Starting phenix.real_space_refine on Mon Oct 26 17:51:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/36pe_77734/10_2026/36pe_77734.cif Found real_map, /net/cci-nas-00/data/ceres_data/36pe_77734/10_2026/36pe_77734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/36pe_77734/10_2026/36pe_77734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/36pe_77734/10_2026/36pe_77734.map" model { file = "/net/cci-nas-00/data/ceres_data/36pe_77734/10_2026/36pe_77734.cif" } default_model = "/net/cci-nas-00/data/ceres_data/36pe_77734/10_2026/36pe_77734.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 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 141 5.49 5 S 156 5.16 5 C 13162 2.51 5 N 3669 2.21 5 O 4413 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s 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: 21541 Number of models: 1 Model: "" Number of chains: 15 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: "N" 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: "O" 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: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1989 Classifications: {'RNA': 92} Modifications used: {'rna2p_pur': 24, 'rna2p_pyr': 16, 'rna3p_pur': 32, 'rna3p_pyr': 20} Link IDs: {'rna2p': 39, 'rna3p': 52} Chain: "B" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 711 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} 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: 4.79, per 1000 atoms: 0.22 Number of scatterers: 21541 At special positions: 0 Unit cell: (98.04, 102.6, 222.3, 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 156 16.00 P 141 15.00 O 4413 8.00 N 3669 7.00 C 13162 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: 1.70 Conformation dependent library (CDL) restraints added in 962.3 milliseconds 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4392 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 38 sheets defined 41.9% alpha, 35.6% beta 33 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 2.94 Creating SS restraints... Processing helix chain 'D' and resid 19 through 23 removed outlier: 3.563A 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 removed outlier: 3.550A pdb=" N THR D 56 " --> pdb=" O SER D 52 " (cutoff:3.500A) 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 122 removed outlier: 3.816A pdb=" N ILE D 122 " --> pdb=" O GLN D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 173 Processing helix chain 'E' and resid 18 through 23 removed outlier: 4.669A pdb=" N LEU E 21 " --> pdb=" O ALA E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 37 Processing helix chain 'E' and resid 42 through 57 removed outlier: 3.589A 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: 6.607A 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: 3.619A 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: 3.575A pdb=" N SER F 57 " --> pdb=" O GLN F 53 " (cutoff:3.500A) removed outlier: 3.871A 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 removed outlier: 3.549A pdb=" N ARG F 92 " --> pdb=" O LYS F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 116 Processing helix chain 'F' and resid 118 through 120 No H-bonds generated for 'chain 'F' and resid 118 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 86 through 93 Processing helix chain 'G' and resid 111 through 116 Processing helix chain 'G' and resid 117 through 120 removed outlier: 6.537A pdb=" N ASP G 120 " --> pdb=" O LYS G 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 117 through 120' Processing helix chain 'G' and resid 158 through 173 Processing helix chain 'H' and resid 19 through 23 removed outlier: 3.523A pdb=" N SER H 22 " --> pdb=" O ASP H 19 " (cutoff:3.500A) removed outlier: 3.506A 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 57 Processing helix chain 'H' and resid 70 through 82 Processing helix chain 'H' and resid 83 through 85 No H-bonds generated for 'chain 'H' and resid 83 through 85' Processing helix chain 'H' and resid 86 through 93 removed outlier: 3.620A pdb=" N ARG H 92 " --> pdb=" O LYS H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 116 Processing helix chain 'H' and resid 117 through 122 removed outlier: 6.393A pdb=" N ASP H 120 " --> pdb=" O LYS H 117 " (cutoff:3.500A) removed outlier: 3.661A 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 117 through 122' Processing helix chain 'H' and resid 158 through 173 Processing helix chain 'I' and resid 19 through 23 removed outlier: 3.519A 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: 3.565A 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 83 through 85 No H-bonds generated for 'chain 'J' and resid 83 through 85' Processing helix chain 'J' and resid 86 through 93 Processing helix chain 'J' and resid 111 through 116 Processing helix chain 'J' and resid 117 through 120 removed outlier: 6.287A 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: 6.392A 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: 3.581A 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 86 through 92 Processing helix chain 'L' and resid 111 through 116 Processing helix chain 'L' and resid 117 through 120 removed outlier: 6.317A 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: 3.603A 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 86 through 92 Processing helix chain 'M' and resid 111 through 116 Processing helix chain 'M' and resid 117 through 120 removed outlier: 6.362A pdb=" N ASP M 120 " --> pdb=" O LYS M 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 117 through 120' Processing helix chain 'M' and resid 158 through 173 Processing helix chain 'N' and resid 19 through 23 removed outlier: 3.541A pdb=" N ASP N 23 " --> pdb=" O THR N 20 " (cutoff:3.500A) Processing helix chain 'N' and resid 26 through 37 Processing helix chain 'N' and resid 42 through 56 Processing helix chain 'N' and resid 70 through 82 Processing helix chain 'N' and resid 83 through 85 No H-bonds generated for 'chain 'N' and resid 83 through 85' Processing helix chain 'N' and resid 86 through 93 Processing helix chain 'N' and resid 111 through 116 Processing helix chain 'N' and resid 118 through 120 No H-bonds generated for 'chain 'N' and resid 118 through 120' Processing helix chain 'N' and resid 158 through 173 Processing helix chain 'O' and resid 19 through 23 removed outlier: 3.528A pdb=" N ASP O 23 " --> pdb=" O THR O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 26 through 37 Processing helix chain 'O' and resid 42 through 57 removed outlier: 3.520A pdb=" N THR O 56 " --> pdb=" O SER O 52 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 82 Processing helix chain 'O' and resid 83 through 85 No H-bonds generated for 'chain 'O' and resid 83 through 85' Processing helix chain 'O' and resid 86 through 94 removed outlier: 3.553A pdb=" N ILE O 94 " --> pdb=" O ILE O 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 117 removed outlier: 3.771A pdb=" N LYS O 117 " --> pdb=" O GLN O 113 " (cutoff:3.500A) Processing helix chain 'O' and resid 118 through 120 No H-bonds generated for 'chain 'O' and resid 118 through 120' Processing helix chain 'O' and resid 158 through 173 Processing sheet with id=AA1, first strand: chain 'D' and resid 60 through 61 removed outlier: 5.486A pdb=" N PHE D 66 " --> pdb=" O MET D 103 " (cutoff:3.500A) removed outlier: 9.793A pdb=" N VAL D 100 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N GLY D 149 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 4.626A 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: 5.486A pdb=" N PHE D 66 " --> pdb=" O MET D 103 " (cutoff:3.500A) removed outlier: 9.793A pdb=" N VAL D 100 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N GLY D 149 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLU D 147 " --> pdb=" O PRO D 102 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N TRP D 144 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU D 3 " --> pdb=" O GLU D 192 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLU D 192 " --> pdb=" O LEU D 3 " (cutoff:3.500A) removed outlier: 7.035A 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 'D' and resid 123 through 129 Processing sheet with id=AA5, first strand: chain 'E' and resid 60 through 61 removed outlier: 5.382A pdb=" N PHE E 66 " --> pdb=" O MET E 103 " (cutoff:3.500A) removed outlier: 9.706A pdb=" N VAL E 100 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N GLY E 149 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLU E 147 " --> pdb=" O PRO E 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 60 through 61 removed outlier: 5.382A pdb=" N PHE E 66 " --> pdb=" O MET E 103 " (cutoff:3.500A) removed outlier: 9.706A pdb=" N VAL E 100 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N GLY E 149 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLU E 147 " --> pdb=" O PRO E 102 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N TRP E 144 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE E 152 " --> pdb=" O LYS E 2 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU E 3 " --> pdb=" O GLU E 192 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N GLU E 192 " --> pdb=" O LEU E 3 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ASN E 5 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 14 through 15 Processing sheet with id=AA8, first strand: chain 'F' and resid 60 through 61 removed outlier: 5.271A pdb=" N PHE F 66 " --> pdb=" O MET F 103 " (cutoff:3.500A) removed outlier: 9.554A pdb=" N VAL F 100 " --> pdb=" O GLY F 149 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N GLY F 149 " --> pdb=" O VAL F 100 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLU F 147 " --> pdb=" O PRO F 102 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 60 through 61 removed outlier: 5.271A pdb=" N PHE F 66 " --> pdb=" O MET F 103 " (cutoff:3.500A) removed outlier: 9.554A pdb=" N VAL F 100 " --> pdb=" O GLY F 149 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N GLY F 149 " --> pdb=" O VAL F 100 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLU F 147 " --> pdb=" O PRO F 102 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N TRP F 144 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU F 3 " --> pdb=" O GLU F 192 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLU F 192 " --> pdb=" O LEU F 3 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASN F 5 " --> pdb=" O MET F 190 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 14 through 15 Processing sheet with id=AB2, first strand: chain 'G' and resid 60 through 61 removed outlier: 5.271A pdb=" N PHE G 66 " --> pdb=" O MET G 103 " (cutoff:3.500A) removed outlier: 9.533A pdb=" N VAL G 100 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N GLY G 149 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLU G 147 " --> pdb=" O PRO G 102 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 60 through 61 removed outlier: 5.271A pdb=" N PHE G 66 " --> pdb=" O MET G 103 " (cutoff:3.500A) removed outlier: 9.533A pdb=" N VAL G 100 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N GLY G 149 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLU G 147 " --> pdb=" O PRO G 102 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N TRP G 144 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU G 3 " --> pdb=" O GLU G 192 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLU G 192 " --> pdb=" O LEU G 3 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN G 5 " --> pdb=" O MET G 190 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 14 through 15 Processing sheet with id=AB5, first strand: chain 'H' and resid 60 through 61 removed outlier: 5.254A pdb=" N PHE H 66 " --> pdb=" O MET H 103 " (cutoff:3.500A) removed outlier: 9.822A pdb=" N VAL H 100 " --> pdb=" O GLY H 149 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N GLY H 149 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLU H 147 " --> pdb=" O PRO H 102 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 60 through 61 removed outlier: 5.254A pdb=" N PHE H 66 " --> pdb=" O MET H 103 " (cutoff:3.500A) removed outlier: 9.822A pdb=" N VAL H 100 " --> pdb=" O GLY H 149 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N GLY H 149 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLU H 147 " --> pdb=" O PRO H 102 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N TRP H 144 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU H 3 " --> pdb=" O GLU H 192 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLU H 192 " --> pdb=" O LEU H 3 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ASN H 5 " --> pdb=" O MET H 190 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 14 through 15 Processing sheet with id=AB8, first strand: chain 'H' and resid 123 through 129 Processing sheet with id=AB9, first strand: chain 'I' and resid 60 through 61 removed outlier: 5.354A pdb=" N PHE I 66 " --> pdb=" O MET I 103 " (cutoff:3.500A) removed outlier: 9.621A pdb=" N VAL I 100 " --> pdb=" O GLY I 149 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N GLY I 149 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLU I 147 " --> pdb=" O PRO I 102 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 60 through 61 removed outlier: 5.354A pdb=" N PHE I 66 " --> pdb=" O MET I 103 " (cutoff:3.500A) removed outlier: 9.621A pdb=" N VAL I 100 " --> pdb=" O GLY I 149 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N GLY I 149 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLU I 147 " --> pdb=" O PRO I 102 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N TRP I 144 " --> pdb=" O GLY I 10 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU I 3 " --> pdb=" O GLU I 192 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLU I 192 " --> pdb=" O LEU I 3 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ASN I 5 " --> pdb=" O MET I 190 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 14 through 15 Processing sheet with id=AC3, first strand: chain 'J' and resid 60 through 61 removed outlier: 5.455A pdb=" N PHE J 66 " --> pdb=" O MET J 103 " (cutoff:3.500A) removed outlier: 9.673A pdb=" N VAL J 100 " --> pdb=" O GLY J 149 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N GLY J 149 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU J 147 " --> pdb=" O PRO J 102 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 60 through 61 removed outlier: 5.455A pdb=" N PHE J 66 " --> pdb=" O MET J 103 " (cutoff:3.500A) removed outlier: 9.673A pdb=" N VAL J 100 " --> pdb=" O GLY J 149 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N GLY J 149 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU J 147 " --> pdb=" O PRO J 102 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N TRP J 144 " --> pdb=" O GLY J 10 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU J 3 " --> pdb=" O GLU J 192 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLU J 192 " --> pdb=" O LEU J 3 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN J 5 " --> pdb=" O MET J 190 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 14 through 15 Processing sheet with id=AC6, first strand: chain 'K' and resid 60 through 61 removed outlier: 5.329A pdb=" N PHE K 66 " --> pdb=" O MET K 103 " (cutoff:3.500A) removed outlier: 9.646A pdb=" N VAL K 100 " --> pdb=" O GLY K 149 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N GLY K 149 " --> pdb=" O VAL K 100 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU K 147 " --> pdb=" O PRO K 102 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 60 through 61 removed outlier: 5.329A pdb=" N PHE K 66 " --> pdb=" O MET K 103 " (cutoff:3.500A) removed outlier: 9.646A pdb=" N VAL K 100 " --> pdb=" O GLY K 149 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N GLY K 149 " --> pdb=" O VAL K 100 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU K 147 " --> pdb=" O PRO K 102 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N TRP K 144 " --> pdb=" O GLY K 10 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU K 3 " --> pdb=" O GLU K 192 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLU K 192 " --> pdb=" O LEU K 3 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ASN K 5 " --> pdb=" O MET K 190 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 14 through 15 Processing sheet with id=AC9, first strand: chain 'L' and resid 60 through 61 removed outlier: 5.380A pdb=" N PHE L 66 " --> pdb=" O MET L 103 " (cutoff:3.500A) removed outlier: 9.722A pdb=" N VAL L 100 " --> pdb=" O GLY L 149 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N GLY L 149 " --> pdb=" O VAL L 100 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLU L 147 " --> pdb=" O PRO L 102 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TRP L 144 " --> pdb=" O GLY L 10 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 95 through 96 removed outlier: 5.176A pdb=" N TRP L 144 " --> pdb=" O GLY L 10 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN L 5 " --> pdb=" O MET L 190 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 14 through 15 Processing sheet with id=AD3, first strand: chain 'M' and resid 60 through 61 removed outlier: 5.256A pdb=" N PHE M 66 " --> pdb=" O MET M 103 " (cutoff:3.500A) removed outlier: 9.833A pdb=" N VAL M 100 " --> pdb=" O GLY M 149 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N GLY M 149 " --> pdb=" O VAL M 100 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU M 147 " --> pdb=" O PRO M 102 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 60 through 61 removed outlier: 5.256A pdb=" N PHE M 66 " --> pdb=" O MET M 103 " (cutoff:3.500A) removed outlier: 9.833A pdb=" N VAL M 100 " --> pdb=" O GLY M 149 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N GLY M 149 " --> pdb=" O VAL M 100 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU M 147 " --> pdb=" O PRO M 102 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N TRP M 144 " --> pdb=" O GLY M 10 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LEU M 3 " --> pdb=" O GLU M 192 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N GLU M 192 " --> pdb=" O LEU M 3 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASN M 5 " --> pdb=" O MET M 190 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 14 through 15 Processing sheet with id=AD6, first strand: chain 'N' and resid 60 through 61 removed outlier: 5.415A pdb=" N PHE N 66 " --> pdb=" O MET N 103 " (cutoff:3.500A) removed outlier: 9.619A pdb=" N VAL N 100 " --> pdb=" O GLY N 149 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N GLY N 149 " --> pdb=" O VAL N 100 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLU N 147 " --> pdb=" O PRO N 102 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 60 through 61 removed outlier: 5.415A pdb=" N PHE N 66 " --> pdb=" O MET N 103 " (cutoff:3.500A) removed outlier: 9.619A pdb=" N VAL N 100 " --> pdb=" O GLY N 149 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N GLY N 149 " --> pdb=" O VAL N 100 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLU N 147 " --> pdb=" O PRO N 102 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N TRP N 144 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER N 191 " --> pdb=" O ASN N 5 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LYS N 7 " --> pdb=" O ILE N 189 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ILE N 189 " --> pdb=" O LYS N 7 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N THR N 9 " --> pdb=" O VAL N 187 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N VAL N 187 " --> pdb=" O THR N 9 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 14 through 15 Processing sheet with id=AD9, first strand: chain 'O' and resid 60 through 61 removed outlier: 5.315A pdb=" N PHE O 66 " --> pdb=" O MET O 103 " (cutoff:3.500A) removed outlier: 9.554A pdb=" N VAL O 100 " --> pdb=" O GLY O 149 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N GLY O 149 " --> pdb=" O VAL O 100 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU O 147 " --> pdb=" O PRO O 102 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 60 through 61 removed outlier: 5.315A pdb=" N PHE O 66 " --> pdb=" O MET O 103 " (cutoff:3.500A) removed outlier: 9.554A pdb=" N VAL O 100 " --> pdb=" O GLY O 149 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N GLY O 149 " --> pdb=" O VAL O 100 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU O 147 " --> pdb=" O PRO O 102 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N TRP O 144 " --> pdb=" O GLY O 10 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU O 3 " --> pdb=" O GLY O 193 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER O 191 " --> pdb=" O ASN O 5 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LYS O 7 " --> pdb=" O ILE O 189 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE O 189 " --> pdb=" O LYS O 7 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N THR O 9 " --> pdb=" O VAL O 187 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N VAL O 187 " --> pdb=" O THR O 9 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 14 through 15 1033 hydrogen bonds defined for protein. 2859 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 80 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 4.57 Time building geometry restraints manager: 2.30 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: 5038 1.33 - 1.45: 4812 1.45 - 1.57: 11850 1.57 - 1.69: 279 1.69 - 1.81: 264 Bond restraints: 22243 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 1.540 -0.024 8.00e-03 1.56e+04 9.37e+00 bond pdb=" N9 A A 1 " pdb=" C4 A A 1 " ideal model delta sigma weight residual 1.374 1.392 -0.018 6.00e-03 2.78e+04 9.31e+00 bond pdb=" C3' DA B 9 " pdb=" O3' DA B 9 " ideal model delta sigma weight residual 1.435 1.470 -0.035 1.30e-02 5.92e+03 7.37e+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 7.05e+00 ... (remaining 22238 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 30119 2.22 - 4.44: 493 4.44 - 6.66: 38 6.66 - 8.88: 6 8.88 - 11.10: 3 Bond angle restraints: 30659 Sorted by residual: angle pdb=" O4' A A 1 " pdb=" C1' A A 1 " pdb=" N9 A A 1 " ideal model delta sigma weight residual 108.20 116.62 -8.42 8.00e-01 1.56e+00 1.11e+02 angle pdb=" O5' U A 2 " pdb=" C5' U A 2 " pdb=" C4' U A 2 " ideal model delta sigma weight residual 109.40 114.04 -4.64 8.00e-01 1.56e+00 3.36e+01 angle pdb=" O4' DT C 24 " pdb=" C1' DT C 24 " pdb=" N1 DT C 24 " ideal model delta sigma weight residual 108.00 111.63 -3.63 7.00e-01 2.04e+00 2.68e+01 angle pdb=" C3' G A 78 " pdb=" O3' G A 78 " pdb=" P U A 79 " ideal model delta sigma weight residual 119.70 125.68 -5.98 1.20e+00 6.94e-01 2.48e+01 angle pdb=" O4' DG C 26 " pdb=" C1' DG C 26 " pdb=" N9 DG C 26 " ideal model delta sigma weight residual 108.00 111.34 -3.34 7.00e-01 2.04e+00 2.27e+01 ... (remaining 30654 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.57: 13072 35.57 - 71.15: 484 71.15 - 106.72: 17 106.72 - 142.29: 2 142.29 - 177.87: 8 Dihedral angle restraints: 13583 sinusoidal: 6791 harmonic: 6792 Sorted by residual: dihedral pdb=" C5' A A 1 " pdb=" C4' A A 1 " pdb=" C3' A A 1 " pdb=" O3' A A 1 " ideal model delta sinusoidal sigma weight residual 147.00 83.37 63.63 1 8.00e+00 1.56e-02 8.34e+01 dihedral pdb=" C4' A A 1 " pdb=" C3' A A 1 " pdb=" C2' A A 1 " pdb=" C1' A A 1 " ideal model delta sinusoidal sigma weight residual -35.00 25.91 -60.91 1 8.00e+00 1.56e-02 7.71e+01 dihedral pdb=" O4' A A 1 " pdb=" C4' A A 1 " pdb=" C3' A A 1 " pdb=" C2' A A 1 " ideal model delta sinusoidal sigma weight residual 24.00 -32.66 56.66 1 8.00e+00 1.56e-02 6.76e+01 ... (remaining 13580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 3413 0.127 - 0.254: 68 0.254 - 0.381: 2 0.381 - 0.509: 4 0.509 - 0.636: 13 Chirality restraints: 3500 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 -2.97 -0.64 2.00e-01 2.50e+01 1.01e+01 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 -2.92 -0.59 2.00e-01 2.50e+01 8.65e+00 chirality pdb=" P DG C 17 " pdb=" OP1 DG C 17 " pdb=" OP2 DG C 17 " pdb=" O5' DG C 17 " both_signs ideal model delta sigma weight residual True 2.34 -2.92 -0.58 2.00e-01 2.50e+01 8.48e+00 ... (remaining 3497 not shown) Planarity restraints: 3381 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U A 52 " 0.035 2.00e-02 2.50e+03 1.87e-02 7.90e+00 pdb=" N1 U A 52 " -0.041 2.00e-02 2.50e+03 pdb=" C2 U A 52 " -0.001 2.00e-02 2.50e+03 pdb=" O2 U A 52 " -0.005 2.00e-02 2.50e+03 pdb=" N3 U A 52 " 0.003 2.00e-02 2.50e+03 pdb=" C4 U A 52 " 0.006 2.00e-02 2.50e+03 pdb=" O4 U A 52 " 0.011 2.00e-02 2.50e+03 pdb=" C5 U A 52 " -0.006 2.00e-02 2.50e+03 pdb=" C6 U A 52 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A 12 " 0.033 2.00e-02 2.50e+03 1.69e-02 6.46e+00 pdb=" N1 U A 12 " -0.037 2.00e-02 2.50e+03 pdb=" C2 U A 12 " -0.003 2.00e-02 2.50e+03 pdb=" O2 U A 12 " -0.003 2.00e-02 2.50e+03 pdb=" N3 U A 12 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U A 12 " 0.005 2.00e-02 2.50e+03 pdb=" O4 U A 12 " 0.010 2.00e-02 2.50e+03 pdb=" C5 U A 12 " -0.003 2.00e-02 2.50e+03 pdb=" C6 U A 12 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 37 " -0.033 2.00e-02 2.50e+03 1.50e-02 6.18e+00 pdb=" N9 A A 37 " 0.035 2.00e-02 2.50e+03 pdb=" C8 A A 37 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A A 37 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A A 37 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A A 37 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A A 37 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A A 37 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A A 37 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A A 37 " 0.006 2.00e-02 2.50e+03 pdb=" C4 A A 37 " 0.004 2.00e-02 2.50e+03 ... (remaining 3378 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 7970 2.93 - 3.42: 18698 3.42 - 3.91: 35908 3.91 - 4.41: 41126 4.41 - 4.90: 69456 Nonbonded interactions: 173158 Sorted by model distance: nonbonded pdb=" O2' A A 1 " pdb=" O5' U A 2 " model vdw 2.433 3.040 nonbonded pdb=" N GLY J 87 " pdb=" OP1 DG C 20 " model vdw 2.478 3.120 nonbonded pdb=" O4' DT C 24 " pdb=" O2 DT C 24 " model vdw 2.521 3.040 nonbonded pdb=" O4' C A 74 " pdb=" C6 C A 74 " model vdw 2.558 2.672 nonbonded pdb=" O5' DA B 30 " pdb=" O4' DA B 30 " model vdw 2.574 2.432 ... (remaining 173153 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 23.320 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.070 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:9.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22243 Z= 0.241 Angle : 0.630 11.095 30659 Z= 0.469 Chirality : 0.062 0.636 3500 Planarity : 0.004 0.036 3381 Dihedral : 16.666 177.865 9191 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.18), residues: 2316 helix: 1.40 (0.18), residues: 912 sheet: 0.93 (0.21), residues: 588 loop : -0.44 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 39 TYR 0.010 0.001 TYR F 59 PHE 0.010 0.001 PHE F 14 TRP 0.007 0.001 TRP H 144 HIS 0.003 0.001 HIS E 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.24 (22243) covalent geometry : angle 0.63023 / 0.47 (30659) hydrogen bonds : bond 0.16178 / 10.83 ( 1027) hydrogen bonds : angle 7.03651 / 4.94 ( 3013) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 397 time to evaluate : 0.712 Fit side-chains REVERT: D 128 LYS cc_start: 0.8579 (tttp) cc_final: 0.8328 (ttpt) REVERT: D 135 MET cc_start: 0.8298 (tpp) cc_final: 0.8084 (mmt) REVERT: D 151 MET cc_start: 0.8154 (mtp) cc_final: 0.7837 (mtm) REVERT: E 98 ASP cc_start: 0.8208 (t0) cc_final: 0.7915 (t70) REVERT: E 99 VAL cc_start: 0.9366 (t) cc_final: 0.8970 (m) REVERT: E 151 MET cc_start: 0.8771 (mtp) cc_final: 0.8545 (mtp) REVERT: F 153 ASP cc_start: 0.8353 (t0) cc_final: 0.8040 (t70) REVERT: F 154 GLU cc_start: 0.8128 (pm20) cc_final: 0.7521 (tp30) REVERT: F 192 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7693 (tt0) REVERT: G 2 LYS cc_start: 0.8087 (mtpt) cc_final: 0.7769 (tttm) REVERT: G 68 MET cc_start: 0.9018 (ttm) cc_final: 0.8778 (ttm) REVERT: H 88 LYS cc_start: 0.8820 (mttp) cc_final: 0.8584 (mtpt) REVERT: H 95 MET cc_start: 0.8681 (ptm) cc_final: 0.8456 (ptm) REVERT: H 119 GLN cc_start: 0.8381 (mm-40) cc_final: 0.8162 (mm110) REVERT: I 103 MET cc_start: 0.8920 (ttt) cc_final: 0.8621 (ttt) REVERT: I 155 GLU cc_start: 0.8414 (tt0) cc_final: 0.7972 (tp30) REVERT: J 39 ARG cc_start: 0.8490 (ttm-80) cc_final: 0.8098 (ttm170) REVERT: J 98 ASP cc_start: 0.8339 (t0) cc_final: 0.8108 (t0) REVERT: K 51 GLU cc_start: 0.8412 (tt0) cc_final: 0.8128 (tt0) REVERT: L 71 GLU cc_start: 0.7467 (tt0) cc_final: 0.6864 (mp0) REVERT: L 78 LYS cc_start: 0.8783 (tttt) cc_final: 0.8582 (tttt) REVERT: L 135 MET cc_start: 0.8643 (mmm) cc_final: 0.8276 (tpt) REVERT: M 156 GLN cc_start: 0.8151 (mt0) cc_final: 0.7946 (tt0) REVERT: N 1 MET cc_start: 0.8157 (mmt) cc_final: 0.7529 (mmt) REVERT: N 113 GLN cc_start: 0.8206 (mp10) cc_final: 0.7901 (mm-40) REVERT: N 151 MET cc_start: 0.8401 (mtm) cc_final: 0.8182 (mtp) REVERT: O 151 MET cc_start: 0.7196 (ttt) cc_final: 0.6849 (tpt) outliers start: 0 outliers final: 0 residues processed: 397 average time/residue: 0.6769 time to fit residues: 300.5049 Evaluate side-chains 298 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: [216, 98, 194, 227, 107, 10, 66, 130, 124, 103, 235] chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 235 optimal weight: 30.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 84 ASN D 107 ASN D 119 GLN E 53 GLN E 107 ASN E 171 ASN H 107 ASN H 171 ASN I 107 ASN K 63 GLN M 113 GLN N 118 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.128770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.097637 restraints weight = 23541.281| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.21 r_work: 0.2905 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 22243 Z= 0.274 Angle : 0.665 7.751 30659 Z= 0.363 Chirality : 0.052 0.450 3500 Planarity : 0.005 0.045 3381 Dihedral : 20.157 176.717 4499 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 2.33 % Allowed : 7.85 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.17), residues: 2316 helix: 1.37 (0.18), residues: 912 sheet: 0.57 (0.21), residues: 612 loop : -0.91 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 179 TYR 0.016 0.002 TYR F 59 PHE 0.018 0.002 PHE M 148 TRP 0.009 0.002 TRP H 144 HIS 0.006 0.002 HIS J 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00664 / 0.27 (22243) covalent geometry : angle 0.66539 / 0.36 (30659) hydrogen bonds : bond 0.05204 / 3.49 ( 1027) hydrogen bonds : angle 5.33741 / 3.76 ( 3013) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 314 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: D 2 LYS cc_start: 0.8179 (mttt) cc_final: 0.7170 (mtpt) REVERT: D 113 GLN cc_start: 0.7469 (OUTLIER) cc_final: 0.6580 (mm-40) REVERT: D 128 LYS cc_start: 0.8356 (tttp) cc_final: 0.7924 (ttpt) REVERT: D 151 MET cc_start: 0.8257 (mtp) cc_final: 0.7942 (mtm) REVERT: E 98 ASP cc_start: 0.8440 (t0) cc_final: 0.8169 (t70) REVERT: E 99 VAL cc_start: 0.9330 (t) cc_final: 0.8911 (m) REVERT: E 106 LYS cc_start: 0.8531 (ttpt) cc_final: 0.8321 (ttpp) REVERT: E 151 MET cc_start: 0.8892 (mtp) cc_final: 0.8648 (mtp) REVERT: F 154 GLU cc_start: 0.7991 (pm20) cc_final: 0.6997 (tp30) REVERT: F 156 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8286 (mt0) REVERT: F 192 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7496 (tt0) REVERT: G 2 LYS cc_start: 0.7618 (mtpt) cc_final: 0.7037 (tttm) REVERT: G 68 MET cc_start: 0.9116 (ttm) cc_final: 0.8851 (ttm) REVERT: G 114 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7788 (mp0) REVERT: H 88 LYS cc_start: 0.8594 (mttp) cc_final: 0.8047 (mtpt) REVERT: H 95 MET cc_start: 0.8522 (ptm) cc_final: 0.8248 (ptm) REVERT: I 98 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.8117 (t0) REVERT: I 103 MET cc_start: 0.9178 (ttt) cc_final: 0.8894 (ttt) REVERT: I 155 GLU cc_start: 0.8327 (tt0) cc_final: 0.7713 (tp30) REVERT: I 163 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7528 (mp) REVERT: J 39 ARG cc_start: 0.8622 (ttm-80) cc_final: 0.8128 (ttm170) REVERT: J 61 ASP cc_start: 0.8612 (t0) cc_final: 0.8179 (t70) REVERT: J 88 LYS cc_start: 0.8138 (mmtm) cc_final: 0.7934 (mmtp) REVERT: J 98 ASP cc_start: 0.8464 (t0) cc_final: 0.8262 (t0) REVERT: K 51 GLU cc_start: 0.8218 (tt0) cc_final: 0.7990 (tt0) REVERT: K 71 GLU cc_start: 0.7112 (tt0) cc_final: 0.6899 (pt0) REVERT: K 91 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.7952 (m-30) REVERT: L 45 ASP cc_start: 0.8500 (m-30) cc_final: 0.8205 (m-30) REVERT: L 71 GLU cc_start: 0.7041 (tt0) cc_final: 0.6087 (mp0) REVERT: L 135 MET cc_start: 0.8746 (mmm) cc_final: 0.8539 (tpt) REVERT: M 68 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8629 (ttp) REVERT: N 1 MET cc_start: 0.8166 (mmt) cc_final: 0.7884 (mmt) REVERT: N 9 THR cc_start: 0.8776 (m) cc_final: 0.8500 (p) REVERT: N 68 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8174 (tpp) REVERT: O 82 LYS cc_start: 0.6991 (mmmt) cc_final: 0.6667 (tptp) REVERT: O 151 MET cc_start: 0.7316 (ttt) cc_final: 0.6780 (tpt) outliers start: 48 outliers final: 21 residues processed: 333 average time/residue: 0.6380 time to fit residues: 239.1309 Evaluate side-chains 319 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 290 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain F residue 156 GLN Chi-restraints excluded: chain F residue 188 GLU Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 151 MET Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain J residue 63 GLN Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 164 MET Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 72 MET Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain L residue 163 LEU Chi-restraints excluded: chain L residue 164 MET Chi-restraints excluded: chain M residue 68 MET Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 68 MET Chi-restraints excluded: chain O residue 20 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: [40, 18, 161, 21, 114, 85, 195, 93, 99, 235, 61] chunk 40 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 161 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 195 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 99 optimal weight: 0.5980 chunk 235 optimal weight: 20.0000 chunk 61 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 84 ASN E 107 ASN I 107 ASN J 113 GLN N 118 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.131823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.101601 restraints weight = 23524.436| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.16 r_work: 0.2949 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22243 Z= 0.119 Angle : 0.509 6.839 30659 Z= 0.292 Chirality : 0.046 0.440 3500 Planarity : 0.004 0.035 3381 Dihedral : 20.066 175.801 4499 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 1.70 % Allowed : 9.74 % Favored : 88.57 % 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: 0.99 (0.18), residues: 2316 helix: 1.67 (0.18), residues: 912 sheet: 0.94 (0.25), residues: 492 loop : -0.51 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 12 TYR 0.012 0.001 TYR H 59 PHE 0.008 0.001 PHE D 152 TRP 0.006 0.001 TRP H 144 HIS 0.003 0.001 HIS O 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (22243) covalent geometry : angle 0.50926 / 0.29 (30659) hydrogen bonds : bond 0.03568 / 2.41 ( 1027) hydrogen bonds : angle 4.94730 / 3.47 ( 3013) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 291 time to evaluate : 0.788 Fit side-chains revert: symmetry clash REVERT: D 2 LYS cc_start: 0.8144 (mttt) cc_final: 0.7216 (mtpt) REVERT: D 88 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7353 (mttm) REVERT: D 113 GLN cc_start: 0.7327 (OUTLIER) cc_final: 0.6402 (mm-40) REVERT: D 128 LYS cc_start: 0.8328 (tttp) cc_final: 0.7889 (ttpt) REVERT: D 151 MET cc_start: 0.8251 (mtp) cc_final: 0.8045 (mtp) REVERT: E 99 VAL cc_start: 0.9334 (t) cc_final: 0.8945 (m) REVERT: E 151 MET cc_start: 0.8868 (mtp) cc_final: 0.8615 (mtp) REVERT: F 153 ASP cc_start: 0.8352 (t0) cc_final: 0.7929 (t70) REVERT: F 154 GLU cc_start: 0.8009 (pm20) cc_final: 0.7131 (tp30) REVERT: F 156 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8266 (mt0) REVERT: F 192 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7386 (tt0) REVERT: G 2 LYS cc_start: 0.7541 (mtpt) cc_final: 0.6985 (tttm) REVERT: G 114 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7701 (mp0) REVERT: H 88 LYS cc_start: 0.8520 (mttp) cc_final: 0.7999 (mtpt) REVERT: H 95 MET cc_start: 0.8528 (ptm) cc_final: 0.8283 (ptm) REVERT: I 98 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.8014 (t0) REVERT: I 103 MET cc_start: 0.9169 (ttt) cc_final: 0.8850 (ttt) REVERT: I 155 GLU cc_start: 0.8324 (tt0) cc_final: 0.7724 (tp30) REVERT: J 39 ARG cc_start: 0.8595 (ttm-80) cc_final: 0.8138 (ttm170) REVERT: J 61 ASP cc_start: 0.8609 (t0) cc_final: 0.8028 (t70) REVERT: K 91 ASP cc_start: 0.8291 (t0) cc_final: 0.7937 (m-30) REVERT: K 188 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7542 (tt0) REVERT: L 71 GLU cc_start: 0.6951 (tt0) cc_final: 0.5984 (mp0) REVERT: L 114 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8445 (mt-10) REVERT: L 135 MET cc_start: 0.8846 (mmm) cc_final: 0.8556 (tpt) REVERT: L 151 MET cc_start: 0.8874 (mtm) cc_final: 0.8096 (mpt) REVERT: L 188 GLU cc_start: 0.8478 (tt0) cc_final: 0.8263 (tt0) REVERT: N 1 MET cc_start: 0.8144 (mmt) cc_final: 0.7836 (mmt) REVERT: N 9 THR cc_start: 0.8742 (m) cc_final: 0.8522 (p) REVERT: N 68 MET cc_start: 0.8400 (ttt) cc_final: 0.8127 (tpp) REVERT: O 20 THR cc_start: 0.8341 (OUTLIER) cc_final: 0.8004 (p) REVERT: O 82 LYS cc_start: 0.7044 (mmmt) cc_final: 0.6706 (tptp) REVERT: O 151 MET cc_start: 0.7344 (ttt) cc_final: 0.6918 (tpt) outliers start: 35 outliers final: 14 residues processed: 305 average time/residue: 0.6294 time to fit residues: 216.5037 Evaluate side-chains 298 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 277 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain F residue 156 GLN Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain J residue 63 GLN Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 164 MET Chi-restraints excluded: chain K residue 188 GLU Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain L residue 163 LEU Chi-restraints excluded: chain L residue 164 MET Chi-restraints excluded: chain M residue 68 MET Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain O residue 20 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: [126, 196, 231, 201, 149, 18, 152, 177, 158, 131, 86] chunk 126 optimal weight: 0.0670 chunk 196 optimal weight: 5.9990 chunk 231 optimal weight: 10.0000 chunk 201 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 152 optimal weight: 6.9990 chunk 177 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 84 ASN D 171 ASN E 107 ASN I 107 ASN K 171 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.150937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.120872 restraints weight = 23069.651| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.23 r_work: 0.3247 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22243 Z= 0.121 Angle : 0.500 6.918 30659 Z= 0.285 Chirality : 0.045 0.438 3500 Planarity : 0.004 0.034 3381 Dihedral : 20.011 174.663 4499 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.33 % Allowed : 10.03 % Favored : 87.65 % 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: 1.19 (0.18), residues: 2316 helix: 1.79 (0.18), residues: 912 sheet: 0.96 (0.21), residues: 588 loop : -0.45 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 12 TYR 0.012 0.001 TYR H 59 PHE 0.009 0.001 PHE G 148 TRP 0.007 0.001 TRP H 144 HIS 0.002 0.001 HIS K 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (22243) covalent geometry : angle 0.49973 / 0.28 (30659) hydrogen bonds : bond 0.03405 / 2.30 ( 1027) hydrogen bonds : angle 4.73308 / 3.32 ( 3013) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 293 time to evaluate : 0.737 Fit side-chains revert: symmetry clash REVERT: D 2 LYS cc_start: 0.8356 (mttt) cc_final: 0.7655 (mtpt) REVERT: D 88 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7678 (mttm) REVERT: D 113 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.6843 (mm-40) REVERT: D 128 LYS cc_start: 0.8433 (tttp) cc_final: 0.8112 (ttpt) REVERT: E 98 ASP cc_start: 0.8433 (t0) cc_final: 0.8137 (t70) REVERT: E 99 VAL cc_start: 0.9341 (t) cc_final: 0.8908 (m) REVERT: E 151 MET cc_start: 0.8889 (mtp) cc_final: 0.8668 (mtp) REVERT: F 153 ASP cc_start: 0.8399 (t0) cc_final: 0.7978 (t70) REVERT: F 154 GLU cc_start: 0.8123 (pm20) cc_final: 0.7394 (tp30) REVERT: F 156 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8356 (mt0) REVERT: F 192 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7627 (tt0) REVERT: G 2 LYS cc_start: 0.7746 (mtpt) cc_final: 0.7303 (tttm) REVERT: G 114 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8127 (mp0) REVERT: H 88 LYS cc_start: 0.8766 (mttp) cc_final: 0.8338 (mtpt) REVERT: H 95 MET cc_start: 0.8615 (ptm) cc_final: 0.8380 (ptm) REVERT: I 98 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.8136 (t0) REVERT: I 103 MET cc_start: 0.9176 (ttt) cc_final: 0.8831 (ttt) REVERT: I 155 GLU cc_start: 0.8388 (tt0) cc_final: 0.7911 (tp30) REVERT: I 163 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7839 (mp) REVERT: J 39 ARG cc_start: 0.8577 (ttm-80) cc_final: 0.8141 (ttm170) REVERT: J 61 ASP cc_start: 0.8697 (t0) cc_final: 0.8140 (t70) REVERT: K 2 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7116 (mttm) REVERT: K 91 ASP cc_start: 0.8088 (OUTLIER) cc_final: 0.7820 (m-30) REVERT: K 188 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7816 (tt0) REVERT: L 71 GLU cc_start: 0.7174 (tt0) cc_final: 0.6423 (mp0) REVERT: L 114 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8593 (mt-10) REVERT: L 135 MET cc_start: 0.8665 (mmm) cc_final: 0.8397 (tpt) REVERT: L 188 GLU cc_start: 0.8489 (tt0) cc_final: 0.8274 (tt0) REVERT: N 68 MET cc_start: 0.8474 (ttt) cc_final: 0.8250 (tpp) REVERT: O 20 THR cc_start: 0.8263 (OUTLIER) cc_final: 0.8000 (p) REVERT: O 82 LYS cc_start: 0.7262 (mmmt) cc_final: 0.6969 (tptp) outliers start: 48 outliers final: 22 residues processed: 316 average time/residue: 0.6157 time to fit residues: 219.6756 Evaluate side-chains 316 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 284 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 156 GLN Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 151 MET Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain J residue 63 GLN Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain K residue 2 LYS Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 164 MET Chi-restraints excluded: chain K residue 188 GLU Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain L residue 163 LEU Chi-restraints excluded: chain L residue 164 MET Chi-restraints excluded: chain M residue 68 MET Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 95 MET Chi-restraints excluded: chain O residue 20 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: [183, 80, 23, 83, 171, 149, 101, 147, 68, 229, 135] chunk 183 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 171 optimal weight: 7.9990 chunk 149 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 229 optimal weight: 10.0000 chunk 135 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 84 ASN D 171 ASN E 107 ASN I 107 ASN K 171 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.147573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.117561 restraints weight = 22803.156| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.23 r_work: 0.3207 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 22243 Z= 0.170 Angle : 0.540 6.877 30659 Z= 0.302 Chirality : 0.047 0.442 3500 Planarity : 0.004 0.035 3381 Dihedral : 20.004 173.964 4499 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 2.42 % Allowed : 11.19 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.18), residues: 2316 helix: 1.71 (0.18), residues: 912 sheet: 0.89 (0.21), residues: 588 loop : -0.54 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 12 TYR 0.013 0.001 TYR I 59 PHE 0.012 0.002 PHE H 182 TRP 0.008 0.001 TRP H 144 HIS 0.003 0.001 HIS J 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (22243) covalent geometry : angle 0.54049 / 0.30 (30659) hydrogen bonds : bond 0.03855 / 2.60 ( 1027) hydrogen bonds : angle 4.74717 / 3.34 ( 3013) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 288 time to evaluate : 0.754 Fit side-chains revert: symmetry clash REVERT: D 2 LYS cc_start: 0.8445 (mttt) cc_final: 0.7764 (mtpt) REVERT: D 88 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7681 (mttm) REVERT: D 113 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.6820 (mm-40) REVERT: D 128 LYS cc_start: 0.8458 (tttp) cc_final: 0.8126 (ttpt) REVERT: E 99 VAL cc_start: 0.9350 (t) cc_final: 0.8983 (m) REVERT: E 151 MET cc_start: 0.8914 (mtp) cc_final: 0.8705 (mtp) REVERT: F 98 ASP cc_start: 0.8653 (OUTLIER) cc_final: 0.8373 (t0) REVERT: F 153 ASP cc_start: 0.8494 (t0) cc_final: 0.8142 (t70) REVERT: F 154 GLU cc_start: 0.8123 (pm20) cc_final: 0.7381 (tp30) REVERT: F 156 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8379 (mt0) REVERT: F 192 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7664 (tt0) REVERT: G 2 LYS cc_start: 0.7844 (mtpt) cc_final: 0.7368 (tttm) REVERT: G 114 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8149 (mp0) REVERT: H 88 LYS cc_start: 0.8781 (mttp) cc_final: 0.8348 (mtpt) REVERT: H 95 MET cc_start: 0.8644 (ptm) cc_final: 0.8404 (ptm) REVERT: I 98 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.8140 (t0) REVERT: I 103 MET cc_start: 0.9188 (ttt) cc_final: 0.8865 (ttt) REVERT: I 155 GLU cc_start: 0.8491 (tt0) cc_final: 0.8047 (tp30) REVERT: I 163 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.7914 (mp) REVERT: J 39 ARG cc_start: 0.8654 (ttm-80) cc_final: 0.8201 (ttm170) REVERT: J 61 ASP cc_start: 0.8707 (t0) cc_final: 0.8146 (t70) REVERT: K 2 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7207 (mttm) REVERT: K 91 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7938 (m-30) REVERT: L 71 GLU cc_start: 0.7292 (tt0) cc_final: 0.6478 (mp0) REVERT: L 135 MET cc_start: 0.8672 (mmm) cc_final: 0.8404 (tpt) REVERT: N 68 MET cc_start: 0.8472 (ttt) cc_final: 0.8249 (tpp) REVERT: O 20 THR cc_start: 0.8237 (OUTLIER) cc_final: 0.7973 (p) REVERT: O 82 LYS cc_start: 0.7312 (mmmt) cc_final: 0.7032 (tptp) outliers start: 50 outliers final: 27 residues processed: 312 average time/residue: 0.6233 time to fit residues: 219.3159 Evaluate side-chains 315 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 278 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 156 GLN Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 151 MET Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain H residue 151 MET Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain J residue 63 GLN Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain K residue 2 LYS Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 164 MET Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain L residue 163 LEU Chi-restraints excluded: chain L residue 164 MET Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 68 MET Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 98 ASP Chi-restraints excluded: chain O residue 20 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: [23, 38, 16, 132, 48, 199, 87, 216, 137, 31, 220] chunk 23 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 199 optimal weight: 5.9990 chunk 87 optimal weight: 0.4980 chunk 216 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 220 optimal weight: 7.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 84 ASN D 171 ASN E 107 ASN I 107 ASN K 171 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.148996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.120766 restraints weight = 22775.484| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.06 r_work: 0.3243 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22243 Z= 0.126 Angle : 0.498 6.905 30659 Z= 0.283 Chirality : 0.045 0.433 3500 Planarity : 0.004 0.035 3381 Dihedral : 19.962 174.006 4499 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.42 % Allowed : 11.92 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.18), residues: 2316 helix: 1.81 (0.18), residues: 912 sheet: 0.92 (0.21), residues: 588 loop : -0.45 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 12 TYR 0.011 0.001 TYR H 59 PHE 0.010 0.001 PHE F 14 TRP 0.007 0.001 TRP H 144 HIS 0.002 0.001 HIS M 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (22243) covalent geometry : angle 0.49780 / 0.28 (30659) hydrogen bonds : bond 0.03349 / 2.26 ( 1027) hydrogen bonds : angle 4.62753 / 3.25 ( 3013) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 289 time to evaluate : 0.740 Fit side-chains revert: symmetry clash REVERT: D 2 LYS cc_start: 0.8422 (mttt) cc_final: 0.7762 (mtpt) REVERT: D 88 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7675 (mttm) REVERT: D 113 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.6783 (mm-40) REVERT: D 128 LYS cc_start: 0.8444 (tttp) cc_final: 0.8131 (ttpt) REVERT: E 95 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8803 (ptm) REVERT: E 98 ASP cc_start: 0.8448 (t0) cc_final: 0.8166 (t70) REVERT: E 99 VAL cc_start: 0.9329 (t) cc_final: 0.8877 (m) REVERT: E 151 MET cc_start: 0.8864 (mtp) cc_final: 0.8648 (mtp) REVERT: F 153 ASP cc_start: 0.8432 (t0) cc_final: 0.7989 (t70) REVERT: F 154 GLU cc_start: 0.8133 (pm20) cc_final: 0.7383 (tp30) REVERT: F 156 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8356 (mt0) REVERT: F 192 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7623 (tt0) REVERT: G 2 LYS cc_start: 0.7801 (mtpt) cc_final: 0.7327 (tttm) REVERT: G 114 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8160 (mp0) REVERT: G 155 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8078 (tp30) REVERT: H 88 LYS cc_start: 0.8769 (mttp) cc_final: 0.8346 (mtpt) REVERT: H 95 MET cc_start: 0.8632 (ptm) cc_final: 0.8395 (ptm) REVERT: I 98 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.8106 (t0) REVERT: I 103 MET cc_start: 0.9181 (ttt) cc_final: 0.8779 (ttt) REVERT: I 155 GLU cc_start: 0.8436 (tt0) cc_final: 0.8128 (tp30) REVERT: I 163 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.7873 (mp) REVERT: J 39 ARG cc_start: 0.8608 (ttm-80) cc_final: 0.8159 (ttm170) REVERT: J 61 ASP cc_start: 0.8681 (t0) cc_final: 0.8135 (t70) REVERT: J 88 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7785 (mmtp) REVERT: K 2 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7181 (mttm) REVERT: K 91 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7706 (m-30) REVERT: L 71 GLU cc_start: 0.7222 (tt0) cc_final: 0.6475 (mp0) REVERT: L 135 MET cc_start: 0.8646 (mmm) cc_final: 0.8368 (tpt) REVERT: L 151 MET cc_start: 0.9014 (mtm) cc_final: 0.8640 (mpp) REVERT: N 68 MET cc_start: 0.8446 (ttt) cc_final: 0.8219 (tpp) REVERT: O 20 THR cc_start: 0.8127 (OUTLIER) cc_final: 0.7894 (p) REVERT: O 82 LYS cc_start: 0.7330 (mmmt) cc_final: 0.6965 (tptp) outliers start: 50 outliers final: 23 residues processed: 311 average time/residue: 0.6440 time to fit residues: 225.5545 Evaluate side-chains 314 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 279 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain F residue 156 GLN Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 151 MET Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain J residue 63 GLN Chi-restraints excluded: chain J residue 88 LYS Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain K residue 2 LYS Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 164 MET Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain L residue 163 LEU Chi-restraints excluded: chain L residue 164 MET Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain O residue 20 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: [149, 94, 116, 51, 63, 71, 213, 19, 110, 60, 205] chunk 149 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 71 optimal weight: 0.0020 chunk 213 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 205 optimal weight: 7.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 84 ASN D 171 ASN E 107 ASN I 107 ASN K 171 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.146277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.116307 restraints weight = 22988.301| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.22 r_work: 0.3253 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22243 Z= 0.118 Angle : 0.494 6.913 30659 Z= 0.281 Chirality : 0.045 0.429 3500 Planarity : 0.004 0.035 3381 Dihedral : 19.930 174.138 4499 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 2.42 % Allowed : 12.45 % Favored : 85.13 % 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: 1.25 (0.18), residues: 2316 helix: 1.87 (0.18), residues: 912 sheet: 0.93 (0.21), residues: 588 loop : -0.40 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 39 TYR 0.011 0.001 TYR H 59 PHE 0.009 0.001 PHE F 14 TRP 0.008 0.001 TRP H 144 HIS 0.002 0.001 HIS N 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (22243) covalent geometry : angle 0.49382 / 0.28 (30659) hydrogen bonds : bond 0.03235 / 2.18 ( 1027) hydrogen bonds : angle 4.56029 / 3.20 ( 3013) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 285 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 2 LYS cc_start: 0.8405 (mttt) cc_final: 0.7741 (mtpt) REVERT: D 88 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7665 (mttm) REVERT: D 113 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.6779 (mm-40) REVERT: D 128 LYS cc_start: 0.8433 (tttp) cc_final: 0.8133 (ttpt) REVERT: E 95 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8766 (ptm) REVERT: E 98 ASP cc_start: 0.8468 (t0) cc_final: 0.8175 (t70) REVERT: E 99 VAL cc_start: 0.9316 (t) cc_final: 0.8861 (m) REVERT: E 151 MET cc_start: 0.8853 (mtp) cc_final: 0.8628 (mtp) REVERT: F 38 LYS cc_start: 0.8139 (mtpp) cc_final: 0.7730 (mttt) REVERT: F 153 ASP cc_start: 0.8409 (t0) cc_final: 0.7962 (t70) REVERT: F 154 GLU cc_start: 0.8098 (pm20) cc_final: 0.7366 (tp30) REVERT: F 156 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8334 (mt0) REVERT: F 190 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.7950 (mtp) REVERT: F 192 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7606 (tt0) REVERT: G 2 LYS cc_start: 0.7800 (mtpt) cc_final: 0.7331 (tttm) REVERT: G 155 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8106 (tp30) REVERT: H 88 LYS cc_start: 0.8762 (mttp) cc_final: 0.8374 (mtpt) REVERT: H 95 MET cc_start: 0.8607 (ptm) cc_final: 0.8369 (ptm) REVERT: I 79 SER cc_start: 0.8568 (OUTLIER) cc_final: 0.8366 (m) REVERT: I 103 MET cc_start: 0.9172 (ttt) cc_final: 0.8774 (ttt) REVERT: I 155 GLU cc_start: 0.8463 (tt0) cc_final: 0.8161 (tp30) REVERT: J 39 ARG cc_start: 0.8610 (ttm-80) cc_final: 0.8165 (ttm170) REVERT: J 61 ASP cc_start: 0.8664 (t0) cc_final: 0.8103 (t70) REVERT: J 88 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7760 (mmtp) REVERT: K 2 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7189 (mttm) REVERT: K 91 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7525 (m-30) REVERT: L 71 GLU cc_start: 0.7189 (tt0) cc_final: 0.6431 (mp0) REVERT: L 135 MET cc_start: 0.8628 (mmm) cc_final: 0.8346 (tpt) REVERT: L 151 MET cc_start: 0.8996 (mtm) cc_final: 0.8649 (mpp) REVERT: M 7 LYS cc_start: 0.8725 (tttt) cc_final: 0.8441 (ttpt) REVERT: O 20 THR cc_start: 0.8050 (OUTLIER) cc_final: 0.7690 (p) REVERT: O 82 LYS cc_start: 0.7248 (mmmt) cc_final: 0.6908 (tptp) REVERT: O 95 MET cc_start: 0.7258 (mmm) cc_final: 0.6930 (mmm) outliers start: 50 outliers final: 29 residues processed: 310 average time/residue: 0.6315 time to fit residues: 221.2429 Evaluate side-chains 318 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 278 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain F residue 156 GLN Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 188 GLU Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain H residue 151 MET Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain J residue 63 GLN Chi-restraints excluded: chain J residue 88 LYS Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain K residue 2 LYS Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 164 MET Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain L residue 163 LEU Chi-restraints excluded: chain L residue 164 MET Chi-restraints excluded: chain L residue 175 VAL Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain O residue 20 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: [235, 147, 97, 61, 122, 167, 182, 187, 93, 87, 69] chunk 235 optimal weight: 20.0000 chunk 147 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 167 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 84 ASN D 171 ASN E 107 ASN I 107 ASN K 63 GLN K 171 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.145906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.114392 restraints weight = 22841.478| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.17 r_work: 0.3144 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 22243 Z= 0.234 Angle : 0.593 7.184 30659 Z= 0.325 Chirality : 0.050 0.441 3500 Planarity : 0.005 0.044 3381 Dihedral : 19.969 173.573 4499 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.62 % Allowed : 12.69 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.17), residues: 2316 helix: 1.64 (0.18), residues: 912 sheet: 0.80 (0.21), residues: 588 loop : -0.62 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 39 TYR 0.015 0.002 TYR F 59 PHE 0.015 0.002 PHE M 148 TRP 0.007 0.001 TRP H 144 HIS 0.005 0.001 HIS J 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.23 (22243) covalent geometry : angle 0.59307 / 0.33 (30659) hydrogen bonds : bond 0.04306 / 2.90 ( 1027) hydrogen bonds : angle 4.72416 / 3.33 ( 3013) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 288 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 2 LYS cc_start: 0.8403 (mttt) cc_final: 0.7719 (mtpt) REVERT: D 88 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7658 (mttm) REVERT: D 113 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.6797 (mm-40) REVERT: D 128 LYS cc_start: 0.8388 (tttp) cc_final: 0.8026 (ttpt) REVERT: E 99 VAL cc_start: 0.9331 (t) cc_final: 0.8941 (m) REVERT: F 38 LYS cc_start: 0.8109 (mtpp) cc_final: 0.7707 (mttt) REVERT: F 68 MET cc_start: 0.9060 (ttm) cc_final: 0.8851 (ttm) REVERT: F 153 ASP cc_start: 0.8488 (t0) cc_final: 0.8248 (t0) REVERT: F 154 GLU cc_start: 0.8073 (pm20) cc_final: 0.7282 (tp30) REVERT: F 156 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8345 (mt0) REVERT: F 190 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.7902 (mtp) REVERT: F 192 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7588 (tt0) REVERT: G 2 LYS cc_start: 0.7877 (mtpt) cc_final: 0.7374 (tttm) REVERT: H 88 LYS cc_start: 0.8750 (mttp) cc_final: 0.8333 (mtpt) REVERT: I 103 MET cc_start: 0.9172 (ttt) cc_final: 0.8814 (ttt) REVERT: I 155 GLU cc_start: 0.8406 (tt0) cc_final: 0.8116 (tp30) REVERT: J 39 ARG cc_start: 0.8553 (ttm-80) cc_final: 0.8086 (ttm170) REVERT: J 61 ASP cc_start: 0.8631 (t0) cc_final: 0.8079 (t70) REVERT: J 88 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7668 (mmtp) REVERT: K 2 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7207 (mttm) REVERT: K 91 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7832 (m-30) REVERT: L 71 GLU cc_start: 0.7218 (tt0) cc_final: 0.6433 (mp0) REVERT: L 135 MET cc_start: 0.8636 (mmm) cc_final: 0.8364 (tpt) REVERT: L 151 MET cc_start: 0.8975 (mtm) cc_final: 0.8592 (mpp) REVERT: M 1 MET cc_start: 0.7451 (mtt) cc_final: 0.7148 (mtt) REVERT: M 7 LYS cc_start: 0.8761 (tttt) cc_final: 0.8466 (ttpt) REVERT: O 1 MET cc_start: 0.5384 (ttt) cc_final: 0.4988 (ttp) REVERT: O 20 THR cc_start: 0.8133 (OUTLIER) cc_final: 0.7857 (p) REVERT: O 82 LYS cc_start: 0.7316 (mmmt) cc_final: 0.6962 (tptp) REVERT: O 95 MET cc_start: 0.7222 (mmm) cc_final: 0.6937 (mmm) outliers start: 54 outliers final: 35 residues processed: 315 average time/residue: 0.5976 time to fit residues: 213.6157 Evaluate side-chains 330 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 287 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain F residue 156 GLN Chi-restraints excluded: chain F residue 188 GLU Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 151 MET Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain J residue 63 GLN Chi-restraints excluded: chain J residue 88 LYS Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain K residue 2 LYS Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 164 MET Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain L residue 163 LEU Chi-restraints excluded: chain L residue 164 MET Chi-restraints excluded: chain L residue 175 VAL Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 98 ASP Chi-restraints excluded: chain O residue 20 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: [69, 61, 70, 96, 72, 145, 12, 112, 117, 128, 177] chunk 69 optimal weight: 0.8980 chunk 61 optimal weight: 0.0170 chunk 70 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 112 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 177 optimal weight: 1.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 84 ASN D 171 ASN E 107 ASN I 107 ASN J 113 GLN K 63 GLN N 5 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.146712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.118842 restraints weight = 22915.030| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.05 r_work: 0.3266 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22243 Z= 0.106 Angle : 0.484 7.255 30659 Z= 0.277 Chirality : 0.044 0.424 3500 Planarity : 0.004 0.035 3381 Dihedral : 19.893 173.868 4499 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.65 % Allowed : 13.95 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.18), residues: 2316 helix: 1.78 (0.18), residues: 924 sheet: 0.93 (0.24), residues: 492 loop : -0.33 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 39 TYR 0.010 0.001 TYR I 59 PHE 0.008 0.001 PHE F 66 TRP 0.006 0.001 TRP G 178 HIS 0.003 0.001 HIS N 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.11 (22243) covalent geometry : angle 0.48430 / 0.28 (30659) hydrogen bonds : bond 0.03054 / 2.06 ( 1027) hydrogen bonds : angle 4.51160 / 3.17 ( 3013) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 295 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 2 LYS cc_start: 0.8408 (mttt) cc_final: 0.7750 (mtpt) REVERT: D 88 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7629 (mttm) REVERT: D 113 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.6806 (mm-40) REVERT: D 128 LYS cc_start: 0.8388 (tttp) cc_final: 0.8041 (ttpt) REVERT: E 51 GLU cc_start: 0.8206 (tt0) cc_final: 0.7608 (pt0) REVERT: E 98 ASP cc_start: 0.8412 (t0) cc_final: 0.8137 (t70) REVERT: E 99 VAL cc_start: 0.9323 (t) cc_final: 0.8875 (m) REVERT: F 38 LYS cc_start: 0.8145 (mtpp) cc_final: 0.7743 (mttt) REVERT: F 153 ASP cc_start: 0.8407 (t0) cc_final: 0.7939 (t70) REVERT: F 154 GLU cc_start: 0.8116 (pm20) cc_final: 0.7376 (tp30) REVERT: F 156 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8321 (mt0) REVERT: F 192 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7548 (tt0) REVERT: G 2 LYS cc_start: 0.7855 (mtpt) cc_final: 0.7384 (tttm) REVERT: G 155 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8138 (tp30) REVERT: H 88 LYS cc_start: 0.8744 (mttp) cc_final: 0.8316 (mtpt) REVERT: I 79 SER cc_start: 0.8566 (OUTLIER) cc_final: 0.8357 (m) REVERT: I 103 MET cc_start: 0.9167 (ttt) cc_final: 0.8789 (ttt) REVERT: I 155 GLU cc_start: 0.8408 (tt0) cc_final: 0.8094 (tp30) REVERT: J 39 ARG cc_start: 0.8595 (ttm-80) cc_final: 0.8157 (ttm170) REVERT: J 61 ASP cc_start: 0.8643 (t0) cc_final: 0.8085 (t70) REVERT: K 2 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7243 (mttm) REVERT: K 91 ASP cc_start: 0.8005 (t0) cc_final: 0.7672 (m-30) REVERT: L 71 GLU cc_start: 0.7181 (tt0) cc_final: 0.6458 (mp0) REVERT: L 151 MET cc_start: 0.8962 (mtm) cc_final: 0.8639 (mpp) REVERT: M 1 MET cc_start: 0.7442 (mtt) cc_final: 0.7177 (mtt) REVERT: M 7 LYS cc_start: 0.8725 (tttt) cc_final: 0.8457 (ttpt) REVERT: N 190 MET cc_start: 0.6761 (mmm) cc_final: 0.6515 (mmp) REVERT: O 1 MET cc_start: 0.5022 (ttt) cc_final: 0.4783 (ttp) REVERT: O 20 THR cc_start: 0.7954 (OUTLIER) cc_final: 0.7579 (p) REVERT: O 82 LYS cc_start: 0.7270 (mmmt) cc_final: 0.6957 (tptp) REVERT: O 95 MET cc_start: 0.7241 (mmm) cc_final: 0.6922 (mmm) outliers start: 34 outliers final: 23 residues processed: 318 average time/residue: 0.6015 time to fit residues: 217.0833 Evaluate side-chains 309 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 279 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain F residue 156 GLN Chi-restraints excluded: chain F residue 188 GLU Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain J residue 63 GLN Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain K residue 2 LYS Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 164 MET Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 163 LEU Chi-restraints excluded: chain L residue 164 MET Chi-restraints excluded: chain L residue 175 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain O residue 20 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: [227, 28, 181, 94, 3, 220, 229, 68, 37, 194, 95] chunk 227 optimal weight: 1.9990 chunk 28 optimal weight: 0.0670 chunk 181 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 3 optimal weight: 0.4980 chunk 220 optimal weight: 4.9990 chunk 229 optimal weight: 9.9990 chunk 68 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 84 ASN D 171 ASN E 107 ASN I 107 ASN J 113 GLN K 63 GLN K 171 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.148207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.116525 restraints weight = 23028.486| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.17 r_work: 0.3215 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 22243 Z= 0.100 Angle : 0.475 7.499 30659 Z= 0.271 Chirality : 0.043 0.417 3500 Planarity : 0.004 0.035 3381 Dihedral : 19.815 173.865 4499 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.41 % Allowed : 14.44 % Favored : 84.16 % 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: 1.37 (0.18), residues: 2316 helix: 1.99 (0.18), residues: 912 sheet: 0.97 (0.24), residues: 492 loop : -0.20 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 12 TYR 0.010 0.001 TYR I 59 PHE 0.009 0.001 PHE F 14 TRP 0.005 0.001 TRP H 144 HIS 0.002 0.001 HIS E 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.10 (22243) covalent geometry : angle 0.47549 / 0.27 (30659) hydrogen bonds : bond 0.02934 / 1.98 ( 1027) hydrogen bonds : angle 4.36612 / 3.07 ( 3013) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 282 time to evaluate : 0.787 Fit side-chains revert: symmetry clash REVERT: D 2 LYS cc_start: 0.8351 (mttt) cc_final: 0.7672 (mtpt) REVERT: D 88 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7594 (mttm) REVERT: D 128 LYS cc_start: 0.8277 (tttp) cc_final: 0.7919 (ttpt) REVERT: E 51 GLU cc_start: 0.8165 (tt0) cc_final: 0.7559 (pt0) REVERT: E 95 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8768 (ptm) REVERT: E 98 ASP cc_start: 0.8409 (t0) cc_final: 0.8139 (t70) REVERT: E 99 VAL cc_start: 0.9291 (t) cc_final: 0.8834 (m) REVERT: F 38 LYS cc_start: 0.8084 (mtpp) cc_final: 0.7664 (mttt) REVERT: F 114 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7472 (mm-30) REVERT: F 153 ASP cc_start: 0.8310 (t0) cc_final: 0.7880 (t70) REVERT: F 154 GLU cc_start: 0.8037 (pm20) cc_final: 0.7318 (tp30) REVERT: F 156 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8278 (mt0) REVERT: F 190 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.7822 (mtp) REVERT: G 2 LYS cc_start: 0.7770 (mtpt) cc_final: 0.7307 (tttm) REVERT: G 114 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7940 (mp0) REVERT: G 155 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7969 (tp30) REVERT: H 88 LYS cc_start: 0.8694 (mttp) cc_final: 0.8306 (mtpt) REVERT: I 103 MET cc_start: 0.9156 (ttt) cc_final: 0.8787 (ttt) REVERT: I 155 GLU cc_start: 0.8380 (tt0) cc_final: 0.8078 (tp30) REVERT: J 39 ARG cc_start: 0.8585 (ttm-80) cc_final: 0.8135 (ttm170) REVERT: J 61 ASP cc_start: 0.8557 (t0) cc_final: 0.8004 (t70) REVERT: K 2 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7266 (mttm) REVERT: L 71 GLU cc_start: 0.7093 (tt0) cc_final: 0.6358 (mp0) REVERT: L 151 MET cc_start: 0.8949 (mtm) cc_final: 0.8616 (mpp) REVERT: M 7 LYS cc_start: 0.8689 (tttt) cc_final: 0.8402 (ttpt) REVERT: N 190 MET cc_start: 0.6813 (mmm) cc_final: 0.6562 (mmp) REVERT: O 1 MET cc_start: 0.4866 (ttt) cc_final: 0.4656 (ttp) REVERT: O 20 THR cc_start: 0.7820 (OUTLIER) cc_final: 0.7416 (p) REVERT: O 82 LYS cc_start: 0.7338 (mmmt) cc_final: 0.6972 (tptp) outliers start: 29 outliers final: 17 residues processed: 300 average time/residue: 0.6141 time to fit residues: 208.8634 Evaluate side-chains 296 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 271 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain F residue 156 GLN Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain J residue 63 GLN Chi-restraints excluded: chain K residue 2 LYS Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 164 MET Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 163 LEU Chi-restraints excluded: chain L residue 164 MET Chi-restraints excluded: chain L residue 175 VAL Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain O residue 20 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: [135, 13, 86, 214, 91, 82, 54, 136, 41, 24, 114] chunk 135 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 214 optimal weight: 7.9990 chunk 91 optimal weight: 0.4980 chunk 82 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 84 ASN D 171 ASN E 107 ASN I 107 ASN K 171 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.146651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.114757 restraints weight = 23048.671| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.21 r_work: 0.3201 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22243 Z= 0.135 Angle : 0.505 7.156 30659 Z= 0.284 Chirality : 0.045 0.421 3500 Planarity : 0.004 0.035 3381 Dihedral : 19.816 173.206 4499 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.65 % Allowed : 14.73 % Favored : 83.62 % 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: 1.30 (0.18), residues: 2316 helix: 1.95 (0.18), residues: 912 sheet: 0.94 (0.24), residues: 492 loop : -0.27 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 12 TYR 0.012 0.001 TYR H 59 PHE 0.009 0.001 PHE H 182 TRP 0.009 0.001 TRP H 178 HIS 0.002 0.001 HIS J 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (22243) covalent geometry : angle 0.50545 / 0.28 (30659) hydrogen bonds : bond 0.03334 / 2.25 ( 1027) hydrogen bonds : angle 4.42854 / 3.11 ( 3013) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6426.85 seconds wall clock time: 110 minutes 13.92 seconds (6613.92 seconds total)