Starting phenix.real_space_refine on Wed Jul 30 13:15:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6f2d_4173/07_2025/6f2d_4173.cif Found real_map, /net/cci-nas-00/data/ceres_data/6f2d_4173/07_2025/6f2d_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_4173/07_2025/6f2d_4173.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6f2d_4173/07_2025/6f2d_4173.map" model { file = "/net/cci-nas-00/data/ceres_data/6f2d_4173/07_2025/6f2d_4173.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6f2d_4173/07_2025/6f2d_4173.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.64, per 1000 atoms: 0.61 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: 3.37 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.27 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: 3.89 Time building geometry restraints manager: 4.03 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.820 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.800 ------------------------------------------------------------------------------- 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 : 26.29 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.023 0.003 TRP F 18 HIS 0.011 0.004 HIS F 14 PHE 0.031 0.003 PHE A 64 TYR 0.029 0.004 TYR C 174 ARG 0.011 0.002 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.16552 ( 787) hydrogen bonds : angle 11.04719 ( 2346) covalent geometry : bond 0.00989 (12820) covalent geometry : angle 1.19431 (17476) *********************** 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 : 1.481 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: 0.7553 (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: 0.6977 (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: 0.6193 (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: 0.7396 (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: 0.2697 time to fit residues: 169.1782 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 : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 80 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 74 optimal weight: 0.2980 chunk 91 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3676 r_free = 0.3676 target = 0.086802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.072978 restraints weight = 42344.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.074751 restraints weight = 25932.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.076010 restraints weight = 18234.014| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12820 Z= 0.196 Angle : 0.896 8.938 17476 Z= 0.450 Chirality : 0.048 0.277 2189 Planarity : 0.007 0.078 2130 Dihedral : 7.290 29.660 1695 Min Nonbonded Distance : 2.439 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.19), residues: 1609 helix: -1.14 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : -3.90 (0.26), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 232 HIS 0.006 0.002 HIS F 143 PHE 0.037 0.002 PHE D 64 TYR 0.020 0.002 TYR A 109 ARG 0.005 0.001 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.05696 ( 787) hydrogen bonds : angle 6.03391 ( 2346) covalent geometry : bond 0.00406 (12820) covalent geometry : angle 0.89551 (17476) *********************** 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 367 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 1.342 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 49 THR cc_start: 0.7755 (m) cc_final: 0.7330 (p) REVERT: A 53 PHE cc_start: 0.6833 (m-80) cc_final: 0.6302 (m-80) REVERT: B 54 LEU cc_start: 0.7754 (tp) cc_final: 0.7323 (tp) REVERT: B 124 GLN cc_start: 0.7837 (mm-40) cc_final: 0.7453 (mt0) REVERT: B 129 LYS cc_start: 0.8886 (tttm) cc_final: 0.8643 (mtmm) REVERT: C 49 THR cc_start: 0.7937 (m) cc_final: 0.7585 (p) REVERT: C 128 ASP cc_start: 0.8202 (m-30) cc_final: 0.7661 (t0) REVERT: C 129 LYS cc_start: 0.8571 (tttm) cc_final: 0.8156 (ttpp) REVERT: C 155 ASN cc_start: 0.7295 (m-40) cc_final: 0.7060 (p0) REVERT: C 168 ARG cc_start: 0.8515 (ptt90) cc_final: 0.8076 (ptp-170) REVERT: D 54 LEU cc_start: 0.8930 (tp) cc_final: 0.8662 (pp) REVERT: E 163 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7125 (pm20) REVERT: E 174 TYR cc_start: 0.8196 (t80) cc_final: 0.7790 (t80) REVERT: F 22 ARG cc_start: 0.7668 (mtt180) cc_final: 0.7396 (ttm-80) REVERT: G 7 MET cc_start: 0.8609 (mmm) cc_final: 0.8275 (mmp) REVERT: G 15 LYS cc_start: 0.8415 (mttt) cc_final: 0.8071 (tmtt) REVERT: G 87 ILE cc_start: 0.8583 (mm) cc_final: 0.8314 (mt) REVERT: H 11 THR cc_start: 0.8698 (p) cc_final: 0.8485 (t) REVERT: H 69 MET cc_start: 0.8449 (mtt) cc_final: 0.8004 (ttm) REVERT: J 9 MET cc_start: 0.9009 (mmp) cc_final: 0.8652 (mmm) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.2294 time to fit residues: 121.1561 Evaluate side-chains 241 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 53 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 153 optimal weight: 0.3980 chunk 23 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 111 optimal weight: 0.3980 overall best weight: 2.5184 ------------------------------------------------------------------------------- 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 39 GLN ** 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 = 0.3665 r_free = 0.3665 target = 0.086436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.072008 restraints weight = 43652.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.073794 restraints weight = 26653.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.075069 restraints weight = 18855.938| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4565 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= 0.185 Angle : 0.834 9.280 17476 Z= 0.414 Chirality : 0.047 0.256 2189 Planarity : 0.007 0.075 2130 Dihedral : 6.848 28.129 1695 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.68 % Allowed : 8.39 % Favored : 90.93 % Rotamer: Outliers : 0.07 % Allowed : 3.42 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.20), residues: 1609 helix: -0.03 (0.15), residues: 1190 sheet: None (None), residues: 0 loop : -3.72 (0.26), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 68 HIS 0.008 0.001 HIS F 14 PHE 0.034 0.002 PHE D 64 TYR 0.022 0.002 TYR C 174 ARG 0.007 0.001 ARG A 75 Details of bonding type rmsd hydrogen bonds : bond 0.04872 ( 787) hydrogen bonds : angle 5.41601 ( 2346) covalent geometry : bond 0.00408 (12820) covalent geometry : angle 0.83440 (17476) *********************** 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 310 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 309 time to evaluate : 1.509 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: 0.7802 (m) cc_final: 0.7448 (p) REVERT: A 53 PHE cc_start: 0.6993 (m-80) cc_final: 0.6601 (m-80) REVERT: B 95 PHE cc_start: 0.7827 (m-10) cc_final: 0.7378 (m-80) REVERT: C 128 ASP cc_start: 0.8234 (m-30) cc_final: 0.7830 (t0) REVERT: C 129 LYS cc_start: 0.8524 (tttm) cc_final: 0.8201 (ttpp) REVERT: C 155 ASN cc_start: 0.7316 (m-40) cc_final: 0.7046 (p0) REVERT: D 210 MET cc_start: 0.7083 (pmm) cc_final: 0.6456 (pmm) REVERT: D 211 MET cc_start: 0.7777 (mmt) cc_final: 0.7294 (mmt) REVERT: E 163 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7149 (pm20) REVERT: E 174 TYR cc_start: 0.8110 (t80) cc_final: 0.7749 (t80) REVERT: F 36 ARG cc_start: 0.7539 (mtt90) cc_final: 0.7245 (mtm-85) REVERT: G 7 MET cc_start: 0.8626 (mmm) cc_final: 0.8280 (mmp) REVERT: G 15 LYS cc_start: 0.8390 (mttt) cc_final: 0.8176 (tmtt) REVERT: G 87 ILE cc_start: 0.8597 (mm) cc_final: 0.8283 (mt) REVERT: H 69 MET cc_start: 0.8558 (mtt) cc_final: 0.8054 (ttm) REVERT: I 29 LEU cc_start: 0.8139 (mm) cc_final: 0.7873 (mm) outliers start: 1 outliers final: 0 residues processed: 310 average time/residue: 0.2282 time to fit residues: 102.8117 Evaluate side-chains 223 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 152 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 153 optimal weight: 9.9990 chunk 140 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 chunk 111 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 ASN D 155 ASN E 132 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.084058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.069504 restraints weight = 44196.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.071281 restraints weight = 26991.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.072540 restraints weight = 18927.754| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12820 Z= 0.225 Angle : 0.866 9.695 17476 Z= 0.430 Chirality : 0.048 0.197 2189 Planarity : 0.007 0.072 2130 Dihedral : 6.735 29.380 1695 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.75 % Allowed : 8.33 % Favored : 90.93 % Rotamer: Outliers : 0.07 % Allowed : 4.00 % Favored : 95.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.20), residues: 1609 helix: 0.06 (0.14), residues: 1206 sheet: None (None), residues: 0 loop : -3.79 (0.26), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 72 HIS 0.006 0.001 HIS F 14 PHE 0.034 0.002 PHE D 64 TYR 0.023 0.002 TYR C 174 ARG 0.010 0.001 ARG A 75 Details of bonding type rmsd hydrogen bonds : bond 0.04890 ( 787) hydrogen bonds : angle 5.29762 ( 2346) covalent geometry : bond 0.00514 (12820) covalent geometry : angle 0.86551 (17476) *********************** 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 290 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 289 time to evaluate : 1.445 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: 0.7767 (m) cc_final: 0.7412 (p) REVERT: A 60 MET cc_start: 0.8837 (mmm) cc_final: 0.8611 (mpp) REVERT: A 139 LEU cc_start: 0.9237 (tp) cc_final: 0.8984 (pp) REVERT: B 95 PHE cc_start: 0.7655 (m-10) cc_final: 0.7369 (m-80) REVERT: B 123 MET cc_start: 0.8094 (mtt) cc_final: 0.7877 (mtp) REVERT: C 134 LEU cc_start: 0.9361 (tp) cc_final: 0.9140 (tt) REVERT: C 155 ASN cc_start: 0.7316 (m-40) cc_final: 0.7055 (p0) REVERT: D 210 MET cc_start: 0.7177 (pmm) cc_final: 0.6374 (pmm) REVERT: E 163 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7109 (pm20) REVERT: F 36 ARG cc_start: 0.7631 (mtt90) cc_final: 0.7306 (mtm-85) REVERT: F 101 PHE cc_start: 0.7738 (m-80) cc_final: 0.7064 (m-80) REVERT: F 129 MET cc_start: 0.9184 (mpp) cc_final: 0.8983 (mpp) REVERT: F 233 MET cc_start: 0.7539 (mmm) cc_final: 0.7224 (mmm) REVERT: G 7 MET cc_start: 0.8688 (mmm) cc_final: 0.8386 (mmm) REVERT: G 15 LYS cc_start: 0.8489 (mttt) cc_final: 0.8275 (tmtt) REVERT: G 87 ILE cc_start: 0.8591 (mm) cc_final: 0.8373 (mt) REVERT: H 69 MET cc_start: 0.8633 (mtt) cc_final: 0.8141 (ttm) REVERT: I 29 LEU cc_start: 0.8027 (mm) cc_final: 0.7776 (mm) REVERT: I 45 ASN cc_start: 0.8468 (p0) cc_final: 0.8211 (p0) outliers start: 1 outliers final: 0 residues processed: 290 average time/residue: 0.2173 time to fit residues: 93.4500 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 : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 122 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 70 optimal weight: 0.0070 chunk 44 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 52 optimal weight: 0.1980 chunk 146 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.088555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.074050 restraints weight = 42816.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.075952 restraints weight = 26263.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.077326 restraints weight = 18222.443| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.5589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 12820 Z= 0.154 Angle : 0.808 9.928 17476 Z= 0.394 Chirality : 0.045 0.161 2189 Planarity : 0.006 0.070 2130 Dihedral : 6.284 27.668 1695 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.75 % Allowed : 7.27 % Favored : 91.98 % Rotamer: Outliers : 0.15 % Allowed : 2.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.21), residues: 1609 helix: 0.54 (0.15), residues: 1212 sheet: None (None), residues: 0 loop : -3.35 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP F 72 HIS 0.003 0.001 HIS F 14 PHE 0.044 0.002 PHE D 64 TYR 0.020 0.001 TYR C 174 ARG 0.010 0.001 ARG A 75 Details of bonding type rmsd hydrogen bonds : bond 0.04053 ( 787) hydrogen bonds : angle 4.79912 ( 2346) covalent geometry : bond 0.00316 (12820) covalent geometry : angle 0.80775 (17476) *********************** 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 322 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 320 time to evaluate : 1.387 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: A 49 THR cc_start: 0.7722 (m) cc_final: 0.7468 (p) REVERT: B 95 PHE cc_start: 0.7803 (m-10) cc_final: 0.7455 (m-80) REVERT: B 125 GLU cc_start: 0.7368 (mm-30) cc_final: 0.6855 (mm-30) REVERT: C 114 GLN cc_start: 0.8149 (tt0) cc_final: 0.7814 (tm-30) REVERT: C 168 ARG cc_start: 0.8478 (ptt90) cc_final: 0.7931 (ptp-170) REVERT: D 118 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7887 (mp0) REVERT: E 167 MET cc_start: 0.7611 (pmm) cc_final: 0.7207 (pmm) REVERT: F 14 HIS cc_start: 0.6356 (m-70) cc_final: 0.6116 (m-70) REVERT: F 185 MET cc_start: 0.8388 (mtm) cc_final: 0.8163 (mtm) REVERT: F 233 MET cc_start: 0.7453 (mmm) cc_final: 0.7146 (mmm) REVERT: G 7 MET cc_start: 0.8551 (mmm) cc_final: 0.8249 (mmm) REVERT: G 15 LYS cc_start: 0.8526 (mttt) cc_final: 0.8295 (tmtt) REVERT: G 87 ILE cc_start: 0.8737 (mm) cc_final: 0.8397 (mt) REVERT: H 69 MET cc_start: 0.8528 (mtt) cc_final: 0.8047 (ttm) REVERT: I 29 LEU cc_start: 0.7892 (mm) cc_final: 0.7618 (mm) outliers start: 2 outliers final: 0 residues processed: 321 average time/residue: 0.2202 time to fit residues: 103.6905 Evaluate side-chains 236 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 128 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 125 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 HIS I 45 ASN ** 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 = 0.3631 r_free = 0.3631 target = 0.084893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.070493 restraints weight = 45476.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.072297 restraints weight = 27558.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.073546 restraints weight = 19315.238| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.5736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 12820 Z= 0.205 Angle : 0.848 9.889 17476 Z= 0.414 Chirality : 0.046 0.203 2189 Planarity : 0.007 0.126 2130 Dihedral : 6.259 27.378 1695 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.75 % Allowed : 7.96 % Favored : 91.30 % Rotamer: Outliers : 0.15 % Allowed : 2.62 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.21), residues: 1609 helix: 0.46 (0.14), residues: 1225 sheet: None (None), residues: 0 loop : -3.63 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 72 HIS 0.004 0.001 HIS F 14 PHE 0.044 0.002 PHE D 64 TYR 0.023 0.002 TYR C 174 ARG 0.016 0.001 ARG E 75 Details of bonding type rmsd hydrogen bonds : bond 0.04366 ( 787) hydrogen bonds : angle 4.92031 ( 2346) covalent geometry : bond 0.00471 (12820) covalent geometry : angle 0.84780 (17476) *********************** 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 282 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 280 time to evaluate : 1.313 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: 0.7772 (m) cc_final: 0.7496 (p) REVERT: A 60 MET cc_start: 0.8579 (mpp) cc_final: 0.8372 (mpp) REVERT: A 209 MET cc_start: 0.6744 (mpp) cc_final: 0.6211 (mpp) REVERT: B 95 PHE cc_start: 0.7804 (m-10) cc_final: 0.7340 (m-80) REVERT: B 125 GLU cc_start: 0.7545 (mm-30) cc_final: 0.6997 (mm-30) REVERT: C 61 MET cc_start: 0.8370 (ptp) cc_final: 0.7934 (ptp) REVERT: C 114 GLN cc_start: 0.8186 (tt0) cc_final: 0.7703 (tm-30) REVERT: C 168 ARG cc_start: 0.8665 (ptt90) cc_final: 0.8071 (ptp-170) REVERT: D 211 MET cc_start: 0.7493 (mmt) cc_final: 0.6579 (tpp) REVERT: F 101 PHE cc_start: 0.7900 (m-80) cc_final: 0.7685 (m-80) REVERT: F 233 MET cc_start: 0.7623 (mmm) cc_final: 0.6853 (mmm) REVERT: G 7 MET cc_start: 0.8598 (mmm) cc_final: 0.8090 (mmt) REVERT: G 15 LYS cc_start: 0.8597 (mttt) cc_final: 0.8380 (tmtt) REVERT: G 87 ILE cc_start: 0.8779 (mm) cc_final: 0.8482 (mt) REVERT: H 69 MET cc_start: 0.8613 (mtt) cc_final: 0.8062 (ttm) REVERT: I 29 LEU cc_start: 0.7947 (mm) cc_final: 0.7737 (mm) outliers start: 2 outliers final: 0 residues processed: 280 average time/residue: 0.2147 time to fit residues: 88.5863 Evaluate side-chains 212 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 70 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 47 optimal weight: 20.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 GLN F 77 GLN F 89 GLN I 45 ASN ** 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 = 0.3590 r_free = 0.3590 target = 0.082965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.068588 restraints weight = 46367.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.070310 restraints weight = 28617.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.071542 restraints weight = 20157.237| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.5854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12820 Z= 0.236 Angle : 0.887 9.289 17476 Z= 0.438 Chirality : 0.049 0.266 2189 Planarity : 0.007 0.076 2130 Dihedral : 6.374 28.142 1695 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.81 % Allowed : 8.39 % Favored : 90.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.21), residues: 1609 helix: 0.34 (0.14), residues: 1226 sheet: None (None), residues: 0 loop : -3.47 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 232 HIS 0.014 0.003 HIS F 14 PHE 0.049 0.002 PHE D 64 TYR 0.027 0.002 TYR E 174 ARG 0.013 0.001 ARG A 75 Details of bonding type rmsd hydrogen bonds : bond 0.04663 ( 787) hydrogen bonds : angle 5.06272 ( 2346) covalent geometry : bond 0.00543 (12820) covalent geometry : angle 0.88712 (17476) *********************** 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 272 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 270 time to evaluate : 1.496 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: 0.7882 (m) cc_final: 0.7680 (p) REVERT: A 209 MET cc_start: 0.6871 (mpp) cc_final: 0.6468 (mpp) REVERT: B 138 MET cc_start: 0.8632 (mmt) cc_final: 0.8029 (mmt) REVERT: B 205 MET cc_start: 0.7772 (mtp) cc_final: 0.6720 (mtp) REVERT: C 61 MET cc_start: 0.8508 (ptp) cc_final: 0.8052 (mtm) REVERT: C 114 GLN cc_start: 0.8213 (tt0) cc_final: 0.7865 (tm-30) REVERT: C 168 ARG cc_start: 0.8804 (ptt90) cc_final: 0.8208 (ptp-170) REVERT: C 230 ASP cc_start: 0.7546 (t0) cc_final: 0.6650 (t0) REVERT: D 118 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7810 (mp0) REVERT: D 211 MET cc_start: 0.7025 (mmt) cc_final: 0.6682 (tpp) REVERT: E 210 MET cc_start: 0.7774 (pmm) cc_final: 0.7398 (pmm) REVERT: F 185 MET cc_start: 0.8657 (mtm) cc_final: 0.8414 (mtm) REVERT: F 233 MET cc_start: 0.7533 (mmm) cc_final: 0.7220 (mmm) REVERT: G 15 LYS cc_start: 0.8714 (mttt) cc_final: 0.8464 (tmtt) REVERT: H 30 ILE cc_start: 0.9218 (mm) cc_final: 0.8975 (tp) REVERT: H 69 MET cc_start: 0.8721 (mtt) cc_final: 0.8136 (ttm) REVERT: I 29 LEU cc_start: 0.8036 (mm) cc_final: 0.7742 (mm) outliers start: 2 outliers final: 0 residues processed: 272 average time/residue: 0.2254 time to fit residues: 90.0829 Evaluate side-chains 208 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 25 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 38 optimal weight: 0.7980 chunk 67 optimal weight: 0.0980 chunk 54 optimal weight: 0.0570 chunk 151 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 111 optimal weight: 0.0170 chunk 132 optimal weight: 7.9990 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 ASN C 160 GLN C 233 GLN E 124 GLN F 143 HIS I 45 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.087750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.072860 restraints weight = 44557.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.074708 restraints weight = 27304.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.076012 restraints weight = 19253.282| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.6295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 12820 Z= 0.154 Angle : 0.809 8.029 17476 Z= 0.396 Chirality : 0.045 0.225 2189 Planarity : 0.006 0.076 2130 Dihedral : 6.015 27.316 1695 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.68 % Allowed : 6.84 % Favored : 92.48 % Rotamer: Outliers : 0.07 % Allowed : 0.73 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.21), residues: 1609 helix: 0.66 (0.15), residues: 1231 sheet: None (None), residues: 0 loop : -3.33 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 232 HIS 0.014 0.002 HIS F 14 PHE 0.043 0.002 PHE D 64 TYR 0.018 0.001 TYR E 174 ARG 0.011 0.001 ARG C 140 Details of bonding type rmsd hydrogen bonds : bond 0.03958 ( 787) hydrogen bonds : angle 4.67256 ( 2346) covalent geometry : bond 0.00326 (12820) covalent geometry : angle 0.80862 (17476) *********************** 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 300 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 299 time to evaluate : 1.347 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: A 49 THR cc_start: 0.7857 (m) cc_final: 0.7597 (p) REVERT: A 53 PHE cc_start: 0.7030 (m-80) cc_final: 0.6818 (m-80) REVERT: A 209 MET cc_start: 0.6643 (mpp) cc_final: 0.6309 (mpp) REVERT: B 61 MET cc_start: 0.8719 (mtp) cc_final: 0.8417 (mtp) REVERT: B 205 MET cc_start: 0.7284 (mtp) cc_final: 0.5907 (mtp) REVERT: C 114 GLN cc_start: 0.8188 (tt0) cc_final: 0.7783 (tm-30) REVERT: C 168 ARG cc_start: 0.8567 (ptt90) cc_final: 0.8025 (ptp-170) REVERT: C 210 MET cc_start: 0.7995 (pmm) cc_final: 0.7723 (pmm) REVERT: D 118 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7723 (mp0) REVERT: D 211 MET cc_start: 0.7018 (mmt) cc_final: 0.6716 (tpp) REVERT: F 185 MET cc_start: 0.8411 (mtm) cc_final: 0.8183 (mtm) REVERT: G 15 LYS cc_start: 0.8685 (mttt) cc_final: 0.8426 (tmtt) REVERT: G 87 ILE cc_start: 0.8660 (mm) cc_final: 0.8423 (mt) REVERT: H 30 ILE cc_start: 0.9179 (mm) cc_final: 0.8971 (tp) REVERT: H 69 MET cc_start: 0.8611 (mtt) cc_final: 0.8108 (ttm) REVERT: I 29 LEU cc_start: 0.7959 (mm) cc_final: 0.7675 (mm) outliers start: 1 outliers final: 1 residues processed: 299 average time/residue: 0.2350 time to fit residues: 102.2511 Evaluate side-chains 217 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 121 optimal weight: 0.6980 chunk 128 optimal weight: 5.9990 chunk 143 optimal weight: 0.0970 chunk 108 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 chunk 12 optimal weight: 0.0270 chunk 10 optimal weight: 0.9980 chunk 140 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 160 GLN F 89 GLN I 45 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.088331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.073863 restraints weight = 43110.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.075782 restraints weight = 26069.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.077085 restraints weight = 18096.881| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.6564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12820 Z= 0.152 Angle : 0.807 8.061 17476 Z= 0.396 Chirality : 0.045 0.256 2189 Planarity : 0.006 0.072 2130 Dihedral : 5.774 27.103 1695 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.75 % Allowed : 7.27 % Favored : 91.98 % Rotamer: Outliers : 0.07 % Allowed : 0.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.22), residues: 1609 helix: 0.91 (0.15), residues: 1224 sheet: None (None), residues: 0 loop : -3.06 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 18 HIS 0.017 0.003 HIS F 14 PHE 0.046 0.002 PHE D 64 TYR 0.033 0.002 TYR E 174 ARG 0.011 0.001 ARG C 140 Details of bonding type rmsd hydrogen bonds : bond 0.03794 ( 787) hydrogen bonds : angle 4.55551 ( 2346) covalent geometry : bond 0.00318 (12820) covalent geometry : angle 0.80687 (17476) *********************** 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 284 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 283 time to evaluate : 1.418 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: symmetry clash REVERT: A 49 THR cc_start: 0.7977 (m) cc_final: 0.7759 (p) REVERT: A 53 PHE cc_start: 0.6923 (m-80) cc_final: 0.6716 (m-80) REVERT: A 86 ASN cc_start: 0.8138 (m-40) cc_final: 0.7781 (t0) REVERT: A 209 MET cc_start: 0.6994 (mpp) cc_final: 0.6762 (mpp) REVERT: B 205 MET cc_start: 0.7957 (mtp) cc_final: 0.7224 (mtt) REVERT: C 114 GLN cc_start: 0.8184 (tt0) cc_final: 0.7762 (tm-30) REVERT: C 168 ARG cc_start: 0.8428 (ptt90) cc_final: 0.7923 (ptp-170) REVERT: C 211 MET cc_start: 0.6606 (mtp) cc_final: 0.6132 (mtp) REVERT: D 211 MET cc_start: 0.7424 (mmt) cc_final: 0.6713 (tpp) REVERT: F 129 MET cc_start: 0.9085 (mpp) cc_final: 0.8868 (mpp) REVERT: F 185 MET cc_start: 0.8478 (mtm) cc_final: 0.8226 (mtm) REVERT: F 207 MET cc_start: 0.7812 (tpp) cc_final: 0.7604 (tpp) REVERT: F 233 MET cc_start: 0.7674 (mmm) cc_final: 0.7356 (mmm) REVERT: G 15 LYS cc_start: 0.8701 (mttt) cc_final: 0.8433 (tmtt) REVERT: H 69 MET cc_start: 0.8559 (mtt) cc_final: 0.8081 (ttm) REVERT: I 29 LEU cc_start: 0.8014 (mm) cc_final: 0.7672 (mm) outliers start: 1 outliers final: 0 residues processed: 283 average time/residue: 0.2161 time to fit residues: 90.3662 Evaluate side-chains 211 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 83 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 10 optimal weight: 0.0070 chunk 128 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 overall best weight: 3.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 143 HIS I 45 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.085326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.070755 restraints weight = 45040.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.072488 restraints weight = 27706.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.073712 restraints weight = 19600.830| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.6492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12820 Z= 0.182 Angle : 0.831 10.631 17476 Z= 0.410 Chirality : 0.047 0.283 2189 Planarity : 0.006 0.074 2130 Dihedral : 5.869 25.457 1695 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.96 % Favored : 91.42 % Rotamer: Outliers : 0.07 % Allowed : 0.73 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.21), residues: 1609 helix: 0.78 (0.15), residues: 1235 sheet: None (None), residues: 0 loop : -3.30 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 68 HIS 0.018 0.003 HIS F 14 PHE 0.049 0.002 PHE D 64 TYR 0.027 0.002 TYR E 174 ARG 0.007 0.001 ARG C 140 Details of bonding type rmsd hydrogen bonds : bond 0.04176 ( 787) hydrogen bonds : angle 4.70259 ( 2346) covalent geometry : bond 0.00420 (12820) covalent geometry : angle 0.83074 (17476) ********************** 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 263 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 262 time to evaluate : 1.529 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: 0.7925 (m) cc_final: 0.7645 (p) REVERT: A 53 PHE cc_start: 0.6928 (m-80) cc_final: 0.6612 (m-10) REVERT: A 210 MET cc_start: 0.8219 (mtp) cc_final: 0.7818 (mtp) REVERT: A 211 MET cc_start: 0.7543 (mmm) cc_final: 0.7181 (mmm) REVERT: B 205 MET cc_start: 0.8212 (mtp) cc_final: 0.7356 (mtt) REVERT: B 211 MET cc_start: 0.8264 (mpp) cc_final: 0.7651 (mpp) REVERT: C 114 GLN cc_start: 0.8209 (tt0) cc_final: 0.7891 (tm-30) REVERT: C 168 ARG cc_start: 0.8564 (ptt90) cc_final: 0.8078 (ptp-170) REVERT: D 211 MET cc_start: 0.7443 (mmt) cc_final: 0.6720 (tpp) REVERT: F 17 PHE cc_start: 0.7275 (m-10) cc_final: 0.7072 (m-10) REVERT: F 101 PHE cc_start: 0.7615 (m-80) cc_final: 0.7212 (m-80) REVERT: F 129 MET cc_start: 0.9129 (mpp) cc_final: 0.8753 (mpp) REVERT: F 185 MET cc_start: 0.8540 (mtm) cc_final: 0.8319 (mtm) REVERT: F 218 PHE cc_start: 0.6718 (m-80) cc_final: 0.6250 (m-80) REVERT: H 69 MET cc_start: 0.8555 (mtt) cc_final: 0.8093 (ttm) outliers start: 1 outliers final: 1 residues processed: 263 average time/residue: 0.2203 time to fit residues: 85.6898 Evaluate side-chains 202 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 201 time to evaluate : 1.515 ------------------------------------------------------------------------------- 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: 0.9980 chunk 69 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 52 optimal weight: 0.0040 chunk 78 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 4 optimal weight: 0.0670 overall best weight: 0.5330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 233 GLN I 45 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.088418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.073852 restraints weight = 44448.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.075770 restraints weight = 26870.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.077068 restraints weight = 18604.772| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.6839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12820 Z= 0.147 Angle : 0.813 9.895 17476 Z= 0.396 Chirality : 0.046 0.309 2189 Planarity : 0.006 0.071 2130 Dihedral : 5.662 26.427 1695 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.40 % Favored : 91.98 % Rotamer: Outliers : 0.07 % Allowed : 0.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.22), residues: 1609 helix: 0.98 (0.15), residues: 1227 sheet: None (None), residues: 0 loop : -3.03 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 68 HIS 0.019 0.003 HIS F 14 PHE 0.046 0.002 PHE D 64 TYR 0.036 0.002 TYR E 174 ARG 0.008 0.001 ARG C 140 Details of bonding type rmsd hydrogen bonds : bond 0.03759 ( 787) hydrogen bonds : angle 4.57723 ( 2346) covalent geometry : bond 0.00304 (12820) covalent geometry : angle 0.81346 (17476) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3977.00 seconds wall clock time: 70 minutes 24.03 seconds (4224.03 seconds total)