond 0.04794 / 3.15 ( 868) hydrogen bonds : angle 4.99852 / 3.56 ( 2543) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 228 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: E 106 LYS cc_start: 0.8678 (ttpt) cc_final: 0.7779 (mmtt) REVERT: E 135 MET cc_start: 0.9067 (mmt) cc_final: 0.8598 (mmt) REVERT: G 135 MET cc_start: 0.9089 (mmm) cc_final: 0.8763 (mmt) REVERT: G 142 ARG cc_start: 0.8722 (mtt90) cc_final: 0.8435 (mtt-85) REVERT: H 98 ASP cc_start: 0.8423 (t0) cc_final: 0.8115 (t0) REVERT: K 45 ASP cc_start: 0.7806 (m-30) cc_final: 0.7576 (m-30) REVERT: K 153 ASP cc_start: 0.8648 (t0) cc_final: 0.7907 (t0) REVERT: L 2 LYS cc_start: 0.7519 (mttt) cc_final: 0.7287 (ttpt) REVERT: M 135 MET cc_start: 0.8225 (tpt) cc_final: 0.7932 (tpt) outliers start: 27 outliers final: 24 residues processed: 241 average time/residue: 0.1362 time to fit residues: 50.2227 Evaluate side-chains 240 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 216 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 145 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [116, 197, 144, 180, 94, 86, 129, 117, 6, 166, 150] chunk 116 optimal weight: 1.9990 chunk 197 optimal weight: 40.0000 chunk 144 optimal weight: 0.9980 chunk 180 optimal weight: 0.1980 chunk 94 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 166 optimal weight: 0.8980 chunk 150 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 84 ASN E 107 ASN F 171 ASN H 156 GLN K 107 ASN L 84 ASN L 107 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.125710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.097669 restraints weight = 19929.061| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 0.85 r_work: 0.2834 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 18904 Z= 0.116 Angle : 0.498 6.218 26121 Z= 0.285 Chirality : 0.045 0.312 2988 Planarity : 0.004 0.035 2833 Dihedral : 20.583 175.423 3965 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.10 % Allowed : 8.31 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.20), residues: 1930 helix: 1.71 (0.20), residues: 760 sheet: 0.74 (0.23), residues: 510 loop : -0.66 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 39 TYR 0.012 0.001 TYR F 59 PHE 0.009 0.001 PHE D 152 TRP 0.006 0.001 TRP H 144 HIS 0.001 0.000 HIS L 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 (18904) covalent geometry : angle 0.49775 / 0.28 (26121) hydrogen bonds : bond 0.03248 / 2.09 ( 868) hydrogen bonds : angle 4.72582 / 3.37 ( 2543) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 231 time to evaluate : 0.612 Fit side-chains REVERT: E 106 LYS cc_start: 0.8617 (ttpt) cc_final: 0.7733 (mmtt) REVERT: E 135 MET cc_start: 0.9036 (mmt) cc_final: 0.8577 (mmt) REVERT: G 135 MET cc_start: 0.8961 (mmm) cc_final: 0.8502 (mmt) REVERT: G 142 ARG cc_start: 0.8708 (mtt90) cc_final: 0.8441 (mtt-85) REVERT: H 98 ASP cc_start: 0.8359 (t0) cc_final: 0.8019 (t0) REVERT: H 147 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8527 (mt-10) REVERT: I 103 MET cc_start: 0.9072 (ttt) cc_final: 0.8823 (ttp) REVERT: K 153 ASP cc_start: 0.8506 (t0) cc_final: 0.7725 (t0) outliers start: 19 outliers final: 17 residues processed: 239 average time/residue: 0.1338 time to fit residues: 48.9870 Evaluate side-chains 238 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 221 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 145 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [7, 125, 77, 144, 3, 17, 117, 114, 121, 29, 104] chunk 7 optimal weight: 1.9990 chunk 125 optimal weight: 0.3980 chunk 77 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 114 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 84 ASN E 107 ASN F 171 ASN K 107 ASN L 84 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 = 0.3343 r_free = 0.3343 target = 0.125306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.096855 restraints weight = 20071.927| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 0.85 r_work: 0.2816 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18904 Z= 0.162 Angle : 0.527 6.373 26121 Z= 0.297 Chirality : 0.046 0.312 2988 Planarity : 0.004 0.036 2833 Dihedral : 20.569 175.897 3965 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.22 % Allowed : 8.49 % Favored : 90.29 % 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: 0.94 (0.19), residues: 1930 helix: 1.69 (0.20), residues: 760 sheet: 0.71 (0.23), residues: 510 loop : -0.66 (0.23), residues: 660 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 0.011 0.002 PHE E 148 TRP 0.007 0.001 TRP H 144 HIS 0.004 0.001 HIS L 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (18904) covalent geometry : angle 0.52663 / 0.30 (26121) hydrogen bonds : bond 0.03611 / 2.34 ( 868) hydrogen bonds : angle 4.71186 / 3.36 ( 2543) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 223 time to evaluate : 0.634 Fit side-chains REVERT: E 106 LYS cc_start: 0.8594 (ttpt) cc_final: 0.7731 (mmtt) REVERT: E 135 MET cc_start: 0.9049 (mmt) cc_final: 0.8592 (mmt) REVERT: G 135 MET cc_start: 0.8969 (mmm) cc_final: 0.8535 (mmt) REVERT: G 142 ARG cc_start: 0.8725 (mtt90) cc_final: 0.8454 (mtt-85) REVERT: H 98 ASP cc_start: 0.8302 (t0) cc_final: 0.7961 (t0) REVERT: K 153 ASP cc_start: 0.8513 (t0) cc_final: 0.7724 (t0) outliers start: 21 outliers final: 19 residues processed: 232 average time/residue: 0.1317 time to fit residues: 47.2380 Evaluate side-chains 238 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 219 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 145 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [166, 117, 149, 130, 72, 98, 29, 14, 121, 165, 188] chunk 166 optimal weight: 3.9990 chunk 117 optimal weight: 0.4980 chunk 149 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 29 optimal weight: 0.0980 chunk 14 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 165 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 84 ASN E 107 ASN F 171 ASN K 107 ASN L 84 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 = 0.3369 r_free = 0.3369 target = 0.127402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.098968 restraints weight = 19965.813| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 0.86 r_work: 0.2849 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 18904 Z= 0.107 Angle : 0.479 6.172 26121 Z= 0.275 Chirality : 0.044 0.306 2988 Planarity : 0.004 0.035 2833 Dihedral : 20.534 174.540 3965 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 1.40 % Allowed : 8.84 % Favored : 89.77 % 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: 1.12 (0.20), residues: 1930 helix: 1.82 (0.20), residues: 760 sheet: 0.79 (0.23), residues: 510 loop : -0.51 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 39 TYR 0.011 0.001 TYR F 59 PHE 0.008 0.001 PHE D 152 TRP 0.006 0.001 TRP H 144 HIS 0.001 0.000 HIS H 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.11 (18904) covalent geometry : angle 0.47867 / 0.27 (26121) hydrogen bonds : bond 0.03002 / 1.93 ( 868) hydrogen bonds : angle 4.55934 / 3.25 ( 2543) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 241 time to evaluate : 0.611 Fit side-chains REVERT: E 106 LYS cc_start: 0.8599 (ttpt) cc_final: 0.7698 (mmtt) REVERT: E 135 MET cc_start: 0.9032 (mmt) cc_final: 0.8610 (mmt) REVERT: G 135 MET cc_start: 0.8951 (mmm) cc_final: 0.8514 (mmt) REVERT: G 142 ARG cc_start: 0.8714 (mtt90) cc_final: 0.8451 (mtt-85) REVERT: H 98 ASP cc_start: 0.8291 (t0) cc_final: 0.7932 (t0) REVERT: H 147 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8532 (mt-10) REVERT: I 103 MET cc_start: 0.9038 (ttt) cc_final: 0.8821 (ttp) REVERT: K 153 ASP cc_start: 0.8472 (t0) cc_final: 0.7691 (t0) REVERT: L 59 TYR cc_start: 0.8603 (m-80) cc_final: 0.7940 (m-80) REVERT: M 167 GLU cc_start: 0.7256 (mm-30) cc_final: 0.7049 (mm-30) outliers start: 24 outliers final: 20 residues processed: 254 average time/residue: 0.1291 time to fit residues: 50.7503 Evaluate side-chains 247 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 227 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 145 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [81, 144, 29, 156, 183, 0, 50, 88, 63, 74, 125] chunk 81 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 63 optimal weight: 0.4980 chunk 74 optimal weight: 0.0980 chunk 125 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 84 ASN E 107 ASN F 171 ASN G 84 ASN K 107 ASN L 84 ASN L 107 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.125839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.097054 restraints weight = 19951.719| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 0.88 r_work: 0.2835 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18904 Z= 0.152 Angle : 0.517 6.630 26121 Z= 0.291 Chirality : 0.046 0.311 2988 Planarity : 0.004 0.036 2833 Dihedral : 20.524 174.803 3965 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.34 % Allowed : 9.24 % Favored : 89.42 % 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: 1.06 (0.20), residues: 1930 helix: 1.77 (0.20), residues: 760 sheet: 0.77 (0.23), residues: 510 loop : -0.57 (0.23), residues: 660 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 0.011 0.001 PHE E 148 TRP 0.006 0.001 TRP H 144 HIS 0.003 0.001 HIS J 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (18904) covalent geometry : angle 0.51671 / 0.29 (26121) hydrogen bonds : bond 0.03422 / 2.22 ( 868) hydrogen bonds : angle 4.57743 / 3.26 ( 2543) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 228 time to evaluate : 0.659 Fit side-chains REVERT: E 106 LYS cc_start: 0.8630 (ttpt) cc_final: 0.7774 (mmtt) REVERT: E 135 MET cc_start: 0.9038 (mmt) cc_final: 0.8578 (mmt) REVERT: G 135 MET cc_start: 0.8933 (mmm) cc_final: 0.8596 (mmt) REVERT: G 142 ARG cc_start: 0.8728 (mtt90) cc_final: 0.8456 (mtt-85) REVERT: H 98 ASP cc_start: 0.8287 (t0) cc_final: 0.7949 (t0) REVERT: K 153 ASP cc_start: 0.8513 (t0) cc_final: 0.7775 (t0) outliers start: 23 outliers final: 23 residues processed: 241 average time/residue: 0.1325 time to fit residues: 49.4612 Evaluate side-chains 244 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 221 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain L residue 84 ASN Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 145 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [52, 37, 190, 57, 112, 45, 72, 171, 162, 156, 41] chunk 52 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 190 optimal weight: 20.0000 chunk 57 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 171 optimal weight: 10.0000 chunk 162 optimal weight: 0.9980 chunk 156 optimal weight: 0.6980 chunk 41 optimal weight: 0.0270 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 84 ASN E 107 ASN F 171 ASN K 107 ASN L 107 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.126028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.097260 restraints weight = 19997.776| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 0.92 r_work: 0.2832 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.151 18904 Z= 0.159 Angle : 0.700 59.193 26121 Z= 0.416 Chirality : 0.046 0.413 2988 Planarity : 0.004 0.037 2833 Dihedral : 20.525 174.791 3965 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.28 % Allowed : 9.42 % Favored : 89.30 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.20), residues: 1930 helix: 1.79 (0.20), residues: 760 sheet: 0.76 (0.23), residues: 510 loop : -0.56 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 39 TYR 0.013 0.001 TYR H 59 PHE 0.010 0.001 PHE E 148 TRP 0.007 0.001 TRP H 144 HIS 0.002 0.001 HIS J 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (18904) covalent geometry : angle 0.70036 / 0.42 (26121) hydrogen bonds : bond 0.03352 / 2.17 ( 868) hydrogen bonds : angle 4.57506 / 3.26 ( 2543) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 223 time to evaluate : 0.574 Fit side-chains REVERT: E 106 LYS cc_start: 0.8605 (ttpt) cc_final: 0.7707 (mmtt) REVERT: E 135 MET cc_start: 0.9042 (mmt) cc_final: 0.8570 (mmt) REVERT: G 135 MET cc_start: 0.8946 (mmm) cc_final: 0.8551 (mmt) REVERT: G 142 ARG cc_start: 0.8732 (mtt90) cc_final: 0.8466 (mtt-85) REVERT: H 98 ASP cc_start: 0.8298 (t0) cc_final: 0.7946 (t0) REVERT: K 153 ASP cc_start: 0.8488 (t0) cc_final: 0.7700 (t0) outliers start: 22 outliers final: 22 residues processed: 235 average time/residue: 0.1310 time to fit residues: 47.7457 Evaluate side-chains 244 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 222 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 145 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [129, 80, 4, 109, 120, 38, 36, 9, 26, 184, 41] chunk 129 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 36 optimal weight: 0.0020 chunk 9 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 184 optimal weight: 0.0030 chunk 41 optimal weight: 0.0270 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 107 ASN F 171 ASN K 107 ASN L 107 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.126023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.097254 restraints weight = 20009.473| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 0.92 r_work: 0.2837 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.151 18904 Z= 0.159 Angle : 0.700 59.193 26121 Z= 0.416 Chirality : 0.046 0.413 2988 Planarity : 0.004 0.037 2833 Dihedral : 20.525 174.791 3965 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.28 % Allowed : 9.42 % Favored : 89.30 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.20), residues: 1930 helix: 1.79 (0.20), residues: 760 sheet: 0.76 (0.23), residues: 510 loop : -0.56 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 39 TYR 0.013 0.001 TYR H 59 PHE 0.010 0.001 PHE E 148 TRP 0.007 0.001 TRP H 144 HIS 0.002 0.001 HIS J 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (18904) covalent geometry : angle 0.70036 / 0.42 (26121) hydrogen bonds : bond 0.03352 / 2.17 ( 868) hydrogen bonds : angle 4.57506 / 3.26 ( 2543) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4221.49 seconds wall clock time: 72 minutes 53.28 seconds (4373.28 seconds total)