Starting phenix.real_space_refine on Thu Jun 4 10:26:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6f2d_4173/06_2026/6f2d_4173.cif Found real_map, /net/cci-nas-00/data/ceres_data/6f2d_4173/06_2026/6f2d_4173.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6f2d_4173/06_2026/6f2d_4173.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6f2d_4173/06_2026/6f2d_4173.map" model { file = "/net/cci-nas-00/data/ceres_data/6f2d_4173/06_2026/6f2d_4173.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6f2d_4173/06_2026/6f2d_4173.cif" } resolution = 4.2 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= 0.012 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 99 5.16 5 C 8390 2.51 5 N 1934 2.21 5 O 2118 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12541 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1575 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 15, 'TRANS': 187} Chain: "B" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1575 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 15, 'TRANS': 187} Chain: "C" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1575 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 15, 'TRANS': 187} Chain: "D" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1575 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 15, 'TRANS': 187} Chain: "E" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1575 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 15, 'TRANS': 187} Chain: "F" Number of atoms: 1986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1986 Classifications: {'peptide': 258} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 240} Chain: "G" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "H" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "I" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "J" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Time building chain proxies: 3.21, per 1000 atoms: 0.26 Number of scatterers: 12541 At special positions: 0 Unit cell: (105.78, 107.5, 131.58, 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 99 16.00 O 2118 8.00 N 1934 7.00 C 8390 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: 1.01 Conformation dependent library (CDL) restraints added in 619.1 milliseconds 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3094 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 0 sheets defined 82.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 44 through 61 removed outlier: 4.414A pdb=" N THR A 52 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N PHE A 53 " --> pdb=" O THR A 49 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) Proline residue: A 55 - end of helix Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.801A pdb=" N ILE A 68 " --> pdb=" O PHE A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 101 removed outlier: 4.043A pdb=" N THR A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 112 Processing helix chain 'A' and resid 112 through 117 Processing helix chain 'A' and resid 126 through 142 Proline residue: A 133 - end of helix removed outlier: 4.094A pdb=" N GLN A 141 " --> pdb=" O PHE A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 154 removed outlier: 3.571A pdb=" N LEU A 147 " --> pdb=" O ARG A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 207 removed outlier: 3.522A pdb=" N LEU A 170 " --> pdb=" O PRO A 166 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 171 " --> pdb=" O MET A 167 " (cutoff:3.500A) Proline residue: A 172 - end of helix removed outlier: 3.883A pdb=" N GLN A 184 " --> pdb=" O LYS A 180 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR A 188 " --> pdb=" O GLN A 184 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 190 " --> pdb=" O GLY A 186 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE A 191 " --> pdb=" O PHE A 187 " (cutoff:3.500A) Proline residue: A 192 - end of helix removed outlier: 3.706A pdb=" N LEU A 207 " --> pdb=" O VAL A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 228 Proline residue: A 220 - end of helix removed outlier: 3.675A pdb=" N PHE A 226 " --> pdb=" O LYS A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 245 removed outlier: 3.820A pdb=" N PHE A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR A 244 " --> pdb=" O ALA A 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 62 removed outlier: 3.969A pdb=" N PHE B 53 " --> pdb=" O THR B 49 " (cutoff:3.500A) Proline residue: B 55 - end of helix removed outlier: 3.658A pdb=" N LEU B 59 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 77 removed outlier: 3.585A pdb=" N ILE B 69 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN B 76 " --> pdb=" O GLY B 72 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 101 removed outlier: 3.536A pdb=" N THR B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 112 Processing helix chain 'B' and resid 112 through 119 removed outlier: 4.221A pdb=" N GLU B 118 " --> pdb=" O GLN B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 142 removed outlier: 3.744A pdb=" N ASP B 128 " --> pdb=" O GLN B 124 " (cutoff:3.500A) Proline residue: B 133 - end of helix removed outlier: 3.697A pdb=" N GLN B 141 " --> pdb=" O PHE B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 155 removed outlier: 4.101A pdb=" N LEU B 147 " --> pdb=" O ARG B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 207 Proline residue: B 172 - end of helix removed outlier: 3.936A pdb=" N PHE B 190 " --> pdb=" O GLY B 186 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE B 191 " --> pdb=" O PHE B 187 " (cutoff:3.500A) Proline residue: B 192 - end of helix removed outlier: 3.913A pdb=" N LEU B 207 " --> pdb=" O VAL B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 228 removed outlier: 4.141A pdb=" N ILE B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) Proline residue: B 220 - end of helix removed outlier: 3.815A pdb=" N PHE B 226 " --> pdb=" O LYS B 222 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 245 removed outlier: 4.065A pdb=" N VAL B 236 " --> pdb=" O TRP B 232 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR B 244 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER B 245 " --> pdb=" O GLN B 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 61 Proline residue: C 55 - end of helix Processing helix chain 'C' and resid 64 through 75 removed outlier: 3.877A pdb=" N VAL C 70 " --> pdb=" O ARG C 66 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE C 71 " --> pdb=" O ILE C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 101 removed outlier: 3.715A pdb=" N GLY C 91 " --> pdb=" O GLN C 87 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR C 97 " --> pdb=" O ALA C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 112 Processing helix chain 'C' and resid 112 through 117 Processing helix chain 'C' and resid 123 through 141 removed outlier: 4.120A pdb=" N LEU C 127 " --> pdb=" O MET C 123 " (cutoff:3.500A) Proline residue: C 133 - end of helix removed outlier: 4.118A pdb=" N GLN C 141 " --> pdb=" O PHE C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 155 removed outlier: 3.687A pdb=" N ALA C 148 " --> pdb=" O GLU C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 207 Proline residue: C 172 - end of helix removed outlier: 4.022A pdb=" N PHE C 190 " --> pdb=" O GLY C 186 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ILE C 191 " --> pdb=" O PHE C 187 " (cutoff:3.500A) Proline residue: C 192 - end of helix Processing helix chain 'C' and resid 214 through 228 removed outlier: 3.615A pdb=" N ALA C 218 " --> pdb=" O PRO C 214 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU C 219 " --> pdb=" O ALA C 215 " (cutoff:3.500A) Proline residue: C 220 - end of helix removed outlier: 3.597A pdb=" N PHE C 226 " --> pdb=" O LYS C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 244 removed outlier: 3.846A pdb=" N VAL C 236 " --> pdb=" O TRP C 232 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TYR C 244 " --> pdb=" O ALA C 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 61 removed outlier: 4.025A pdb=" N PHE D 53 " --> pdb=" O THR D 49 " (cutoff:3.500A) Proline residue: D 55 - end of helix Processing helix chain 'D' and resid 64 through 75 removed outlier: 3.528A pdb=" N ARG D 75 " --> pdb=" O PHE D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 112 removed outlier: 3.591A pdb=" N THR D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) Proline residue: D 103 - end of helix Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 124 through 142 removed outlier: 3.723A pdb=" N ASP D 128 " --> pdb=" O GLN D 124 " (cutoff:3.500A) Proline residue: D 133 - end of helix Processing helix chain 'D' and resid 143 through 154 removed outlier: 4.014A pdb=" N LEU D 147 " --> pdb=" O ARG D 143 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 208 removed outlier: 3.921A pdb=" N LEU D 171 " --> pdb=" O MET D 167 " (cutoff:3.500A) Proline residue: D 172 - end of helix removed outlier: 3.864A pdb=" N PHE D 190 " --> pdb=" O GLY D 186 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE D 191 " --> pdb=" O PHE D 187 " (cutoff:3.500A) Proline residue: D 192 - end of helix Processing helix chain 'D' and resid 213 through 218 Processing helix chain 'D' and resid 218 through 228 Processing helix chain 'D' and resid 231 through 245 removed outlier: 3.783A pdb=" N VAL D 236 " --> pdb=" O TRP D 232 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA D 240 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE D 243 " --> pdb=" O LEU D 239 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR D 244 " --> pdb=" O ALA D 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 61 Proline residue: E 55 - end of helix removed outlier: 3.943A pdb=" N LEU E 59 " --> pdb=" O PRO E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 77 removed outlier: 4.310A pdb=" N ILE E 69 " --> pdb=" O THR E 65 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL E 70 " --> pdb=" O ARG E 66 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE E 71 " --> pdb=" O ILE E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 112 removed outlier: 3.931A pdb=" N ALA E 93 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR E 97 " --> pdb=" O ALA E 93 " (cutoff:3.500A) Proline residue: E 103 - end of helix Processing helix chain 'E' and resid 112 through 117 Processing helix chain 'E' and resid 124 through 142 Proline residue: E 133 - end of helix removed outlier: 3.884A pdb=" N GLN E 141 " --> pdb=" O PHE E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 154 removed outlier: 3.627A pdb=" N ALA E 148 " --> pdb=" O GLU E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 207 removed outlier: 4.081A pdb=" N LEU E 170 " --> pdb=" O PRO E 166 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU E 171 " --> pdb=" O MET E 167 " (cutoff:3.500A) Proline residue: E 172 - end of helix removed outlier: 3.726A pdb=" N ILE E 191 " --> pdb=" O PHE E 187 " (cutoff:3.500A) Proline residue: E 192 - end of helix removed outlier: 3.604A pdb=" N LEU E 207 " --> pdb=" O VAL E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 228 removed outlier: 4.305A pdb=" N PHE E 221 " --> pdb=" O ILE E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 242 Processing helix chain 'F' and resid 7 through 16 removed outlier: 3.900A pdb=" N TRP F 12 " --> pdb=" O GLN F 8 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TYR F 16 " --> pdb=" O TRP F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 29 Processing helix chain 'F' and resid 39 through 44 Processing helix chain 'F' and resid 44 through 55 removed outlier: 4.366A pdb=" N ILE F 48 " --> pdb=" O LEU F 44 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU F 52 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL F 53 " --> pdb=" O MET F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 104 removed outlier: 3.840A pdb=" N GLN F 76 " --> pdb=" O TRP F 72 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN F 77 " --> pdb=" O LEU F 73 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE F 78 " --> pdb=" O ALA F 74 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU F 79 " --> pdb=" O MET F 75 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE F 80 " --> pdb=" O GLN F 76 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY F 85 " --> pdb=" O GLY F 81 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N PHE F 90 " --> pdb=" O PHE F 86 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ALA F 91 " --> pdb=" O THR F 87 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE F 92 " --> pdb=" O MET F 88 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE F 101 " --> pdb=" O THR F 97 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE F 102 " --> pdb=" O ALA F 98 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY F 103 " --> pdb=" O GLY F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 106 No H-bonds generated for 'chain 'F' and resid 105 through 106' Processing helix chain 'F' and resid 107 through 112 removed outlier: 4.071A pdb=" N PHE F 110 " --> pdb=" O GLY F 107 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA F 111 " --> pdb=" O LEU F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 137 removed outlier: 3.875A pdb=" N MET F 129 " --> pdb=" O LEU F 125 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET F 131 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA F 133 " --> pdb=" O MET F 129 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET F 134 " --> pdb=" O ASP F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 157 removed outlier: 3.564A pdb=" N HIS F 155 " --> pdb=" O VAL F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 175 removed outlier: 3.721A pdb=" N ALA F 171 " --> pdb=" O ASN F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 208 removed outlier: 3.923A pdb=" N LEU F 181 " --> pdb=" O GLY F 177 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU F 186 " --> pdb=" O ASN F 182 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA F 187 " --> pdb=" O GLY F 183 " (cutoff:3.500A) Proline residue: F 189 - end of helix removed outlier: 3.989A pdb=" N THR F 196 " --> pdb=" O THR F 192 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU F 197 " --> pdb=" O LEU F 193 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY F 202 " --> pdb=" O ASN F 198 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU F 204 " --> pdb=" O ALA F 200 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASN F 205 " --> pdb=" O LEU F 201 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ARG F 206 " --> pdb=" O GLY F 202 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N MET F 207 " --> pdb=" O LEU F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 215 Processing helix chain 'F' and resid 216 through 232 removed outlier: 3.635A pdb=" N LEU F 220 " --> pdb=" O ILE F 216 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N THR F 223 " --> pdb=" O PRO F 219 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL F 224 " --> pdb=" O LEU F 220 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET F 229 " --> pdb=" O GLY F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 261 removed outlier: 3.607A pdb=" N PHE F 239 " --> pdb=" O LEU F 235 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLU F 241 " --> pdb=" O ALA F 237 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N HIS F 242 " --> pdb=" O PRO F 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU F 243 " --> pdb=" O PHE F 239 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE F 247 " --> pdb=" O LEU F 243 " (cutoff:3.500A) Proline residue: F 259 - end of helix Processing helix chain 'G' and resid 2 through 39 removed outlier: 3.640A pdb=" N GLY G 10 " --> pdb=" O VAL G 6 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS G 15 " --> pdb=" O THR G 11 " (cutoff:3.500A) Proline residue: G 23 - end of helix Processing helix chain 'G' and resid 50 through 65 removed outlier: 3.526A pdb=" N VAL G 58 " --> pdb=" O LYS G 54 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE G 63 " --> pdb=" O PHE G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 88 removed outlier: 3.628A pdb=" N LEU G 70 " --> pdb=" O GLY G 66 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU G 73 " --> pdb=" O MET G 69 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG G 78 " --> pdb=" O LEU G 74 " (cutoff:3.500A) Proline residue: G 85 - end of helix removed outlier: 3.586A pdb=" N ILE G 88 " --> pdb=" O LEU G 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 39 removed outlier: 3.640A pdb=" N GLY H 10 " --> pdb=" O VAL H 6 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS H 15 " --> pdb=" O THR H 11 " (cutoff:3.500A) Proline residue: H 23 - end of helix Processing helix chain 'H' and resid 50 through 65 removed outlier: 3.525A pdb=" N VAL H 58 " --> pdb=" O LYS H 54 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE H 63 " --> pdb=" O PHE H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 88 removed outlier: 3.629A pdb=" N LEU H 70 " --> pdb=" O GLY H 66 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU H 73 " --> pdb=" O MET H 69 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG H 78 " --> pdb=" O LEU H 74 " (cutoff:3.500A) Proline residue: H 85 - end of helix removed outlier: 3.586A pdb=" N ILE H 88 " --> pdb=" O LEU H 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 39 removed outlier: 3.640A pdb=" N GLY I 10 " --> pdb=" O VAL I 6 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS I 15 " --> pdb=" O THR I 11 " (cutoff:3.500A) Proline residue: I 23 - end of helix Processing helix chain 'I' and resid 50 through 65 removed outlier: 3.526A pdb=" N VAL I 58 " --> pdb=" O LYS I 54 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE I 63 " --> pdb=" O PHE I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 88 removed outlier: 3.628A pdb=" N LEU I 70 " --> pdb=" O GLY I 66 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU I 73 " --> pdb=" O MET I 69 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG I 78 " --> pdb=" O LEU I 74 " (cutoff:3.500A) Proline residue: I 85 - end of helix removed outlier: 3.586A pdb=" N ILE I 88 " --> pdb=" O LEU I 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 39 removed outlier: 3.640A pdb=" N GLY J 10 " --> pdb=" O VAL J 6 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS J 15 " --> pdb=" O THR J 11 " (cutoff:3.500A) Proline residue: J 23 - end of helix Processing helix chain 'J' and resid 50 through 65 removed outlier: 3.526A pdb=" N VAL J 58 " --> pdb=" O LYS J 54 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE J 63 " --> pdb=" O PHE J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 88 removed outlier: 3.628A pdb=" N LEU J 70 " --> pdb=" O GLY J 66 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU J 73 " --> pdb=" O MET J 69 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG J 78 " --> pdb=" O LEU J 74 " (cutoff:3.500A) Proline residue: J 85 - end of helix removed outlier: 3.586A pdb=" N ILE J 88 " --> pdb=" O LEU J 84 " (cutoff:3.500A) 787 hydrogen bonds defined for protein. 2346 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: 2.00 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3742 1.34 - 1.46: 2363 1.46 - 1.58: 6518 1.58 - 1.70: 0 1.70 - 1.81: 197 Bond restraints: 12820 Sorted by residual: bond pdb=" C LEU F 58 " pdb=" N PRO F 59 " ideal model delta sigma weight residual 1.334 1.218 0.115 2.34e-02 1.83e+03 2.43e+01 bond pdb=" CG ARG B 75 " pdb=" CD ARG B 75 " ideal model delta sigma weight residual 1.520 1.439 0.081 3.00e-02 1.11e+03 7.28e+00 bond pdb=" C THR J 2 " pdb=" N PRO J 3 " ideal model delta sigma weight residual 1.335 1.304 0.030 1.19e-02 7.06e+03 6.53e+00 bond pdb=" C THR H 2 " pdb=" N PRO H 3 " ideal model delta sigma weight residual 1.335 1.304 0.030 1.19e-02 7.06e+03 6.42e+00 bond pdb=" C THR G 2 " pdb=" N PRO G 3 " ideal model delta sigma weight residual 1.335 1.305 0.030 1.19e-02 7.06e+03 6.30e+00 ... (remaining 12815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.65: 17136 3.65 - 7.30: 301 7.30 - 10.95: 35 10.95 - 14.59: 3 14.59 - 18.24: 1 Bond angle restraints: 17476 Sorted by residual: angle pdb=" C ASN J 45 " pdb=" N GLU J 46 " pdb=" CA GLU J 46 " ideal model delta sigma weight residual 121.98 113.11 8.87 1.35e+00 5.49e-01 4.32e+01 angle pdb=" C ASN G 45 " pdb=" N GLU G 46 " pdb=" CA GLU G 46 " ideal model delta sigma weight residual 121.98 113.12 8.86 1.35e+00 5.49e-01 4.30e+01 angle pdb=" C ASN H 45 " pdb=" N GLU H 46 " pdb=" CA GLU H 46 " ideal model delta sigma weight residual 121.98 113.14 8.84 1.35e+00 5.49e-01 4.28e+01 angle pdb=" C ASN I 45 " pdb=" N GLU I 46 " pdb=" CA GLU I 46 " ideal model delta sigma weight residual 121.98 113.15 8.83 1.35e+00 5.49e-01 4.28e+01 angle pdb=" CA LEU F 150 " pdb=" CB LEU F 150 " pdb=" CG LEU F 150 " ideal model delta sigma weight residual 116.30 98.06 18.24 3.50e+00 8.16e-02 2.72e+01 ... (remaining 17471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 7462 16.96 - 33.92: 236 33.92 - 50.88: 27 50.88 - 67.84: 1 67.84 - 84.81: 5 Dihedral angle restraints: 7731 sinusoidal: 2988 harmonic: 4743 Sorted by residual: dihedral pdb=" CA SER E 117 " pdb=" C SER E 117 " pdb=" N GLU E 118 " pdb=" CA GLU E 118 " ideal model delta harmonic sigma weight residual -180.00 -150.43 -29.57 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA ASP A 230 " pdb=" C ASP A 230 " pdb=" N GLY A 231 " pdb=" CA GLY A 231 " ideal model delta harmonic sigma weight residual -180.00 -151.02 -28.98 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA ILE C 189 " pdb=" C ILE C 189 " pdb=" N PHE C 190 " pdb=" CA PHE C 190 " ideal model delta harmonic sigma weight residual -180.00 -151.22 -28.78 0 5.00e+00 4.00e-02 3.31e+01 ... (remaining 7728 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1167 0.037 - 0.074: 661 0.074 - 0.111: 263 0.111 - 0.148: 86 0.148 - 0.185: 12 Chirality restraints: 2189 Sorted by residual: chirality pdb=" CA VAL A 165 " pdb=" N VAL A 165 " pdb=" C VAL A 165 " pdb=" CB VAL A 165 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.59e-01 chirality pdb=" CB THR F 112 " pdb=" CA THR F 112 " pdb=" OG1 THR F 112 " pdb=" CG2 THR F 112 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.50e-01 chirality pdb=" CA VAL A 212 " pdb=" N VAL A 212 " pdb=" C VAL A 212 " pdb=" CB VAL A 212 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.18 2.00e-01 2.50e+01 8.46e-01 ... (remaining 2186 not shown) Planarity restraints: 2130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 84 " 0.061 5.00e-02 4.00e+02 9.32e-02 1.39e+01 pdb=" N PRO B 85 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO B 85 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 85 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 212 " -0.049 5.00e-02 4.00e+02 7.44e-02 8.85e+00 pdb=" N PRO D 213 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO D 213 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 213 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 84 " 0.043 5.00e-02 4.00e+02 6.52e-02 6.79e+00 pdb=" N PRO C 85 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 85 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 85 " 0.036 5.00e-02 4.00e+02 ... (remaining 2127 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 260 2.60 - 3.17: 14293 3.17 - 3.75: 18354 3.75 - 4.32: 26776 4.32 - 4.90: 40002 Nonbonded interactions: 99685 Sorted by model distance: nonbonded pdb=" O ALA F 25 " pdb=" OG1 THR F 29 " model vdw 2.023 3.040 nonbonded pdb=" O THR A 62 " pdb=" OH TYR A 174 " model vdw 2.037 3.040 nonbonded pdb=" O LEU C 94 " pdb=" OG1 THR C 97 " model vdw 2.044 3.040 nonbonded pdb=" O THR C 62 " pdb=" OH TYR C 174 " model vdw 2.045 3.040 nonbonded pdb=" O THR C 49 " pdb=" OG1 THR C 52 " model vdw 2.074 3.040 ... (remaining 99680 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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 group one per residue 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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.460 Find NCS groups from input model: 0.200 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 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 : 0.010 0.115 12820 Z= 0.443 Angle : 1.194 18.243 17476 Z= 0.599 Chirality : 0.054 0.185 2189 Planarity : 0.008 0.093 2130 Dihedral : 9.303 84.805 4637 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 26.13 Ramachandran Plot: Outliers : 0.68 % Allowed : 16.35 % Favored : 82.97 % Rotamer: Outliers : 0.51 % Allowed : 1.31 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -6.32 (0.14), residues: 1609 helix: -3.94 (0.09), residues: 1175 sheet: None (None), residues: 0 loop : -4.19 (0.25), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG B 75 TYR 0.029 0.004 TYR C 174 PHE 0.031 0.003 PHE A 64 TRP 0.023 0.003 TRP F 18 HIS 0.011 0.004 HIS F 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00989 / 0.44 (12820) covalent geometry : angle 1.19431 / 0.60 (17476) hydrogen bonds : bond 0.16552 / 10.89 ( 787) hydrogen bonds : angle 11.04719 / 7.80 ( 2346) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 448 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 THR cc_start: 0.7433 (m) cc_final: 0.7067 (p) REVERT: A 53 PHE cc_start: 0.7007 (m-80) cc_final: 0.6696 (m-80) REVERT: A 60 MET cc_start: 0.9353 (mmm) cc_final: 0.8998 (mmt) REVERT: A 205 MET cc_start: 0.8563 (mmt) cc_final: 0.8257 (tpt) REVERT: A 209 MET cc_start: 0.7554 (mmp) cc_final: 0.7052 (mmm) REVERT: B 54 LEU cc_start: 0.8338 (tp) cc_final: 0.8113 (tp) REVERT: B 124 GLN cc_start: 0.8348 (mm-40) cc_final: 0.8141 (mm110) REVERT: B 125 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8568 (mm-30) REVERT: B 128 ASP cc_start: 0.8952 (m-30) cc_final: 0.8737 (t70) REVERT: B 129 LYS cc_start: 0.8883 (tttm) cc_final: 0.8344 (mtmm) REVERT: C 88 VAL cc_start: 0.9091 (t) cc_final: 0.8794 (p) REVERT: C 111 ASP cc_start: 0.8400 (m-30) cc_final: 0.8065 (m-30) REVERT: C 128 ASP cc_start: 0.8328 (m-30) cc_final: 0.7432 (t0) REVERT: C 243 PHE cc_start: 0.7333 (t80) cc_final: 0.6976 (t80) REVERT: D 95 PHE cc_start: 0.8915 (m-10) cc_final: 0.8653 (m-80) REVERT: D 135 ARG cc_start: 0.8761 (mtt-85) cc_final: 0.8438 (mtp-110) REVERT: D 210 MET cc_start: 0.6192 (tpp) cc_final: 0.5323 (tmm) REVERT: D 211 MET cc_start: 0.6839 (mmm) cc_final: 0.6527 (mmt) REVERT: E 114 GLN cc_start: 0.9333 (tt0) cc_final: 0.8917 (tp-100) REVERT: E 128 ASP cc_start: 0.9127 (m-30) cc_final: 0.8842 (t0) REVERT: E 163 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7626 (pm20) REVERT: E 213 PRO cc_start: 0.8660 (Cg_endo) cc_final: 0.8432 (Cg_exo) REVERT: E 230 ASP cc_start: 0.8673 (t0) cc_final: 0.8011 (t0) REVERT: F 22 ARG cc_start: 0.8125 (mtt180) cc_final: 0.7440 (ttm-80) REVERT: F 36 ARG cc_start: 0.7044 (mtt-85) cc_final: 0.6343 (mtm-85) REVERT: F 71 LEU cc_start: 0.8603 (mt) cc_final: 0.8394 (pp) REVERT: F 101 PHE cc_start: 0.8023 (m-80) cc_final: 0.7395 (m-80) REVERT: F 123 PRO cc_start: 0.7755 (Cg_exo) cc_final: 0.7028 (Cg_endo) REVERT: F 143 HIS cc_start: 0.8320 (m-70) cc_final: 0.7745 (m-70) REVERT: F 258 MET cc_start: 0.6722 (ttm) cc_final: 0.6522 (ttm) REVERT: G 7 MET cc_start: 0.8761 (mmm) cc_final: 0.8559 (mmp) REVERT: G 15 LYS cc_start: 0.8406 (mttt) cc_final: 0.7987 (tmtt) REVERT: J 11 THR cc_start: 0.7922 (p) cc_final: 0.7717 (p) REVERT: J 83 ASN cc_start: 0.9166 (m-40) cc_final: 0.8887 (t0) REVERT: J 84 LEU cc_start: 0.8223 (mt) cc_final: 0.7824 (mt) outliers start: 7 outliers final: 3 residues processed: 454 average time/residue: 0.1180 time to fit residues: 74.7719 Evaluate side-chains 250 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 247 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 98 optimal weight: 0.4980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 GLN D 87 GLN ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 HIS J 39 GLN ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.086307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.072485 restraints weight = 43056.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.074256 restraints weight = 26056.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.075524 restraints weight = 18217.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.076375 restraints weight = 14151.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.076854 restraints weight = 11901.623| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12820 Z= 0.199 Angle : 0.909 8.938 17476 Z= 0.455 Chirality : 0.048 0.250 2189 Planarity : 0.007 0.078 2130 Dihedral : 7.326 29.987 1695 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.58 % Favored : 91.05 % Rotamer: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -2.91 (0.19), residues: 1609 helix: -1.18 (0.14), residues: 1203 sheet: None (None), residues: 0 loop : -3.93 (0.26), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 135 TYR 0.022 0.002 TYR A 109 PHE 0.038 0.002 PHE D 64 TRP 0.015 0.002 TRP F 18 HIS 0.007 0.002 HIS F 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.20 (12820) covalent geometry : angle 0.90904 / 0.46 (17476) hydrogen bonds : bond 0.05718 / 3.75 ( 787) hydrogen bonds : angle 6.07677 / 4.33 ( 2346) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 THR cc_start: 0.7795 (m) cc_final: 0.7377 (p) REVERT: A 53 PHE cc_start: 0.6784 (m-80) cc_final: 0.6245 (m-80) REVERT: B 54 LEU cc_start: 0.7747 (tp) cc_final: 0.7323 (tp) REVERT: B 123 MET cc_start: 0.8193 (mtt) cc_final: 0.7984 (mtp) REVERT: B 124 GLN cc_start: 0.7743 (mm-40) cc_final: 0.7394 (mt0) REVERT: B 129 LYS cc_start: 0.8916 (tttm) cc_final: 0.8666 (mtmm) REVERT: C 49 THR cc_start: 0.7874 (m) cc_final: 0.7519 (p) REVERT: C 128 ASP cc_start: 0.8181 (m-30) cc_final: 0.7648 (t0) REVERT: C 129 LYS cc_start: 0.8551 (tttm) cc_final: 0.8148 (ttpp) REVERT: D 54 LEU cc_start: 0.8939 (tp) cc_final: 0.8677 (pp) REVERT: E 163 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7090 (pm20) REVERT: E 174 TYR cc_start: 0.8245 (t80) cc_final: 0.7812 (t80) REVERT: F 22 ARG cc_start: 0.7718 (mtt180) cc_final: 0.7416 (ttm-80) REVERT: F 101 PHE cc_start: 0.7446 (m-80) cc_final: 0.6780 (m-80) REVERT: G 7 MET cc_start: 0.8612 (mmm) cc_final: 0.8304 (mmp) REVERT: G 15 LYS cc_start: 0.8395 (mttt) cc_final: 0.8066 (tmtt) REVERT: G 87 ILE cc_start: 0.8572 (mm) cc_final: 0.8306 (mt) REVERT: H 11 THR cc_start: 0.8701 (p) cc_final: 0.8473 (t) REVERT: H 69 MET cc_start: 0.8396 (mtt) cc_final: 0.8005 (ttm) REVERT: J 9 MET cc_start: 0.9011 (mmp) cc_final: 0.8656 (mmm) outliers start: 0 outliers final: 0 residues processed: 359 average time/residue: 0.1020 time to fit residues: 53.4405 Evaluate side-chains 244 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 16 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 105 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 HIS ** F 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.086887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.072760 restraints weight = 43520.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.074664 restraints weight = 26078.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.075970 restraints weight = 18134.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.076758 restraints weight = 13959.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.077469 restraints weight = 11812.032| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12820 Z= 0.170 Angle : 0.819 10.324 17476 Z= 0.406 Chirality : 0.046 0.258 2189 Planarity : 0.007 0.078 2130 Dihedral : 6.825 28.450 1695 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.68 % Allowed : 8.02 % Favored : 91.30 % Rotamer: Outliers : 0.07 % Allowed : 3.20 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.20), residues: 1609 helix: 0.02 (0.15), residues: 1189 sheet: None (None), residues: 0 loop : -3.75 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 135 TYR 0.021 0.001 TYR C 174 PHE 0.034 0.002 PHE D 64 TRP 0.015 0.002 TRP F 72 HIS 0.007 0.001 HIS F 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (12820) covalent geometry : angle 0.81908 / 0.41 (17476) hydrogen bonds : bond 0.04761 / 3.14 ( 787) hydrogen bonds : angle 5.35574 / 3.82 ( 2346) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 326 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 THR cc_start: 0.7872 (m) cc_final: 0.7488 (p) REVERT: A 53 PHE cc_start: 0.6878 (m-80) cc_final: 0.6432 (m-80) REVERT: B 95 PHE cc_start: 0.7827 (m-10) cc_final: 0.7378 (m-80) REVERT: C 128 ASP cc_start: 0.8169 (m-30) cc_final: 0.7804 (t0) REVERT: C 129 LYS cc_start: 0.8434 (tttm) cc_final: 0.8140 (ttpp) REVERT: C 168 ARG cc_start: 0.8534 (ptt90) cc_final: 0.8007 (ptp-170) REVERT: E 163 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7050 (pm20) REVERT: E 174 TYR cc_start: 0.8071 (t80) cc_final: 0.7746 (t80) REVERT: F 36 ARG cc_start: 0.7481 (mtt90) cc_final: 0.7205 (mtm-85) REVERT: G 7 MET cc_start: 0.8648 (mmm) cc_final: 0.8311 (mmp) REVERT: G 15 LYS cc_start: 0.8397 (mttt) cc_final: 0.8173 (tmtt) REVERT: H 69 MET cc_start: 0.8573 (mtt) cc_final: 0.8042 (ttm) REVERT: I 29 LEU cc_start: 0.8109 (mm) cc_final: 0.7842 (mm) REVERT: J 9 MET cc_start: 0.9013 (mmp) cc_final: 0.8754 (mmm) outliers start: 1 outliers final: 0 residues processed: 327 average time/residue: 0.0957 time to fit residues: 46.2519 Evaluate side-chains 232 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 43 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 71 optimal weight: 0.0670 chunk 104 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 147 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 overall best weight: 2.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 ASN F 77 GLN F 143 HIS ** F 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.087286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.072585 restraints weight = 44353.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.074459 restraints weight = 27184.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.075791 restraints weight = 19079.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.076473 restraints weight = 14900.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.077203 restraints weight = 12861.378| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.5119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 12820 Z= 0.168 Angle : 0.812 8.757 17476 Z= 0.401 Chirality : 0.046 0.176 2189 Planarity : 0.006 0.066 2130 Dihedral : 6.504 28.997 1695 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.81 % Allowed : 7.52 % Favored : 91.67 % Rotamer: Outliers : 0.07 % Allowed : 2.54 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -0.85 (0.21), residues: 1609 helix: 0.37 (0.14), residues: 1208 sheet: None (None), residues: 0 loop : -3.44 (0.28), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 140 TYR 0.019 0.002 TYR C 174 PHE 0.033 0.002 PHE D 64 TRP 0.032 0.002 TRP F 72 HIS 0.007 0.001 HIS F 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (12820) covalent geometry : angle 0.81219 / 0.40 (17476) hydrogen bonds : bond 0.04491 / 2.96 ( 787) hydrogen bonds : angle 5.02190 / 3.58 ( 2346) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 303 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 THR cc_start: 0.7810 (m) cc_final: 0.7428 (p) REVERT: B 95 PHE cc_start: 0.7765 (m-10) cc_final: 0.7478 (m-80) REVERT: B 123 MET cc_start: 0.7920 (mtt) cc_final: 0.7715 (mtp) REVERT: C 168 ARG cc_start: 0.8569 (ptt90) cc_final: 0.7969 (ptp-170) REVERT: D 210 MET cc_start: 0.7061 (pmm) cc_final: 0.6331 (pmm) REVERT: E 210 MET cc_start: 0.7621 (pmm) cc_final: 0.7216 (pmm) REVERT: F 36 ARG cc_start: 0.7522 (mtt90) cc_final: 0.7188 (mtm-85) REVERT: F 211 LEU cc_start: 0.7597 (mp) cc_final: 0.7138 (tt) REVERT: F 218 PHE cc_start: 0.6381 (m-80) cc_final: 0.6150 (m-80) REVERT: F 229 MET cc_start: 0.8300 (tpt) cc_final: 0.8010 (tpt) REVERT: G 9 MET cc_start: 0.7769 (mtm) cc_final: 0.7444 (mtm) REVERT: G 15 LYS cc_start: 0.8452 (mttt) cc_final: 0.8239 (tmtt) REVERT: H 46 GLU cc_start: 0.6476 (mp0) cc_final: 0.5838 (mm-30) REVERT: H 69 MET cc_start: 0.8439 (mtt) cc_final: 0.7977 (ttm) REVERT: I 29 LEU cc_start: 0.7981 (mm) cc_final: 0.7744 (mm) REVERT: I 45 ASN cc_start: 0.8382 (p0) cc_final: 0.8097 (p0) REVERT: J 1 MET cc_start: 0.7713 (ppp) cc_final: 0.7485 (ppp) outliers start: 1 outliers final: 0 residues processed: 304 average time/residue: 0.0882 time to fit residues: 40.5088 Evaluate side-chains 230 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 12 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 47 optimal weight: 30.0000 chunk 3 optimal weight: 0.0270 chunk 1 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 89 optimal weight: 0.0050 overall best weight: 2.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 ASN E 132 GLN F 143 HIS ** F 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.086378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.071817 restraints weight = 44036.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.073677 restraints weight = 26897.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.074971 restraints weight = 18809.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.075864 restraints weight = 14588.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.076489 restraints weight = 12245.326| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.5433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 12820 Z= 0.171 Angle : 0.805 8.876 17476 Z= 0.396 Chirality : 0.045 0.179 2189 Planarity : 0.006 0.072 2130 Dihedral : 6.323 27.768 1695 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.87 % Allowed : 7.58 % Favored : 91.55 % Rotamer: Outliers : 0.15 % Allowed : 2.76 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -0.81 (0.20), residues: 1609 helix: 0.45 (0.15), residues: 1193 sheet: None (None), residues: 0 loop : -3.47 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 75 TYR 0.023 0.002 TYR C 174 PHE 0.044 0.002 PHE D 64 TRP 0.045 0.002 TRP F 72 HIS 0.015 0.003 HIS F 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (12820) covalent geometry : angle 0.80534 / 0.40 (17476) hydrogen bonds : bond 0.04317 / 2.85 ( 787) hydrogen bonds : angle 4.90279 / 3.51 ( 2346) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 284 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 THR cc_start: 0.7802 (m) cc_final: 0.7513 (p) REVERT: A 53 PHE cc_start: 0.7003 (m-80) cc_final: 0.6699 (m-80) REVERT: A 209 MET cc_start: 0.6512 (mpp) cc_final: 0.6012 (mpp) REVERT: B 95 PHE cc_start: 0.7854 (m-10) cc_final: 0.7482 (m-80) REVERT: B 125 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7191 (mm-30) REVERT: B 205 MET cc_start: 0.8281 (mtm) cc_final: 0.7686 (mtm) REVERT: C 114 GLN cc_start: 0.8173 (tt0) cc_final: 0.7737 (tm-30) REVERT: C 168 ARG cc_start: 0.8611 (ptt90) cc_final: 0.7978 (ptp-170) REVERT: F 36 ARG cc_start: 0.7491 (mtt90) cc_final: 0.7082 (mtm-85) REVERT: F 218 PHE cc_start: 0.6502 (m-80) cc_final: 0.6242 (m-80) REVERT: F 233 MET cc_start: 0.7427 (mmm) cc_final: 0.7215 (mmm) REVERT: G 7 MET cc_start: 0.8603 (mmm) cc_final: 0.8299 (mmm) REVERT: G 9 MET cc_start: 0.7866 (mtm) cc_final: 0.7615 (mtm) REVERT: G 15 LYS cc_start: 0.8576 (mttt) cc_final: 0.8328 (tmtt) REVERT: H 69 MET cc_start: 0.8606 (mtt) cc_final: 0.8046 (ttm) REVERT: I 29 LEU cc_start: 0.7951 (mm) cc_final: 0.7670 (mm) REVERT: I 45 ASN cc_start: 0.8134 (p0) cc_final: 0.7905 (p0) outliers start: 2 outliers final: 0 residues processed: 285 average time/residue: 0.0947 time to fit residues: 39.8572 Evaluate side-chains 222 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 125 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 chunk 133 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 142 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 143 HIS ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.084880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.070351 restraints weight = 45875.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.072017 restraints weight = 28308.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.073239 restraints weight = 20266.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.073951 restraints weight = 15965.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.074613 restraints weight = 13709.677| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.5634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12820 Z= 0.195 Angle : 0.832 8.555 17476 Z= 0.408 Chirality : 0.047 0.185 2189 Planarity : 0.007 0.072 2130 Dihedral : 6.309 28.055 1695 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.81 % Allowed : 8.08 % Favored : 91.11 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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 (0.21), residues: 1609 helix: 0.58 (0.15), residues: 1206 sheet: None (None), residues: 0 loop : -3.30 (0.28), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 140 TYR 0.022 0.002 TYR C 174 PHE 0.045 0.002 PHE D 64 TRP 0.032 0.002 TRP F 72 HIS 0.014 0.002 HIS F 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.20 (12820) covalent geometry : angle 0.83207 / 0.41 (17476) hydrogen bonds : bond 0.04357 / 2.89 ( 787) hydrogen bonds : angle 4.91080 / 3.50 ( 2346) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 MET cc_start: 0.6590 (mpp) cc_final: 0.5891 (mpp) REVERT: B 95 PHE cc_start: 0.7861 (m-10) cc_final: 0.7363 (m-80) REVERT: B 125 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7000 (mm-30) REVERT: B 205 MET cc_start: 0.8362 (mtm) cc_final: 0.7365 (mtm) REVERT: B 225 LEU cc_start: 0.8832 (mp) cc_final: 0.8628 (tp) REVERT: C 114 GLN cc_start: 0.8176 (tt0) cc_final: 0.7694 (tm-30) REVERT: C 168 ARG cc_start: 0.8696 (ptt90) cc_final: 0.8129 (ptp-170) REVERT: D 118 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7975 (mp0) REVERT: F 129 MET cc_start: 0.9160 (mpp) cc_final: 0.8836 (mpp) REVERT: F 218 PHE cc_start: 0.6618 (m-80) cc_final: 0.6368 (m-80) REVERT: F 233 MET cc_start: 0.7487 (mmm) cc_final: 0.7152 (mmm) REVERT: G 7 MET cc_start: 0.8566 (mmm) cc_final: 0.8294 (mmm) REVERT: G 15 LYS cc_start: 0.8584 (mttt) cc_final: 0.8345 (tmtt) REVERT: G 87 ILE cc_start: 0.8806 (mm) cc_final: 0.8450 (mt) REVERT: H 69 MET cc_start: 0.8618 (mtt) cc_final: 0.8082 (ttm) REVERT: I 29 LEU cc_start: 0.7992 (mm) cc_final: 0.7781 (mm) REVERT: I 69 MET cc_start: 0.8164 (mtt) cc_final: 0.7936 (mtt) outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.0922 time to fit residues: 37.0048 Evaluate side-chains 218 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 113 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 45 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.087644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.073428 restraints weight = 45497.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.074992 restraints weight = 30058.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.076140 restraints weight = 22202.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.076931 restraints weight = 17871.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.077310 restraints weight = 15334.802| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.6048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12820 Z= 0.151 Angle : 0.787 8.584 17476 Z= 0.386 Chirality : 0.044 0.244 2189 Planarity : 0.006 0.074 2130 Dihedral : 6.001 26.326 1695 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.81 % Allowed : 7.21 % Favored : 91.98 % Rotamer: Outliers : 0.07 % Allowed : 2.03 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -0.36 (0.21), residues: 1609 helix: 0.73 (0.15), residues: 1216 sheet: None (None), residues: 0 loop : -3.35 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 75 TYR 0.023 0.001 TYR C 174 PHE 0.043 0.002 PHE D 64 TRP 0.013 0.001 TRP B 232 HIS 0.010 0.002 HIS F 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (12820) covalent geometry : angle 0.78705 / 0.39 (17476) hydrogen bonds : bond 0.03901 / 2.55 ( 787) hydrogen bonds : angle 4.67291 / 3.32 ( 2346) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 295 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 MET cc_start: 0.6475 (mpp) cc_final: 0.5886 (mpp) REVERT: B 54 LEU cc_start: 0.7224 (mt) cc_final: 0.6972 (mt) REVERT: B 95 PHE cc_start: 0.7902 (m-10) cc_final: 0.7437 (m-80) REVERT: B 125 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7062 (mm-30) REVERT: B 138 MET cc_start: 0.8307 (mmt) cc_final: 0.7793 (mmt) REVERT: B 205 MET cc_start: 0.8188 (mtm) cc_final: 0.7497 (mtm) REVERT: C 134 LEU cc_start: 0.9289 (tp) cc_final: 0.9021 (tp) REVERT: C 168 ARG cc_start: 0.8522 (ptt90) cc_final: 0.7985 (ptp-170) REVERT: D 118 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7842 (mp0) REVERT: F 14 HIS cc_start: 0.6434 (m-70) cc_final: 0.5970 (m-70) REVERT: F 218 PHE cc_start: 0.6403 (m-80) cc_final: 0.6102 (m-80) REVERT: G 15 LYS cc_start: 0.8592 (mttt) cc_final: 0.8360 (tmtt) REVERT: G 87 ILE cc_start: 0.8766 (mm) cc_final: 0.8459 (mt) REVERT: H 69 MET cc_start: 0.8436 (mtt) cc_final: 0.7945 (ttm) REVERT: I 29 LEU cc_start: 0.7987 (mm) cc_final: 0.7702 (mm) REVERT: I 69 MET cc_start: 0.8041 (mtt) cc_final: 0.7832 (mtt) REVERT: J 9 MET cc_start: 0.8756 (mmm) cc_final: 0.8428 (mtt) outliers start: 1 outliers final: 0 residues processed: 295 average time/residue: 0.0931 time to fit residues: 40.9977 Evaluate side-chains 225 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 55 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 chunk 128 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 126 optimal weight: 0.4980 chunk 142 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 137 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 ASN F 89 GLN F 143 HIS I 45 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.086638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.072118 restraints weight = 44105.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.073864 restraints weight = 27127.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.075098 restraints weight = 19249.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.075994 restraints weight = 15153.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.076488 restraints weight = 12839.471| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.6144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 12820 Z= 0.165 Angle : 0.805 8.884 17476 Z= 0.394 Chirality : 0.045 0.244 2189 Planarity : 0.006 0.086 2130 Dihedral : 5.942 25.610 1695 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.81 % Allowed : 7.52 % Favored : 91.67 % Rotamer: Outliers : 0.07 % Allowed : 1.02 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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 (0.21), residues: 1609 helix: 0.88 (0.15), residues: 1202 sheet: None (None), residues: 0 loop : -3.14 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 75 TYR 0.021 0.002 TYR C 174 PHE 0.045 0.002 PHE D 64 TRP 0.032 0.002 TRP F 72 HIS 0.010 0.002 HIS F 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (12820) covalent geometry : angle 0.80532 / 0.39 (17476) hydrogen bonds : bond 0.03973 / 2.62 ( 787) hydrogen bonds : angle 4.69065 / 3.35 ( 2346) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 272 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.8369 (mmm) cc_final: 0.8158 (mtm) REVERT: A 209 MET cc_start: 0.6562 (mpp) cc_final: 0.6006 (mpp) REVERT: B 125 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7075 (mm-30) REVERT: B 138 MET cc_start: 0.8346 (mmt) cc_final: 0.7862 (mmt) REVERT: B 205 MET cc_start: 0.8195 (mtm) cc_final: 0.7524 (mtm) REVERT: C 168 ARG cc_start: 0.8543 (ptt90) cc_final: 0.8037 (ptp-170) REVERT: D 118 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7738 (mp0) REVERT: D 209 MET cc_start: 0.8456 (mmm) cc_final: 0.8130 (mmp) REVERT: D 211 MET cc_start: 0.7084 (mmt) cc_final: 0.6394 (tpp) REVERT: F 185 MET cc_start: 0.8309 (mtm) cc_final: 0.8036 (mtm) REVERT: F 229 MET cc_start: 0.8396 (tpt) cc_final: 0.8086 (tpt) REVERT: G 15 LYS cc_start: 0.8620 (mttt) cc_final: 0.8399 (tmtt) REVERT: G 87 ILE cc_start: 0.8782 (mm) cc_final: 0.8510 (mt) REVERT: H 30 ILE cc_start: 0.9197 (mm) cc_final: 0.8942 (tp) REVERT: H 69 MET cc_start: 0.8456 (mtt) cc_final: 0.7967 (ttm) REVERT: I 29 LEU cc_start: 0.7995 (mm) cc_final: 0.7604 (mt) REVERT: I 69 MET cc_start: 0.8081 (mtt) cc_final: 0.7701 (ttm) outliers start: 1 outliers final: 1 residues processed: 273 average time/residue: 0.0938 time to fit residues: 38.2927 Evaluate side-chains 214 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 213 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 95 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 131 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 78 optimal weight: 0.0170 chunk 98 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 102 optimal weight: 0.6980 chunk 26 optimal weight: 0.3980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 233 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.089398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.074511 restraints weight = 44276.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.076390 restraints weight = 26824.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.077727 restraints weight = 18776.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.078616 restraints weight = 14677.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.079087 restraints weight = 12382.564| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.6504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12820 Z= 0.148 Angle : 0.803 8.422 17476 Z= 0.390 Chirality : 0.044 0.251 2189 Planarity : 0.006 0.075 2130 Dihedral : 5.728 25.529 1695 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.75 % Allowed : 7.09 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -0.08 (0.21), residues: 1609 helix: 0.93 (0.15), residues: 1201 sheet: None (None), residues: 0 loop : -3.06 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 152 TYR 0.021 0.001 TYR E 174 PHE 0.042 0.002 PHE D 64 TRP 0.017 0.002 TRP C 232 HIS 0.010 0.002 HIS F 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 (12820) covalent geometry : angle 0.80258 / 0.39 (17476) hydrogen bonds : bond 0.03710 / 2.46 ( 787) hydrogen bonds : angle 4.55359 / 3.26 ( 2346) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8504 (tpp) cc_final: 0.8103 (mtm) REVERT: A 209 MET cc_start: 0.6554 (mpp) cc_final: 0.5998 (mpp) REVERT: B 138 MET cc_start: 0.8388 (mmt) cc_final: 0.8069 (mmt) REVERT: B 205 MET cc_start: 0.8120 (mtm) cc_final: 0.7477 (mtm) REVERT: C 168 ARG cc_start: 0.8422 (ptt90) cc_final: 0.7909 (ptp-170) REVERT: D 209 MET cc_start: 0.8470 (mmm) cc_final: 0.8250 (mmp) REVERT: D 211 MET cc_start: 0.7002 (mmt) cc_final: 0.6723 (tpp) REVERT: F 185 MET cc_start: 0.8375 (mtm) cc_final: 0.8072 (mtm) REVERT: F 207 MET cc_start: 0.7801 (tpp) cc_final: 0.7586 (tpp) REVERT: G 15 LYS cc_start: 0.8697 (mttt) cc_final: 0.8415 (tmtt) REVERT: G 87 ILE cc_start: 0.8757 (mm) cc_final: 0.8424 (mt) REVERT: H 30 ILE cc_start: 0.9194 (mm) cc_final: 0.8965 (tp) REVERT: H 69 MET cc_start: 0.8521 (mtt) cc_final: 0.7961 (ttm) REVERT: I 29 LEU cc_start: 0.8023 (mm) cc_final: 0.7705 (mm) REVERT: I 69 MET cc_start: 0.8097 (mtt) cc_final: 0.7894 (mtt) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.0977 time to fit residues: 40.6374 Evaluate side-chains 214 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 135 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 126 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 70 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 233 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 HIS H 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.087024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.072448 restraints weight = 44095.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.074323 restraints weight = 26827.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.075421 restraints weight = 18737.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.076456 restraints weight = 14889.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.076976 restraints weight = 12394.444| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.6533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12820 Z= 0.166 Angle : 0.819 10.549 17476 Z= 0.400 Chirality : 0.046 0.220 2189 Planarity : 0.006 0.076 2130 Dihedral : 5.742 27.605 1695 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.58 % Favored : 91.80 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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 (0.21), residues: 1609 helix: 0.94 (0.15), residues: 1211 sheet: None (None), residues: 0 loop : -3.11 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 75 TYR 0.024 0.002 TYR B 109 PHE 0.045 0.002 PHE D 64 TRP 0.019 0.002 TRP F 18 HIS 0.018 0.003 HIS F 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (12820) covalent geometry : angle 0.81860 / 0.40 (17476) hydrogen bonds : bond 0.03938 / 2.60 ( 787) hydrogen bonds : angle 4.60906 / 3.30 ( 2346) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8437 (tpp) cc_final: 0.7999 (ttp) REVERT: A 209 MET cc_start: 0.6706 (mpp) cc_final: 0.6200 (mpp) REVERT: A 210 MET cc_start: 0.8041 (mtp) cc_final: 0.7728 (ttm) REVERT: B 61 MET cc_start: 0.8550 (mtp) cc_final: 0.8051 (mtp) REVERT: B 205 MET cc_start: 0.8238 (mtm) cc_final: 0.7596 (mtm) REVERT: C 134 LEU cc_start: 0.9388 (tp) cc_final: 0.9010 (tp) REVERT: C 168 ARG cc_start: 0.8507 (ptt90) cc_final: 0.8021 (ptp-170) REVERT: F 14 HIS cc_start: 0.7181 (m-70) cc_final: 0.6755 (m90) REVERT: F 207 MET cc_start: 0.7771 (tpp) cc_final: 0.7560 (tpp) REVERT: F 218 PHE cc_start: 0.6510 (m-80) cc_final: 0.6136 (m-80) REVERT: F 233 MET cc_start: 0.7549 (mmm) cc_final: 0.7251 (mmm) REVERT: G 15 LYS cc_start: 0.8732 (mttt) cc_final: 0.8431 (tmtt) REVERT: G 87 ILE cc_start: 0.8756 (mm) cc_final: 0.8492 (mt) REVERT: H 30 ILE cc_start: 0.9180 (mm) cc_final: 0.8974 (tp) REVERT: H 45 ASN cc_start: 0.7327 (p0) cc_final: 0.6933 (p0) REVERT: H 69 MET cc_start: 0.8517 (mtt) cc_final: 0.8004 (ttm) REVERT: I 29 LEU cc_start: 0.7963 (mm) cc_final: 0.7585 (mt) REVERT: I 69 MET cc_start: 0.8099 (mtt) cc_final: 0.7727 (ttm) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.0878 time to fit residues: 35.1051 Evaluate side-chains 210 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 114 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 130 optimal weight: 0.0670 chunk 151 optimal weight: 0.9980 chunk 90 optimal weight: 0.0870 chunk 72 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 137 optimal weight: 0.6980 chunk 12 optimal weight: 10.0000 chunk 145 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.089303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.074548 restraints weight = 43768.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.076437 restraints weight = 26362.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.077774 restraints weight = 18430.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.078685 restraints weight = 14324.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.078940 restraints weight = 12051.379| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.6786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12820 Z= 0.145 Angle : 0.810 10.172 17476 Z= 0.394 Chirality : 0.045 0.210 2189 Planarity : 0.006 0.073 2130 Dihedral : 5.616 26.933 1695 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.15 % Favored : 92.29 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: 0.11 (0.22), residues: 1609 helix: 1.03 (0.15), residues: 1216 sheet: None (None), residues: 0 loop : -3.04 (0.33), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 75 TYR 0.018 0.001 TYR C 174 PHE 0.045 0.002 PHE D 64 TRP 0.017 0.002 TRP F 18 HIS 0.018 0.003 HIS F 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (12820) covalent geometry : angle 0.80997 / 0.39 (17476) hydrogen bonds : bond 0.03732 / 2.47 ( 787) hydrogen bonds : angle 4.51503 / 3.22 ( 2346) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1917.83 seconds wall clock time: 33 minutes 57.82 seconds (2037.82 seconds total)