Starting phenix.real_space_refine on Thu Feb 5 01:28:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m66_63659/02_2026/9m66_63659.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m66_63659/02_2026/9m66_63659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m66_63659/02_2026/9m66_63659.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m66_63659/02_2026/9m66_63659.map" model { file = "/net/cci-nas-00/data/ceres_data/9m66_63659/02_2026/9m66_63659.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m66_63659/02_2026/9m66_63659.cif" } resolution = 3.39 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= -0.002 sd= 0.052 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: 4 Type Number sf(0) Gaussians S 7 5.16 5 C 8897 2.51 5 N 2317 2.21 5 O 2877 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14098 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2014 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 9, 'TRANS': 258} Chain: "B" Number of atoms: 2014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2014 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 9, 'TRANS': 258} Chain: "C" Number of atoms: 2014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2014 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 9, 'TRANS': 258} Chain: "D" Number of atoms: 2014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2014 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 9, 'TRANS': 258} Chain: "E" Number of atoms: 2014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2014 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 9, 'TRANS': 258} Chain: "F" Number of atoms: 2014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2014 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 9, 'TRANS': 258} Chain: "G" Number of atoms: 2014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2014 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 9, 'TRANS': 258} Time building chain proxies: 2.94, per 1000 atoms: 0.21 Number of scatterers: 14098 At special positions: 0 Unit cell: (183.6, 192, 133.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 7 16.00 O 2877 8.00 N 2317 7.00 C 8897 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: 1.10 Conformation dependent library (CDL) restraints added in 655.2 milliseconds 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3458 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 29 sheets defined 26.3% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 91 through 96 Processing helix chain 'A' and resid 100 through 126 removed outlier: 3.614A pdb=" N GLY A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 161 through 172 Processing helix chain 'A' and resid 258 through 260 No H-bonds generated for 'chain 'A' and resid 258 through 260' Processing helix chain 'B' and resid 91 through 96 Processing helix chain 'B' and resid 100 through 126 removed outlier: 3.718A pdb=" N GLY B 110 " --> pdb=" O ASN B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 161 through 176 removed outlier: 3.798A pdb=" N SER B 166 " --> pdb=" O PRO B 162 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS B 167 " --> pdb=" O LEU B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 190 removed outlier: 3.714A pdb=" N ALA B 184 " --> pdb=" O THR B 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'C' and resid 100 through 126 removed outlier: 4.069A pdb=" N GLU C 104 " --> pdb=" O ASP C 100 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER C 105 " --> pdb=" O PRO C 101 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN C 106 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY C 110 " --> pdb=" O ASN C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 161 through 176 removed outlier: 3.584A pdb=" N SER C 166 " --> pdb=" O PRO C 162 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU C 175 " --> pdb=" O SER C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 190 Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 91 through 96 Processing helix chain 'D' and resid 100 through 126 removed outlier: 3.827A pdb=" N GLU D 104 " --> pdb=" O ASP D 100 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER D 105 " --> pdb=" O PRO D 101 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY D 110 " --> pdb=" O ASN D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 161 through 176 Processing helix chain 'D' and resid 180 through 190 Processing helix chain 'E' and resid 91 through 96 Processing helix chain 'E' and resid 100 through 127 removed outlier: 3.681A pdb=" N GLY E 110 " --> pdb=" O ASN E 106 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU E 127 " --> pdb=" O THR E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 161 through 176 removed outlier: 3.597A pdb=" N SER E 166 " --> pdb=" O PRO E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 190 Processing helix chain 'E' and resid 258 through 260 No H-bonds generated for 'chain 'E' and resid 258 through 260' Processing helix chain 'F' and resid 28 through 30 No H-bonds generated for 'chain 'F' and resid 28 through 30' Processing helix chain 'F' and resid 91 through 96 Processing helix chain 'F' and resid 100 through 126 removed outlier: 3.654A pdb=" N GLY F 110 " --> pdb=" O ASN F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 149 removed outlier: 3.655A pdb=" N VAL F 147 " --> pdb=" O THR F 143 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N PHE F 148 " --> pdb=" O ALA F 144 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASN F 149 " --> pdb=" O LEU F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 176 Processing helix chain 'F' and resid 180 through 190 removed outlier: 3.534A pdb=" N ALA F 184 " --> pdb=" O THR F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 260 No H-bonds generated for 'chain 'F' and resid 258 through 260' Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'G' and resid 100 through 126 removed outlier: 3.722A pdb=" N GLY G 110 " --> pdb=" O ASN G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 146 Processing helix chain 'G' and resid 161 through 176 removed outlier: 3.597A pdb=" N ALA G 165 " --> pdb=" O SER G 161 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER G 166 " --> pdb=" O PRO G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 190 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 35 removed outlier: 7.185A pdb=" N VAL A 226 " --> pdb=" O TYR A 255 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N TYR A 255 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N LYS A 228 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 9.569A pdb=" N ALA A 253 " --> pdb=" O LYS A 228 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ALA A 230 " --> pdb=" O HIS A 251 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N HIS A 251 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN A 232 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP A 249 " --> pdb=" O GLN A 232 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 51 Processing sheet with id=AA4, first strand: chain 'A' and resid 131 through 134 removed outlier: 3.673A pdb=" N GLY A 211 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 33 through 35 removed outlier: 6.248A pdb=" N GLN B 33 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N SER B 227 " --> pdb=" O GLN B 33 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASP B 35 " --> pdb=" O SER B 227 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ARG B 229 " --> pdb=" O ASP B 35 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL B 226 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N TYR B 255 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N LYS B 228 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 9.222A pdb=" N ALA B 253 " --> pdb=" O LYS B 228 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ALA B 230 " --> pdb=" O HIS B 251 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N HIS B 251 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN B 232 " --> pdb=" O ASP B 249 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP B 249 " --> pdb=" O GLN B 232 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR C 58 " --> pdb=" O ALA B 84 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 77 through 79 removed outlier: 3.542A pdb=" N LEU B 46 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL G 13 " --> pdb=" O THR B 45 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 50 through 51 Processing sheet with id=AA8, first strand: chain 'B' and resid 58 through 59 removed outlier: 3.501A pdb=" N THR B 58 " --> pdb=" O ALA G 84 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLN G 33 " --> pdb=" O LEU G 225 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N SER G 227 " --> pdb=" O GLN G 33 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASP G 35 " --> pdb=" O SER G 227 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 58 through 59 removed outlier: 3.501A pdb=" N THR B 58 " --> pdb=" O ALA G 84 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP G 249 " --> pdb=" O GLN G 232 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN G 232 " --> pdb=" O ASP G 249 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 131 through 134 removed outlier: 3.663A pdb=" N GLY B 211 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLY B 155 " --> pdb=" O VAL B 216 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.987A pdb=" N VAL C 13 " --> pdb=" O THR D 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 33 through 35 removed outlier: 6.499A pdb=" N GLN C 33 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N SER C 227 " --> pdb=" O GLN C 33 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASP C 35 " --> pdb=" O SER C 227 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ARG C 229 " --> pdb=" O ASP C 35 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL C 226 " --> pdb=" O TYR C 255 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N TYR C 255 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LYS C 228 " --> pdb=" O ALA C 253 " (cutoff:3.500A) removed outlier: 9.225A pdb=" N ALA C 253 " --> pdb=" O LYS C 228 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ALA C 230 " --> pdb=" O HIS C 251 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N HIS C 251 " --> pdb=" O ALA C 230 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN C 232 " --> pdb=" O ASP C 249 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP C 249 " --> pdb=" O GLN C 232 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA C 84 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR D 58 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.535A pdb=" N LEU C 46 " --> pdb=" O VAL C 78 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 50 through 51 Processing sheet with id=AB6, first strand: chain 'C' and resid 133 through 135 removed outlier: 3.525A pdb=" N LEU C 265 " --> pdb=" O GLY C 211 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY C 211 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY C 155 " --> pdb=" O VAL C 216 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 13 through 14 removed outlier: 7.440A pdb=" N VAL D 13 " --> pdb=" O THR E 47 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU E 46 " --> pdb=" O VAL E 78 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 32 through 35 removed outlier: 6.330A pdb=" N GLN D 33 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N SER D 227 " --> pdb=" O GLN D 33 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASP D 35 " --> pdb=" O SER D 227 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ARG D 229 " --> pdb=" O ASP D 35 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL D 226 " --> pdb=" O TYR D 255 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N TYR D 255 " --> pdb=" O VAL D 226 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N LYS D 228 " --> pdb=" O ALA D 253 " (cutoff:3.500A) removed outlier: 9.393A pdb=" N ALA D 253 " --> pdb=" O LYS D 228 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ALA D 230 " --> pdb=" O HIS D 251 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N HIS D 251 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN D 232 " --> pdb=" O ASP D 249 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP D 249 " --> pdb=" O GLN D 232 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR E 58 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 32 through 35 removed outlier: 6.330A pdb=" N GLN D 33 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N SER D 227 " --> pdb=" O GLN D 33 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASP D 35 " --> pdb=" O SER D 227 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ARG D 229 " --> pdb=" O ASP D 35 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL D 226 " --> pdb=" O TYR D 255 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N TYR D 255 " --> pdb=" O VAL D 226 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N LYS D 228 " --> pdb=" O ALA D 253 " (cutoff:3.500A) removed outlier: 9.393A pdb=" N ALA D 253 " --> pdb=" O LYS D 228 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ALA D 230 " --> pdb=" O HIS D 251 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N HIS D 251 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN D 232 " --> pdb=" O ASP D 249 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP D 249 " --> pdb=" O GLN D 232 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP E 69 " --> pdb=" O GLY D 86 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU D 88 " --> pdb=" O ASP E 69 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 50 through 51 Processing sheet with id=AC2, first strand: chain 'D' and resid 131 through 134 removed outlier: 6.670A pdb=" N ALA D 132 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N TYR D 156 " --> pdb=" O GLU D 199 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ILE D 201 " --> pdb=" O TYR D 156 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU D 158 " --> pdb=" O ILE D 201 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 13 through 14 removed outlier: 7.214A pdb=" N VAL E 13 " --> pdb=" O THR F 47 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU F 46 " --> pdb=" O VAL F 78 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL F 78 " --> pdb=" O LEU F 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 33 through 35 removed outlier: 5.959A pdb=" N GLN E 33 " --> pdb=" O LEU E 225 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N SER E 227 " --> pdb=" O GLN E 33 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ASP E 35 " --> pdb=" O SER E 227 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ARG E 229 " --> pdb=" O ASP E 35 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL E 226 " --> pdb=" O TYR E 255 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N TYR E 255 " --> pdb=" O VAL E 226 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LYS E 228 " --> pdb=" O ALA E 253 " (cutoff:3.500A) removed outlier: 9.619A pdb=" N ALA E 253 " --> pdb=" O LYS E 228 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ALA E 230 " --> pdb=" O HIS E 251 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N HIS E 251 " --> pdb=" O ALA E 230 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 50 through 51 Processing sheet with id=AC6, first strand: chain 'E' and resid 131 through 134 removed outlier: 4.542A pdb=" N GLY E 155 " --> pdb=" O VAL E 216 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N TYR E 156 " --> pdb=" O GLU E 199 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ILE E 201 " --> pdb=" O TYR E 156 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU E 158 " --> pdb=" O ILE E 201 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 13 through 14 removed outlier: 7.362A pdb=" N VAL F 13 " --> pdb=" O THR G 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 32 through 35 removed outlier: 3.501A pdb=" N GLN F 33 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER F 227 " --> pdb=" O ASP F 35 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL F 226 " --> pdb=" O TYR F 255 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N TYR F 255 " --> pdb=" O VAL F 226 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LYS F 228 " --> pdb=" O ALA F 253 " (cutoff:3.500A) removed outlier: 9.256A pdb=" N ALA F 253 " --> pdb=" O LYS F 228 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ALA F 230 " --> pdb=" O HIS F 251 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N HIS F 251 " --> pdb=" O ALA F 230 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN F 232 " --> pdb=" O ASP F 249 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP F 249 " --> pdb=" O GLN F 232 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 50 through 51 Processing sheet with id=AD1, first strand: chain 'F' and resid 131 through 134 removed outlier: 4.622A pdb=" N GLY F 155 " --> pdb=" O VAL F 216 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N TYR F 156 " --> pdb=" O GLU F 199 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N ILE F 201 " --> pdb=" O TYR F 156 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU F 158 " --> pdb=" O ILE F 201 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 131 through 134 removed outlier: 7.405A pdb=" N TYR G 156 " --> pdb=" O GLU G 199 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N ILE G 201 " --> pdb=" O TYR G 156 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU G 158 " --> pdb=" O ILE G 201 " (cutoff:3.500A) 578 hydrogen bonds defined for protein. 1659 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.94 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2612 1.32 - 1.44: 3068 1.44 - 1.56: 8572 1.56 - 1.68: 0 1.68 - 1.80: 14 Bond restraints: 14266 Sorted by residual: bond pdb=" CA ASP F 120 " pdb=" C ASP F 120 " ideal model delta sigma weight residual 1.524 1.488 0.036 1.29e-02 6.01e+03 7.66e+00 bond pdb=" C ASP F 120 " pdb=" O ASP F 120 " ideal model delta sigma weight residual 1.237 1.210 0.026 1.19e-02 7.06e+03 4.85e+00 bond pdb=" C THR A 3 " pdb=" O THR A 3 " ideal model delta sigma weight residual 1.233 1.204 0.029 1.36e-02 5.41e+03 4.64e+00 bond pdb=" C ASP D 118 " pdb=" O ASP D 118 " ideal model delta sigma weight residual 1.237 1.212 0.025 1.19e-02 7.06e+03 4.28e+00 bond pdb=" CA THR A 2 " pdb=" C THR A 2 " ideal model delta sigma weight residual 1.525 1.486 0.039 2.10e-02 2.27e+03 3.40e+00 ... (remaining 14261 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 18877 1.42 - 2.84: 430 2.84 - 4.26: 65 4.26 - 5.68: 7 5.68 - 7.10: 4 Bond angle restraints: 19383 Sorted by residual: angle pdb=" C LYS C 4 " pdb=" CA LYS C 4 " pdb=" CB LYS C 4 " ideal model delta sigma weight residual 115.89 109.69 6.20 1.32e+00 5.74e-01 2.20e+01 angle pdb=" C THR G 3 " pdb=" CA THR G 3 " pdb=" CB THR G 3 " ideal model delta sigma weight residual 110.42 116.22 -5.80 1.99e+00 2.53e-01 8.48e+00 angle pdb=" CA GLY F 43 " pdb=" C GLY F 43 " pdb=" O GLY F 43 " ideal model delta sigma weight residual 122.22 120.42 1.80 6.50e-01 2.37e+00 7.65e+00 angle pdb=" N ALA A 218 " pdb=" CA ALA A 218 " pdb=" C ALA A 218 " ideal model delta sigma weight residual 111.07 113.96 -2.89 1.07e+00 8.73e-01 7.30e+00 angle pdb=" C LEU C 5 " pdb=" N VAL C 6 " pdb=" CA VAL C 6 " ideal model delta sigma weight residual 121.97 126.69 -4.72 1.80e+00 3.09e-01 6.87e+00 ... (remaining 19378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 8020 17.97 - 35.94: 557 35.94 - 53.91: 92 53.91 - 71.88: 25 71.88 - 89.85: 7 Dihedral angle restraints: 8701 sinusoidal: 3325 harmonic: 5376 Sorted by residual: dihedral pdb=" CA GLY A 183 " pdb=" C GLY A 183 " pdb=" N ALA A 184 " pdb=" CA ALA A 184 " ideal model delta harmonic sigma weight residual 180.00 161.44 18.56 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA TYR A 192 " pdb=" C TYR A 192 " pdb=" N GLY A 193 " pdb=" CA GLY A 193 " ideal model delta harmonic sigma weight residual -180.00 -162.07 -17.93 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA GLU G 175 " pdb=" C GLU G 175 " pdb=" N TRP G 176 " pdb=" CA TRP G 176 " ideal model delta harmonic sigma weight residual 180.00 -162.35 -17.65 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 8698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1739 0.035 - 0.069: 415 0.069 - 0.104: 164 0.104 - 0.139: 86 0.139 - 0.173: 4 Chirality restraints: 2408 Sorted by residual: chirality pdb=" CA THR E 29 " pdb=" N THR E 29 " pdb=" C THR E 29 " pdb=" CB THR E 29 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.50e-01 chirality pdb=" CA THR F 29 " pdb=" N THR F 29 " pdb=" C THR F 29 " pdb=" CB THR F 29 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.14e-01 chirality pdb=" CA ASP D 118 " pdb=" N ASP D 118 " pdb=" C ASP D 118 " pdb=" CB ASP D 118 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.80e-01 ... (remaining 2405 not shown) Planarity restraints: 2478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 41 " -0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO D 42 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO D 42 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 42 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 41 " 0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO A 42 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 42 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 42 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 29 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO D 30 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 30 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 30 " 0.022 5.00e-02 4.00e+02 ... (remaining 2475 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2040 2.76 - 3.30: 12158 3.30 - 3.83: 20544 3.83 - 4.37: 22575 4.37 - 4.90: 42566 Nonbonded interactions: 99883 Sorted by model distance: nonbonded pdb=" O LYS B 174 " pdb=" ND2 ASN B 178 " model vdw 2.226 3.120 nonbonded pdb=" OD2 ASP F 150 " pdb=" OH TYR F 156 " model vdw 2.251 3.040 nonbonded pdb=" OD2 ASP A 120 " pdb=" OH TYR A 252 " model vdw 2.254 3.040 nonbonded pdb=" OD2 ASP G 120 " pdb=" OH TYR G 252 " model vdw 2.255 3.040 nonbonded pdb=" OD2 ASP B 120 " pdb=" OH TYR B 252 " model vdw 2.264 3.040 ... (remaining 99878 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.750 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: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 12.630 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 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 : 0.002 0.048 14266 Z= 0.139 Angle : 0.532 7.102 19383 Z= 0.310 Chirality : 0.041 0.173 2408 Planarity : 0.004 0.049 2478 Dihedral : 13.000 89.854 5243 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.15 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.19), residues: 1862 helix: 2.64 (0.26), residues: 444 sheet: 0.23 (0.21), residues: 605 loop : -1.50 (0.19), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 204 TYR 0.023 0.001 TYR F 53 PHE 0.008 0.001 PHE G 28 TRP 0.006 0.001 TRP F 176 HIS 0.002 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00245 (14266) covalent geometry : angle 0.53194 (19383) hydrogen bonds : bond 0.21597 ( 551) hydrogen bonds : angle 6.78005 ( 1659) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 208 GLU cc_start: 0.6612 (mt-10) cc_final: 0.6300 (mt-10) REVERT: C 236 ASP cc_start: 0.7416 (m-30) cc_final: 0.7097 (m-30) REVERT: D 151 GLU cc_start: 0.7851 (pt0) cc_final: 0.7535 (pt0) REVERT: E 56 ASP cc_start: 0.8402 (p0) cc_final: 0.7765 (p0) REVERT: F 53 TYR cc_start: 0.8328 (t80) cc_final: 0.8004 (t80) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.1069 time to fit residues: 39.4736 Evaluate side-chains 182 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN C 154 GLN F 33 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.134813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.114677 restraints weight = 21323.332| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.19 r_work: 0.3309 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 14266 Z= 0.300 Angle : 0.691 8.311 19383 Z= 0.366 Chirality : 0.047 0.178 2408 Planarity : 0.005 0.053 2478 Dihedral : 4.702 20.539 1974 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.44 % Favored : 96.51 % Rotamer: Outliers : 1.37 % Allowed : 8.35 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.19), residues: 1862 helix: 2.14 (0.25), residues: 460 sheet: 0.32 (0.22), residues: 543 loop : -1.85 (0.17), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 237 TYR 0.023 0.002 TYR A 53 PHE 0.022 0.003 PHE B 51 TRP 0.005 0.001 TRP F 176 HIS 0.007 0.003 HIS G 251 Details of bonding type rmsd covalent geometry : bond 0.00727 (14266) covalent geometry : angle 0.69054 (19383) hydrogen bonds : bond 0.08027 ( 551) hydrogen bonds : angle 5.22649 ( 1659) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: A 118 ASP cc_start: 0.8867 (t0) cc_final: 0.8597 (t0) REVERT: B 118 ASP cc_start: 0.8740 (t0) cc_final: 0.8524 (t0) REVERT: B 189 SER cc_start: 0.8706 (p) cc_final: 0.8492 (p) REVERT: E 56 ASP cc_start: 0.8683 (p0) cc_final: 0.8196 (p0) REVERT: E 77 GLU cc_start: 0.8077 (pt0) cc_final: 0.7653 (pt0) REVERT: E 127 GLU cc_start: 0.8309 (tt0) cc_final: 0.7742 (pp20) REVERT: F 53 TYR cc_start: 0.8547 (t80) cc_final: 0.8346 (t80) outliers start: 21 outliers final: 17 residues processed: 179 average time/residue: 0.1098 time to fit residues: 30.3045 Evaluate side-chains 163 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 235 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 175 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 148 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN E 178 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.138520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.117729 restraints weight = 21198.052| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.37 r_work: 0.3342 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14266 Z= 0.162 Angle : 0.530 6.416 19383 Z= 0.285 Chirality : 0.042 0.164 2408 Planarity : 0.004 0.051 2478 Dihedral : 4.323 17.895 1974 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.69 % Favored : 97.26 % Rotamer: Outliers : 1.30 % Allowed : 10.57 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.19), residues: 1862 helix: 2.39 (0.26), residues: 460 sheet: 0.31 (0.22), residues: 567 loop : -1.76 (0.18), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 186 TYR 0.019 0.001 TYR A 53 PHE 0.012 0.002 PHE F 28 TRP 0.005 0.001 TRP F 176 HIS 0.004 0.002 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00377 (14266) covalent geometry : angle 0.53045 (19383) hydrogen bonds : bond 0.05935 ( 551) hydrogen bonds : angle 4.66811 ( 1659) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: A 118 ASP cc_start: 0.8936 (t0) cc_final: 0.8639 (t0) REVERT: B 118 ASP cc_start: 0.8752 (t0) cc_final: 0.8551 (t0) REVERT: C 4 LYS cc_start: 0.7815 (mttp) cc_final: 0.7384 (tmtt) REVERT: C 115 ASN cc_start: 0.8717 (t0) cc_final: 0.8324 (t0) REVERT: E 56 ASP cc_start: 0.8769 (p0) cc_final: 0.8333 (p0) REVERT: E 77 GLU cc_start: 0.8035 (pt0) cc_final: 0.7637 (pt0) REVERT: E 127 GLU cc_start: 0.8330 (tt0) cc_final: 0.7703 (pp20) REVERT: E 185 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8674 (mm-30) REVERT: F 53 TYR cc_start: 0.8655 (t80) cc_final: 0.8393 (t80) REVERT: G 7 ASP cc_start: 0.8614 (m-30) cc_final: 0.8157 (m-30) outliers start: 20 outliers final: 15 residues processed: 181 average time/residue: 0.1032 time to fit residues: 29.4204 Evaluate side-chains 172 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 235 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 55 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 162 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 131 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.132523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.112428 restraints weight = 21725.380| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.17 r_work: 0.3277 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 14266 Z= 0.320 Angle : 0.692 8.511 19383 Z= 0.365 Chirality : 0.047 0.172 2408 Planarity : 0.004 0.058 2478 Dihedral : 4.868 19.947 1974 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.14 % Favored : 95.81 % Rotamer: Outliers : 2.35 % Allowed : 11.74 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.19), residues: 1862 helix: 1.93 (0.25), residues: 459 sheet: 0.15 (0.23), residues: 516 loop : -2.04 (0.17), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 169 TYR 0.024 0.002 TYR A 192 PHE 0.017 0.003 PHE G 48 TRP 0.005 0.001 TRP G 176 HIS 0.007 0.003 HIS G 251 Details of bonding type rmsd covalent geometry : bond 0.00782 (14266) covalent geometry : angle 0.69222 (19383) hydrogen bonds : bond 0.08116 ( 551) hydrogen bonds : angle 5.08912 ( 1659) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 154 time to evaluate : 0.570 Fit side-chains REVERT: A 118 ASP cc_start: 0.8944 (t0) cc_final: 0.8631 (t0) REVERT: D 232 GLN cc_start: 0.8402 (mp10) cc_final: 0.7621 (mp10) REVERT: E 127 GLU cc_start: 0.8324 (tt0) cc_final: 0.7827 (pp20) REVERT: E 185 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8654 (mm-30) REVERT: F 44 ASP cc_start: 0.8600 (p0) cc_final: 0.8228 (p0) REVERT: F 53 TYR cc_start: 0.8767 (t80) cc_final: 0.8216 (t80) REVERT: F 187 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8421 (mp) REVERT: G 236 ASP cc_start: 0.7957 (t0) cc_final: 0.7750 (t0) outliers start: 36 outliers final: 30 residues processed: 174 average time/residue: 0.1031 time to fit residues: 28.5025 Evaluate side-chains 176 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 235 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 37 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 ASN D 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.139062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.118504 restraints weight = 21160.246| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.35 r_work: 0.3354 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14266 Z= 0.133 Angle : 0.495 7.687 19383 Z= 0.265 Chirality : 0.041 0.156 2408 Planarity : 0.004 0.050 2478 Dihedral : 4.215 18.037 1974 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.58 % Favored : 97.37 % Rotamer: Outliers : 1.83 % Allowed : 13.11 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.19), residues: 1862 helix: 2.38 (0.26), residues: 460 sheet: 0.17 (0.22), residues: 573 loop : -1.87 (0.18), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 186 TYR 0.014 0.001 TYR A 53 PHE 0.013 0.001 PHE F 28 TRP 0.004 0.001 TRP F 176 HIS 0.004 0.002 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00299 (14266) covalent geometry : angle 0.49461 (19383) hydrogen bonds : bond 0.05096 ( 551) hydrogen bonds : angle 4.43525 ( 1659) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 0.595 Fit side-chains REVERT: A 118 ASP cc_start: 0.8904 (t0) cc_final: 0.8633 (t0) REVERT: C 115 ASN cc_start: 0.8679 (t0) cc_final: 0.8435 (t0) REVERT: D 232 GLN cc_start: 0.8346 (mp10) cc_final: 0.7424 (mp10) REVERT: E 127 GLU cc_start: 0.8227 (tt0) cc_final: 0.7603 (pp20) REVERT: E 146 ASP cc_start: 0.8257 (m-30) cc_final: 0.7971 (m-30) REVERT: E 185 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8649 (mm-30) REVERT: F 44 ASP cc_start: 0.8564 (p0) cc_final: 0.7940 (p0) REVERT: F 53 TYR cc_start: 0.8822 (t80) cc_final: 0.8325 (t80) REVERT: G 149 ASN cc_start: 0.9006 (t0) cc_final: 0.8656 (t0) REVERT: G 236 ASP cc_start: 0.7794 (t0) cc_final: 0.7544 (t0) outliers start: 28 outliers final: 22 residues processed: 184 average time/residue: 0.1032 time to fit residues: 30.0220 Evaluate side-chains 179 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain B residue 33 GLN Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 194 SER Chi-restraints excluded: chain G residue 235 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 46 optimal weight: 7.9990 chunk 142 optimal weight: 8.9990 chunk 96 optimal weight: 8.9990 chunk 172 optimal weight: 8.9990 chunk 118 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 145 optimal weight: 8.9990 chunk 27 optimal weight: 0.1980 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 ASN D 108 GLN D 119 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.136360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.115732 restraints weight = 21265.144| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.35 r_work: 0.3315 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14266 Z= 0.190 Angle : 0.551 7.440 19383 Z= 0.292 Chirality : 0.043 0.157 2408 Planarity : 0.004 0.052 2478 Dihedral : 4.362 17.550 1974 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.60 % Favored : 96.35 % Rotamer: Outliers : 2.54 % Allowed : 13.11 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.19), residues: 1862 helix: 2.30 (0.26), residues: 459 sheet: 0.12 (0.22), residues: 578 loop : -1.92 (0.18), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 229 TYR 0.018 0.001 TYR A 192 PHE 0.012 0.002 PHE A 214 TRP 0.003 0.001 TRP F 176 HIS 0.005 0.002 HIS G 251 Details of bonding type rmsd covalent geometry : bond 0.00452 (14266) covalent geometry : angle 0.55074 (19383) hydrogen bonds : bond 0.06162 ( 551) hydrogen bonds : angle 4.59743 ( 1659) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 158 time to evaluate : 0.545 Fit side-chains REVERT: A 118 ASP cc_start: 0.8957 (t0) cc_final: 0.8668 (t0) REVERT: C 115 ASN cc_start: 0.8733 (t0) cc_final: 0.8413 (t0) REVERT: D 232 GLN cc_start: 0.8416 (mp10) cc_final: 0.7399 (mp10) REVERT: E 127 GLU cc_start: 0.8294 (tt0) cc_final: 0.7640 (pp20) REVERT: F 44 ASP cc_start: 0.8616 (p0) cc_final: 0.8002 (p0) REVERT: F 53 TYR cc_start: 0.8835 (t80) cc_final: 0.8402 (t80) REVERT: F 120 ASP cc_start: 0.8933 (OUTLIER) cc_final: 0.8591 (t0) REVERT: F 187 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8347 (mp) REVERT: G 149 ASN cc_start: 0.9066 (t0) cc_final: 0.8730 (t0) REVERT: G 236 ASP cc_start: 0.7865 (t0) cc_final: 0.7621 (t0) outliers start: 39 outliers final: 29 residues processed: 187 average time/residue: 0.1017 time to fit residues: 30.1831 Evaluate side-chains 186 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain B residue 33 GLN Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 194 SER Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 194 SER Chi-restraints excluded: chain G residue 235 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 12 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 chunk 82 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 117 optimal weight: 0.3980 chunk 138 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.136595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.116038 restraints weight = 21169.784| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.35 r_work: 0.3321 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14266 Z= 0.182 Angle : 0.541 7.897 19383 Z= 0.287 Chirality : 0.042 0.157 2408 Planarity : 0.004 0.052 2478 Dihedral : 4.340 17.586 1974 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.76 % Favored : 96.19 % Rotamer: Outliers : 2.61 % Allowed : 13.57 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.19), residues: 1862 helix: 2.29 (0.26), residues: 459 sheet: 0.12 (0.22), residues: 578 loop : -1.94 (0.18), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 229 TYR 0.018 0.001 TYR A 192 PHE 0.011 0.002 PHE A 214 TRP 0.004 0.001 TRP F 176 HIS 0.005 0.002 HIS G 251 Details of bonding type rmsd covalent geometry : bond 0.00429 (14266) covalent geometry : angle 0.54102 (19383) hydrogen bonds : bond 0.06006 ( 551) hydrogen bonds : angle 4.55631 ( 1659) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 0.597 Fit side-chains REVERT: A 118 ASP cc_start: 0.8950 (t0) cc_final: 0.8652 (t0) REVERT: B 264 ASP cc_start: 0.8249 (t0) cc_final: 0.8028 (p0) REVERT: C 115 ASN cc_start: 0.8732 (t0) cc_final: 0.8410 (t0) REVERT: D 232 GLN cc_start: 0.8412 (mp10) cc_final: 0.7420 (mp10) REVERT: E 127 GLU cc_start: 0.8329 (tt0) cc_final: 0.7618 (pp20) REVERT: F 44 ASP cc_start: 0.8632 (p0) cc_final: 0.8019 (p0) REVERT: F 53 TYR cc_start: 0.8828 (t80) cc_final: 0.8398 (t80) REVERT: F 120 ASP cc_start: 0.8947 (OUTLIER) cc_final: 0.8577 (t0) REVERT: F 187 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8452 (mp) REVERT: G 149 ASN cc_start: 0.9072 (t0) cc_final: 0.8756 (t0) REVERT: G 236 ASP cc_start: 0.7866 (t0) cc_final: 0.7619 (t0) outliers start: 40 outliers final: 32 residues processed: 189 average time/residue: 0.1014 time to fit residues: 30.2700 Evaluate side-chains 188 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain B residue 33 GLN Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 194 SER Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 194 SER Chi-restraints excluded: chain G residue 235 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 149 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 125 optimal weight: 0.5980 chunk 164 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 129 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.143140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.122674 restraints weight = 20921.889| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.35 r_work: 0.3386 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14266 Z= 0.097 Angle : 0.457 8.929 19383 Z= 0.243 Chirality : 0.040 0.145 2408 Planarity : 0.003 0.045 2478 Dihedral : 3.800 17.637 1974 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.85 % Favored : 97.10 % Rotamer: Outliers : 1.44 % Allowed : 14.68 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.20), residues: 1862 helix: 2.56 (0.26), residues: 460 sheet: 0.16 (0.21), residues: 606 loop : -1.76 (0.19), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 229 TYR 0.010 0.001 TYR A 53 PHE 0.009 0.001 PHE G 28 TRP 0.004 0.001 TRP G 176 HIS 0.003 0.001 HIS G 251 Details of bonding type rmsd covalent geometry : bond 0.00206 (14266) covalent geometry : angle 0.45681 (19383) hydrogen bonds : bond 0.03618 ( 551) hydrogen bonds : angle 4.07510 ( 1659) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 180 time to evaluate : 0.657 Fit side-chains REVERT: A 53 TYR cc_start: 0.8735 (t80) cc_final: 0.8381 (t80) REVERT: A 118 ASP cc_start: 0.8869 (t0) cc_final: 0.8624 (t0) REVERT: B 241 ARG cc_start: 0.7181 (OUTLIER) cc_final: 0.6321 (tpt170) REVERT: C 115 ASN cc_start: 0.8679 (t0) cc_final: 0.8373 (t0) REVERT: D 232 GLN cc_start: 0.8403 (mp10) cc_final: 0.7407 (mp10) REVERT: E 56 ASP cc_start: 0.8772 (p0) cc_final: 0.8310 (p0) REVERT: E 261 LYS cc_start: 0.8626 (mptt) cc_final: 0.8123 (mmmm) REVERT: F 44 ASP cc_start: 0.8573 (p0) cc_final: 0.7918 (p0) REVERT: F 53 TYR cc_start: 0.8730 (t80) cc_final: 0.8310 (t80) REVERT: F 149 ASN cc_start: 0.9254 (t0) cc_final: 0.8926 (t0) REVERT: G 149 ASN cc_start: 0.9103 (t0) cc_final: 0.8865 (t0) REVERT: G 236 ASP cc_start: 0.7770 (t0) cc_final: 0.7519 (t0) outliers start: 22 outliers final: 15 residues processed: 191 average time/residue: 0.1103 time to fit residues: 32.6708 Evaluate side-chains 187 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain B residue 33 GLN Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 241 ARG Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 194 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 157 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 48 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 108 GLN D 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.132235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.111338 restraints weight = 21520.707| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.38 r_work: 0.3279 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 14266 Z= 0.281 Angle : 0.645 7.774 19383 Z= 0.340 Chirality : 0.045 0.159 2408 Planarity : 0.004 0.056 2478 Dihedral : 4.575 19.195 1974 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.62 % Favored : 95.33 % Rotamer: Outliers : 2.41 % Allowed : 13.89 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.19), residues: 1862 helix: 2.12 (0.26), residues: 459 sheet: 0.10 (0.22), residues: 578 loop : -2.00 (0.18), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 237 TYR 0.023 0.002 TYR A 192 PHE 0.015 0.002 PHE A 214 TRP 0.005 0.001 TRP A 176 HIS 0.006 0.002 HIS G 251 Details of bonding type rmsd covalent geometry : bond 0.00684 (14266) covalent geometry : angle 0.64481 (19383) hydrogen bonds : bond 0.07337 ( 551) hydrogen bonds : angle 4.84079 ( 1659) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 0.468 Fit side-chains REVERT: A 118 ASP cc_start: 0.9011 (t0) cc_final: 0.8709 (t0) REVERT: B 70 LYS cc_start: 0.6000 (mmtm) cc_final: 0.4486 (mmtt) REVERT: C 7 ASP cc_start: 0.8487 (m-30) cc_final: 0.8078 (t0) REVERT: C 115 ASN cc_start: 0.8769 (t0) cc_final: 0.8427 (t0) REVERT: D 220 GLN cc_start: 0.8735 (mp10) cc_final: 0.8523 (mm110) REVERT: D 232 GLN cc_start: 0.8450 (mp10) cc_final: 0.7437 (mp10) REVERT: E 56 ASP cc_start: 0.8774 (p0) cc_final: 0.8333 (p0) REVERT: E 127 GLU cc_start: 0.8313 (tt0) cc_final: 0.7587 (pp20) REVERT: E 225 LEU cc_start: 0.8952 (tp) cc_final: 0.8742 (tp) REVERT: F 44 ASP cc_start: 0.8696 (p0) cc_final: 0.8095 (p0) REVERT: F 53 TYR cc_start: 0.8831 (t80) cc_final: 0.8470 (t80) REVERT: G 149 ASN cc_start: 0.9060 (t0) cc_final: 0.8723 (t0) REVERT: G 236 ASP cc_start: 0.7962 (t0) cc_final: 0.7717 (t0) outliers start: 37 outliers final: 31 residues processed: 185 average time/residue: 0.0944 time to fit residues: 28.1539 Evaluate side-chains 181 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain B residue 33 GLN Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 194 SER Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 194 SER Chi-restraints excluded: chain G residue 235 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 175 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 179 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 176 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.140989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.120393 restraints weight = 20907.077| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.34 r_work: 0.3404 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 14266 Z= 0.103 Angle : 0.474 9.311 19383 Z= 0.251 Chirality : 0.041 0.152 2408 Planarity : 0.003 0.045 2478 Dihedral : 3.873 17.915 1974 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.24 % Allowed : 15.26 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.20), residues: 1862 helix: 2.47 (0.26), residues: 460 sheet: 0.14 (0.21), residues: 616 loop : -1.76 (0.19), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 186 TYR 0.010 0.001 TYR A 53 PHE 0.010 0.001 PHE G 28 TRP 0.006 0.001 TRP G 176 HIS 0.003 0.001 HIS G 251 Details of bonding type rmsd covalent geometry : bond 0.00220 (14266) covalent geometry : angle 0.47360 (19383) hydrogen bonds : bond 0.03849 ( 551) hydrogen bonds : angle 4.13044 ( 1659) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 0.593 Fit side-chains REVERT: A 118 ASP cc_start: 0.8850 (t0) cc_final: 0.8587 (t0) REVERT: B 70 LYS cc_start: 0.5457 (mmtm) cc_final: 0.4784 (mmtt) REVERT: B 241 ARG cc_start: 0.7217 (OUTLIER) cc_final: 0.6362 (tpt170) REVERT: C 115 ASN cc_start: 0.8673 (t0) cc_final: 0.8365 (t0) REVERT: C 236 ASP cc_start: 0.7563 (m-30) cc_final: 0.6815 (m-30) REVERT: D 232 GLN cc_start: 0.8403 (mp10) cc_final: 0.7404 (mp10) REVERT: E 56 ASP cc_start: 0.8771 (p0) cc_final: 0.8276 (p0) REVERT: E 127 GLU cc_start: 0.8292 (tt0) cc_final: 0.7409 (pp20) REVERT: E 261 LYS cc_start: 0.8611 (mptt) cc_final: 0.8112 (mmmm) REVERT: F 44 ASP cc_start: 0.8603 (p0) cc_final: 0.8005 (p0) REVERT: F 53 TYR cc_start: 0.8739 (t80) cc_final: 0.8299 (t80) REVERT: F 187 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8429 (mp) REVERT: G 149 ASN cc_start: 0.9086 (t0) cc_final: 0.8854 (t0) REVERT: G 236 ASP cc_start: 0.7780 (t0) cc_final: 0.7548 (t0) outliers start: 19 outliers final: 16 residues processed: 187 average time/residue: 0.1071 time to fit residues: 31.0970 Evaluate side-chains 187 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 241 ARG Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 194 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 137 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 108 GLN D 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.136786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.116747 restraints weight = 21323.169| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.19 r_work: 0.3337 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14266 Z= 0.188 Angle : 0.561 8.669 19383 Z= 0.296 Chirality : 0.042 0.153 2408 Planarity : 0.004 0.047 2478 Dihedral : 4.218 17.397 1974 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.89 % Allowed : 14.81 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.19), residues: 1862 helix: 2.34 (0.26), residues: 459 sheet: 0.19 (0.22), residues: 580 loop : -1.89 (0.18), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 186 TYR 0.019 0.002 TYR A 192 PHE 0.012 0.002 PHE A 214 TRP 0.003 0.001 TRP F 176 HIS 0.005 0.002 HIS G 251 Details of bonding type rmsd covalent geometry : bond 0.00447 (14266) covalent geometry : angle 0.56148 (19383) hydrogen bonds : bond 0.05960 ( 551) hydrogen bonds : angle 4.52133 ( 1659) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4158.67 seconds wall clock time: 71 minutes 49.58 seconds (4309.58 seconds total)