Starting phenix.real_space_refine on Fri Mar 15 18:56:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f2d_4173/03_2024/6f2d_4173.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f2d_4173/03_2024/6f2d_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f2d_4173/03_2024/6f2d_4173.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f2d_4173/03_2024/6f2d_4173.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f2d_4173/03_2024/6f2d_4173.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f2d_4173/03_2024/6f2d_4173.pdb" } 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 Residue "E TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 6.24, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 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: 5.39 Conformation dependent library (CDL) restraints added in 2.2 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: 1.06 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: 3.40 Time building geometry restraints manager: 5.79 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: 95.91 - 103.57: 336 103.57 - 111.23: 5811 111.23 - 118.89: 4760 118.89 - 126.55: 6417 126.55 - 134.21: 152 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 2.440 nonbonded pdb=" O THR A 62 " pdb=" OH TYR A 174 " model vdw 2.037 2.440 nonbonded pdb=" O LEU C 94 " pdb=" OG1 THR C 97 " model vdw 2.044 2.440 nonbonded pdb=" O THR C 62 " pdb=" OH TYR C 174 " model vdw 2.045 2.440 nonbonded pdb=" O THR C 49 " pdb=" OG1 THR C 52 " model vdw 2.074 2.440 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.120 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 35.060 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.090 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.090 ------------------------------------------------------------------------------- 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= 0.641 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 *********************** 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 fitting. rotamer outliers: 7 poor density : 448 time to evaluate : 1.383 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: 0.2621 time to fit residues: 163.1724 Evaluate side-chains 250 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 247 time to evaluate : 1.457 ------------------------------------------------------------------------------- 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: 0.9990 chunk 118 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 0.0370 chunk 142 optimal weight: 4.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 GLN ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 HIS J 39 GLN ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12820 Z= 0.282 Angle : 0.899 9.328 17476 Z= 0.448 Chirality : 0.047 0.262 2189 Planarity : 0.007 0.079 2130 Dihedral : 7.409 29.173 1695 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.38 % Favored : 90.18 % Rotamer: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % 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: -3.01 (0.19), residues: 1609 helix: -1.26 (0.13), residues: 1195 sheet: None (None), residues: 0 loop : -3.91 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 232 HIS 0.008 0.002 HIS F 14 PHE 0.036 0.002 PHE D 64 TYR 0.021 0.002 TYR A 109 ARG 0.007 0.001 ARG B 75 *********************** 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 344 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 344 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 THR cc_start: 0.7289 (m) cc_final: 0.6962 (p) REVERT: A 53 PHE cc_start: 0.6843 (m-80) cc_final: 0.6580 (m-80) REVERT: A 60 MET cc_start: 0.9238 (mmm) cc_final: 0.8940 (mmt) REVERT: A 152 ARG cc_start: 0.8591 (tmm-80) cc_final: 0.8182 (tmm-80) REVERT: A 205 MET cc_start: 0.8532 (mmt) cc_final: 0.8097 (tpt) REVERT: A 209 MET cc_start: 0.7717 (mmp) cc_final: 0.7158 (mmm) REVERT: B 54 LEU cc_start: 0.8151 (tp) cc_final: 0.7890 (tp) REVERT: B 73 LEU cc_start: 0.8711 (mp) cc_final: 0.8453 (mp) REVERT: B 80 THR cc_start: 0.7193 (p) cc_final: 0.6823 (p) REVERT: B 124 GLN cc_start: 0.8352 (mm-40) cc_final: 0.7744 (mt0) REVERT: B 128 ASP cc_start: 0.8847 (m-30) cc_final: 0.8513 (t70) REVERT: B 129 LYS cc_start: 0.8939 (tttm) cc_final: 0.8566 (mtmm) REVERT: C 49 THR cc_start: 0.8290 (m) cc_final: 0.8003 (p) REVERT: C 128 ASP cc_start: 0.8231 (m-30) cc_final: 0.7700 (t0) REVERT: C 135 ARG cc_start: 0.9316 (mmt90) cc_final: 0.9014 (mmm-85) REVERT: C 209 MET cc_start: 0.7918 (mmp) cc_final: 0.7542 (mmm) REVERT: C 230 ASP cc_start: 0.8150 (t0) cc_final: 0.7930 (t0) REVERT: C 244 TYR cc_start: 0.7954 (t80) cc_final: 0.7754 (t80) REVERT: D 95 PHE cc_start: 0.8708 (m-10) cc_final: 0.8442 (m-80) REVERT: D 135 ARG cc_start: 0.8516 (mtt-85) cc_final: 0.8289 (mtp85) REVERT: D 211 MET cc_start: 0.6900 (mmm) cc_final: 0.6540 (mmt) REVERT: E 101 MET cc_start: 0.8787 (tpp) cc_final: 0.8583 (tpp) REVERT: E 163 GLU cc_start: 0.8523 (mt-10) cc_final: 0.7579 (pm20) REVERT: E 213 PRO cc_start: 0.8620 (Cg_endo) cc_final: 0.8395 (Cg_exo) REVERT: F 17 PHE cc_start: 0.8327 (m-10) cc_final: 0.8026 (m-10) REVERT: F 22 ARG cc_start: 0.7986 (mtt180) cc_final: 0.7412 (ttm-80) REVERT: F 36 ARG cc_start: 0.6779 (mtt-85) cc_final: 0.6400 (mtt90) REVERT: F 101 PHE cc_start: 0.8252 (m-80) cc_final: 0.7357 (m-80) REVERT: F 143 HIS cc_start: 0.8190 (m-70) cc_final: 0.7827 (m-70) REVERT: F 170 MET cc_start: 0.8778 (ttm) cc_final: 0.8405 (tpp) REVERT: G 15 LYS cc_start: 0.8487 (mttt) cc_final: 0.7961 (tmtt) REVERT: G 26 LEU cc_start: 0.9103 (mt) cc_final: 0.8902 (mt) REVERT: G 47 MET cc_start: 0.8207 (ttt) cc_final: 0.7863 (ttt) REVERT: H 46 GLU cc_start: 0.7606 (tt0) cc_final: 0.7396 (mm-30) REVERT: H 69 MET cc_start: 0.8634 (mtt) cc_final: 0.8301 (ttm) REVERT: J 1 MET cc_start: 0.7972 (ppp) cc_final: 0.7482 (ppp) REVERT: J 7 MET cc_start: 0.8168 (tpp) cc_final: 0.7800 (tpt) REVERT: J 8 MET cc_start: 0.9160 (mtp) cc_final: 0.8921 (mtp) REVERT: J 11 THR cc_start: 0.8032 (p) cc_final: 0.7685 (p) outliers start: 0 outliers final: 0 residues processed: 344 average time/residue: 0.2319 time to fit residues: 114.4501 Evaluate side-chains 246 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 0.1980 chunk 118 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 39 optimal weight: 0.6980 chunk 142 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 114 optimal weight: 0.0770 overall best weight: 1.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12820 Z= 0.220 Angle : 0.794 9.884 17476 Z= 0.392 Chirality : 0.045 0.250 2189 Planarity : 0.006 0.075 2130 Dihedral : 6.835 26.984 1695 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.68 % Allowed : 8.20 % Favored : 91.11 % Rotamer: Outliers : 0.15 % Allowed : 3.12 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.34 (0.20), residues: 1609 helix: 0.08 (0.15), residues: 1207 sheet: None (None), residues: 0 loop : -3.84 (0.26), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 72 HIS 0.006 0.001 HIS F 14 PHE 0.035 0.002 PHE D 64 TYR 0.023 0.002 TYR C 174 ARG 0.006 0.001 ARG B 75 *********************** 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 333 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 331 time to evaluate : 1.465 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: 0.7293 (m) cc_final: 0.7025 (p) REVERT: A 60 MET cc_start: 0.9224 (mmm) cc_final: 0.8962 (mmm) REVERT: A 174 TYR cc_start: 0.8364 (t80) cc_final: 0.7973 (t80) REVERT: A 205 MET cc_start: 0.8460 (mmt) cc_final: 0.8032 (tpt) REVERT: A 209 MET cc_start: 0.7791 (mmp) cc_final: 0.7044 (mmp) REVERT: A 211 MET cc_start: 0.8342 (mmm) cc_final: 0.8107 (mmm) REVERT: B 73 LEU cc_start: 0.8662 (mp) cc_final: 0.8446 (mp) REVERT: B 95 PHE cc_start: 0.8134 (m-10) cc_final: 0.7668 (m-80) REVERT: B 125 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7862 (mm-30) REVERT: B 128 ASP cc_start: 0.8999 (m-30) cc_final: 0.8532 (t70) REVERT: B 129 LYS cc_start: 0.8856 (tttm) cc_final: 0.8592 (mtmm) REVERT: C 128 ASP cc_start: 0.8333 (m-30) cc_final: 0.7921 (t0) REVERT: C 135 ARG cc_start: 0.9321 (mmt90) cc_final: 0.8956 (mmm-85) REVERT: C 168 ARG cc_start: 0.8290 (ptt90) cc_final: 0.7422 (ptp-170) REVERT: C 209 MET cc_start: 0.7873 (mmp) cc_final: 0.7592 (mmm) REVERT: C 230 ASP cc_start: 0.8271 (t0) cc_final: 0.7935 (t0) REVERT: D 95 PHE cc_start: 0.8642 (m-10) cc_final: 0.8413 (m-80) REVERT: D 113 TYR cc_start: 0.8119 (m-10) cc_final: 0.7829 (t80) REVERT: D 135 ARG cc_start: 0.8522 (mtt-85) cc_final: 0.8292 (mtt180) REVERT: D 210 MET cc_start: 0.6185 (pmm) cc_final: 0.5768 (pmm) REVERT: E 101 MET cc_start: 0.8753 (tpp) cc_final: 0.8550 (tpp) REVERT: E 163 GLU cc_start: 0.8442 (mt-10) cc_final: 0.7594 (pm20) REVERT: E 210 MET cc_start: 0.7430 (pmm) cc_final: 0.7227 (pmm) REVERT: E 213 PRO cc_start: 0.8633 (Cg_endo) cc_final: 0.8415 (Cg_exo) REVERT: F 22 ARG cc_start: 0.7954 (mtt180) cc_final: 0.7654 (ttt180) REVERT: F 36 ARG cc_start: 0.6726 (mtt-85) cc_final: 0.6388 (mtt90) REVERT: F 75 MET cc_start: 0.8777 (mpp) cc_final: 0.8550 (mpp) REVERT: F 143 HIS cc_start: 0.8143 (m-70) cc_final: 0.7828 (m-70) REVERT: F 185 MET cc_start: 0.7825 (mmm) cc_final: 0.7372 (mtt) REVERT: F 233 MET cc_start: 0.7654 (mmm) cc_final: 0.6926 (mmm) REVERT: G 7 MET cc_start: 0.8693 (mmp) cc_final: 0.7758 (mmt) REVERT: G 15 LYS cc_start: 0.8538 (mttt) cc_final: 0.8048 (tmtt) REVERT: H 46 GLU cc_start: 0.7477 (tt0) cc_final: 0.7223 (mm-30) REVERT: H 69 MET cc_start: 0.8683 (mtt) cc_final: 0.8216 (ttm) REVERT: I 29 LEU cc_start: 0.8169 (mm) cc_final: 0.7879 (mm) REVERT: J 1 MET cc_start: 0.8080 (ppp) cc_final: 0.7560 (ppp) REVERT: J 7 MET cc_start: 0.8087 (tpp) cc_final: 0.7756 (tpt) outliers start: 2 outliers final: 1 residues processed: 333 average time/residue: 0.2276 time to fit residues: 109.0789 Evaluate side-chains 237 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 236 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 141 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 chunk 151 optimal weight: 9.9990 chunk 135 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 ASN F 262 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12820 Z= 0.232 Angle : 0.779 8.507 17476 Z= 0.383 Chirality : 0.044 0.190 2189 Planarity : 0.006 0.068 2130 Dihedral : 6.528 28.252 1695 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.81 % Allowed : 7.64 % Favored : 91.55 % Rotamer: Outliers : 0.07 % Allowed : 2.25 % 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: -0.81 (0.21), residues: 1609 helix: 0.47 (0.15), residues: 1194 sheet: None (None), residues: 0 loop : -3.55 (0.26), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 72 HIS 0.012 0.002 HIS F 14 PHE 0.033 0.002 PHE D 64 TYR 0.022 0.002 TYR C 174 ARG 0.008 0.001 ARG B 75 *********************** 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 309 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 308 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 THR cc_start: 0.7304 (m) cc_final: 0.7022 (p) REVERT: A 60 MET cc_start: 0.9186 (mmm) cc_final: 0.8959 (mmm) REVERT: A 87 GLN cc_start: 0.8067 (mp10) cc_final: 0.7833 (mp10) REVERT: A 174 TYR cc_start: 0.8322 (t80) cc_final: 0.7906 (t80) REVERT: A 205 MET cc_start: 0.8485 (mmt) cc_final: 0.8046 (tpt) REVERT: A 209 MET cc_start: 0.7573 (mmp) cc_final: 0.7198 (mmp) REVERT: A 211 MET cc_start: 0.8441 (mmm) cc_final: 0.8199 (mmm) REVERT: B 73 LEU cc_start: 0.8610 (mp) cc_final: 0.8358 (mp) REVERT: B 95 PHE cc_start: 0.8121 (m-10) cc_final: 0.7619 (m-80) REVERT: B 125 GLU cc_start: 0.8330 (mm-30) cc_final: 0.7837 (mm-30) REVERT: B 128 ASP cc_start: 0.9008 (m-30) cc_final: 0.8476 (t70) REVERT: B 129 LYS cc_start: 0.8852 (tttm) cc_final: 0.8629 (mtmm) REVERT: B 209 MET cc_start: 0.8395 (mtp) cc_final: 0.8130 (mtp) REVERT: C 128 ASP cc_start: 0.8433 (m-30) cc_final: 0.8147 (t0) REVERT: C 135 ARG cc_start: 0.9360 (mmt90) cc_final: 0.8952 (mmm-85) REVERT: C 168 ARG cc_start: 0.8365 (ptt90) cc_final: 0.7550 (ptp-170) REVERT: C 209 MET cc_start: 0.8003 (mmp) cc_final: 0.7523 (mmm) REVERT: C 230 ASP cc_start: 0.8367 (t0) cc_final: 0.7997 (t0) REVERT: D 113 TYR cc_start: 0.8241 (m-10) cc_final: 0.7948 (t80) REVERT: D 135 ARG cc_start: 0.8510 (mtt-85) cc_final: 0.8293 (mtp85) REVERT: D 167 MET cc_start: 0.8516 (ptm) cc_final: 0.8271 (pmm) REVERT: D 210 MET cc_start: 0.6504 (pmm) cc_final: 0.5850 (pmm) REVERT: D 211 MET cc_start: 0.6060 (mmt) cc_final: 0.5755 (mmt) REVERT: D 230 ASP cc_start: 0.8651 (t0) cc_final: 0.8429 (t0) REVERT: E 53 PHE cc_start: 0.8091 (m-80) cc_final: 0.7883 (m-10) REVERT: E 120 LYS cc_start: 0.7517 (mppt) cc_final: 0.7137 (mmtt) REVERT: E 230 ASP cc_start: 0.8074 (t0) cc_final: 0.7808 (t0) REVERT: F 22 ARG cc_start: 0.7954 (mtt180) cc_final: 0.7626 (ttt90) REVERT: F 36 ARG cc_start: 0.6938 (mtt-85) cc_final: 0.6278 (mtm-85) REVERT: F 75 MET cc_start: 0.8756 (mpp) cc_final: 0.8515 (mtt) REVERT: F 101 PHE cc_start: 0.8520 (m-80) cc_final: 0.7700 (m-80) REVERT: F 185 MET cc_start: 0.7809 (mmm) cc_final: 0.7346 (mtt) REVERT: F 211 LEU cc_start: 0.7371 (mp) cc_final: 0.6961 (tt) REVERT: G 15 LYS cc_start: 0.8623 (mttt) cc_final: 0.8116 (tmtt) REVERT: H 7 MET cc_start: 0.8250 (tpp) cc_final: 0.8036 (mmp) REVERT: H 69 MET cc_start: 0.8663 (mtt) cc_final: 0.8214 (ttm) REVERT: I 29 LEU cc_start: 0.8095 (mm) cc_final: 0.7825 (mm) REVERT: I 44 ILE cc_start: 0.8410 (mp) cc_final: 0.8134 (pt) REVERT: J 1 MET cc_start: 0.8076 (ppp) cc_final: 0.7534 (ppp) REVERT: J 7 MET cc_start: 0.8265 (tpp) cc_final: 0.8000 (tpp) outliers start: 1 outliers final: 0 residues processed: 309 average time/residue: 0.2322 time to fit residues: 103.4504 Evaluate side-chains 231 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 86 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 112 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 51 optimal weight: 0.1980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.5422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12820 Z= 0.208 Angle : 0.765 8.547 17476 Z= 0.374 Chirality : 0.043 0.184 2189 Planarity : 0.006 0.065 2130 Dihedral : 6.235 28.253 1695 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.81 % Allowed : 7.33 % Favored : 91.86 % 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: -0.29 (0.21), residues: 1609 helix: 0.78 (0.15), residues: 1196 sheet: None (None), residues: 0 loop : -3.14 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP F 72 HIS 0.010 0.002 HIS F 14 PHE 0.042 0.002 PHE D 64 TYR 0.023 0.001 TYR C 174 ARG 0.009 0.001 ARG E 140 *********************** 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 310 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 308 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 THR cc_start: 0.7303 (m) cc_final: 0.7097 (p) REVERT: A 87 GLN cc_start: 0.8062 (mp10) cc_final: 0.7743 (mp10) REVERT: A 205 MET cc_start: 0.8514 (mmt) cc_final: 0.8008 (tpt) REVERT: A 209 MET cc_start: 0.7586 (mmp) cc_final: 0.7269 (mmp) REVERT: A 211 MET cc_start: 0.8476 (mmm) cc_final: 0.8233 (mmm) REVERT: B 73 LEU cc_start: 0.8531 (mp) cc_final: 0.8281 (mp) REVERT: B 95 PHE cc_start: 0.8134 (m-10) cc_final: 0.7636 (m-80) REVERT: B 125 GLU cc_start: 0.8452 (mm-30) cc_final: 0.7760 (mm-30) REVERT: B 128 ASP cc_start: 0.8921 (m-30) cc_final: 0.8689 (t70) REVERT: B 129 LYS cc_start: 0.8822 (tttm) cc_final: 0.8607 (mtmm) REVERT: B 209 MET cc_start: 0.8328 (mtp) cc_final: 0.8101 (mtp) REVERT: C 135 ARG cc_start: 0.9377 (mmt90) cc_final: 0.9027 (mmm-85) REVERT: C 168 ARG cc_start: 0.8330 (ptt90) cc_final: 0.7491 (ptp-170) REVERT: C 209 MET cc_start: 0.8189 (mmp) cc_final: 0.7580 (mmm) REVERT: C 230 ASP cc_start: 0.8359 (t0) cc_final: 0.7950 (t0) REVERT: D 55 PRO cc_start: 0.7520 (Cg_exo) cc_final: 0.7311 (Cg_endo) REVERT: D 113 TYR cc_start: 0.8208 (m-10) cc_final: 0.7922 (t80) REVERT: D 118 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8031 (mp0) REVERT: D 167 MET cc_start: 0.8518 (ptm) cc_final: 0.8223 (pmm) REVERT: D 210 MET cc_start: 0.6365 (pmm) cc_final: 0.5529 (pmm) REVERT: D 230 ASP cc_start: 0.8690 (t0) cc_final: 0.8484 (t0) REVERT: E 53 PHE cc_start: 0.8184 (m-80) cc_final: 0.7964 (m-10) REVERT: E 230 ASP cc_start: 0.8094 (t0) cc_final: 0.7836 (t0) REVERT: F 17 PHE cc_start: 0.8530 (t80) cc_final: 0.8269 (t80) REVERT: F 22 ARG cc_start: 0.8023 (mtt180) cc_final: 0.7673 (ttt90) REVERT: F 36 ARG cc_start: 0.6930 (mtt-85) cc_final: 0.6173 (mpt180) REVERT: F 129 MET cc_start: 0.7152 (mpp) cc_final: 0.6865 (mpp) REVERT: F 185 MET cc_start: 0.7738 (mmm) cc_final: 0.7342 (mtt) REVERT: F 233 MET cc_start: 0.7753 (mmm) cc_final: 0.6825 (mmm) REVERT: G 7 MET cc_start: 0.8593 (mmp) cc_final: 0.7650 (mmt) REVERT: G 8 MET cc_start: 0.8491 (tpt) cc_final: 0.8278 (tpt) REVERT: G 15 LYS cc_start: 0.8645 (mttt) cc_final: 0.8139 (tmtt) REVERT: G 87 ILE cc_start: 0.7699 (mm) cc_final: 0.7453 (mt) REVERT: H 69 MET cc_start: 0.8648 (mtt) cc_final: 0.8161 (ttm) REVERT: I 29 LEU cc_start: 0.8057 (mm) cc_final: 0.7756 (mm) REVERT: J 1 MET cc_start: 0.8079 (ppp) cc_final: 0.7444 (ppp) REVERT: J 7 MET cc_start: 0.8251 (tpp) cc_final: 0.7878 (tpp) REVERT: J 9 MET cc_start: 0.8379 (mmm) cc_final: 0.8118 (mtt) REVERT: J 38 LEU cc_start: 0.8959 (mm) cc_final: 0.8744 (mm) REVERT: J 47 MET cc_start: 0.7574 (ptt) cc_final: 0.7164 (pmm) outliers start: 2 outliers final: 0 residues processed: 309 average time/residue: 0.2203 time to fit residues: 100.1184 Evaluate side-chains 238 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 136 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 chunk 126 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 12 optimal weight: 0.2980 chunk 50 optimal weight: 0.1980 chunk 79 optimal weight: 10.0000 chunk 146 optimal weight: 2.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 HIS ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 HIS ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.5770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12820 Z= 0.188 Angle : 0.765 11.677 17476 Z= 0.366 Chirality : 0.043 0.240 2189 Planarity : 0.006 0.065 2130 Dihedral : 5.986 27.569 1695 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.75 % Allowed : 7.09 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % 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: -0.04 (0.21), residues: 1609 helix: 0.96 (0.15), residues: 1195 sheet: None (None), residues: 0 loop : -3.03 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 72 HIS 0.007 0.002 HIS F 14 PHE 0.040 0.002 PHE D 64 TYR 0.021 0.001 TYR C 174 ARG 0.009 0.001 ARG E 140 *********************** 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 313 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 313 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLN cc_start: 0.8135 (mp10) cc_final: 0.7487 (pm20) REVERT: A 205 MET cc_start: 0.8446 (mmt) cc_final: 0.7980 (tpt) REVERT: A 209 MET cc_start: 0.7551 (mmp) cc_final: 0.7253 (mmp) REVERT: A 211 MET cc_start: 0.8500 (mmm) cc_final: 0.8273 (mmm) REVERT: B 73 LEU cc_start: 0.8482 (mp) cc_final: 0.8235 (mp) REVERT: B 95 PHE cc_start: 0.8265 (m-10) cc_final: 0.7673 (m-80) REVERT: B 125 GLU cc_start: 0.8453 (mm-30) cc_final: 0.7705 (mm-30) REVERT: B 128 ASP cc_start: 0.8910 (m-30) cc_final: 0.8687 (t70) REVERT: B 129 LYS cc_start: 0.8806 (tttm) cc_final: 0.8603 (mtmm) REVERT: B 209 MET cc_start: 0.8230 (mtp) cc_final: 0.7969 (mtm) REVERT: C 114 GLN cc_start: 0.8258 (tt0) cc_final: 0.7832 (tm-30) REVERT: C 140 ARG cc_start: 0.8520 (ttm110) cc_final: 0.8317 (mtm-85) REVERT: C 168 ARG cc_start: 0.8129 (ptt90) cc_final: 0.7340 (ptp-170) REVERT: C 209 MET cc_start: 0.7836 (mmp) cc_final: 0.7543 (mmm) REVERT: C 230 ASP cc_start: 0.8401 (t0) cc_final: 0.7192 (t0) REVERT: D 113 TYR cc_start: 0.8186 (m-10) cc_final: 0.7927 (t80) REVERT: D 167 MET cc_start: 0.8525 (ptm) cc_final: 0.8189 (pmm) REVERT: D 210 MET cc_start: 0.6368 (pmm) cc_final: 0.5515 (pmm) REVERT: D 230 ASP cc_start: 0.8649 (t0) cc_final: 0.8289 (t0) REVERT: E 53 PHE cc_start: 0.8176 (m-80) cc_final: 0.7954 (m-10) REVERT: F 17 PHE cc_start: 0.8552 (t80) cc_final: 0.8301 (t80) REVERT: F 22 ARG cc_start: 0.7998 (mtt180) cc_final: 0.7593 (ttt90) REVERT: F 36 ARG cc_start: 0.6857 (mtt-85) cc_final: 0.6135 (mpt180) REVERT: F 101 PHE cc_start: 0.8615 (m-80) cc_final: 0.7666 (m-80) REVERT: F 185 MET cc_start: 0.7633 (mmm) cc_final: 0.7338 (mtt) REVERT: F 233 MET cc_start: 0.7812 (mmm) cc_final: 0.6947 (mmm) REVERT: G 7 MET cc_start: 0.8613 (mmp) cc_final: 0.7592 (mmt) REVERT: G 15 LYS cc_start: 0.8659 (mttt) cc_final: 0.8152 (tmtt) REVERT: G 87 ILE cc_start: 0.7682 (mm) cc_final: 0.7374 (mt) REVERT: H 45 ASN cc_start: 0.7040 (p0) cc_final: 0.6809 (p0) REVERT: I 1 MET cc_start: 0.7885 (ptp) cc_final: 0.7462 (pmm) REVERT: I 29 LEU cc_start: 0.8070 (mm) cc_final: 0.7825 (mm) REVERT: J 1 MET cc_start: 0.7958 (ppp) cc_final: 0.7293 (ppp) REVERT: J 7 MET cc_start: 0.8243 (tpp) cc_final: 0.7883 (tpp) outliers start: 0 outliers final: 0 residues processed: 313 average time/residue: 0.2205 time to fit residues: 100.5513 Evaluate side-chains 232 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 17 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 chunk 85 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 94 optimal weight: 0.0770 chunk 92 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 GLN ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.6056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12820 Z= 0.204 Angle : 0.757 9.088 17476 Z= 0.364 Chirality : 0.043 0.190 2189 Planarity : 0.006 0.069 2130 Dihedral : 5.799 27.406 1695 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.75 % Allowed : 7.09 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % 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 (0.22), residues: 1609 helix: 1.14 (0.15), residues: 1194 sheet: None (None), residues: 0 loop : -2.86 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 72 HIS 0.006 0.001 HIS F 14 PHE 0.041 0.002 PHE D 64 TYR 0.022 0.001 TYR C 174 ARG 0.007 0.001 ARG E 140 *********************** 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 299 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9103 (tp) cc_final: 0.8871 (pp) REVERT: A 205 MET cc_start: 0.8462 (mmt) cc_final: 0.8029 (tpt) REVERT: A 209 MET cc_start: 0.7675 (mmp) cc_final: 0.7368 (mmp) REVERT: A 211 MET cc_start: 0.8491 (mmm) cc_final: 0.8247 (mmm) REVERT: B 73 LEU cc_start: 0.8416 (mp) cc_final: 0.8197 (mp) REVERT: B 95 PHE cc_start: 0.8167 (m-10) cc_final: 0.7573 (m-80) REVERT: B 125 GLU cc_start: 0.8429 (mm-30) cc_final: 0.7268 (mm-30) REVERT: B 128 ASP cc_start: 0.8926 (m-30) cc_final: 0.8642 (t70) REVERT: B 129 LYS cc_start: 0.8778 (tttm) cc_final: 0.8504 (mtmt) REVERT: B 209 MET cc_start: 0.8270 (mtp) cc_final: 0.7945 (mtm) REVERT: C 61 MET cc_start: 0.8542 (tpp) cc_final: 0.8085 (mtp) REVERT: C 114 GLN cc_start: 0.8275 (tt0) cc_final: 0.7803 (tm-30) REVERT: C 138 MET cc_start: 0.8982 (mtt) cc_final: 0.8518 (mtt) REVERT: C 168 ARG cc_start: 0.8119 (ptt90) cc_final: 0.7352 (ptp-170) REVERT: C 209 MET cc_start: 0.8119 (mmp) cc_final: 0.7668 (mmm) REVERT: C 230 ASP cc_start: 0.8455 (t0) cc_final: 0.8012 (t0) REVERT: D 113 TYR cc_start: 0.8165 (m-10) cc_final: 0.7911 (t80) REVERT: D 118 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7913 (mp0) REVERT: D 167 MET cc_start: 0.8460 (ptm) cc_final: 0.8172 (pmm) REVERT: D 209 MET cc_start: 0.7942 (mmp) cc_final: 0.7656 (mmp) REVERT: D 210 MET cc_start: 0.6570 (pmm) cc_final: 0.5643 (pmm) REVERT: D 230 ASP cc_start: 0.8723 (t0) cc_final: 0.8411 (t0) REVERT: E 163 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7296 (pm20) REVERT: F 17 PHE cc_start: 0.8584 (t80) cc_final: 0.8327 (t80) REVERT: F 22 ARG cc_start: 0.7963 (mtt180) cc_final: 0.7590 (ttt90) REVERT: F 36 ARG cc_start: 0.6927 (mtt-85) cc_final: 0.6192 (mpt180) REVERT: F 101 PHE cc_start: 0.8619 (m-80) cc_final: 0.7995 (m-80) REVERT: F 129 MET cc_start: 0.7124 (mpp) cc_final: 0.6811 (mpp) REVERT: F 185 MET cc_start: 0.7611 (mmm) cc_final: 0.7272 (mtt) REVERT: F 233 MET cc_start: 0.7870 (mmm) cc_final: 0.7269 (mmm) REVERT: G 7 MET cc_start: 0.8661 (mmp) cc_final: 0.7635 (mmt) REVERT: G 8 MET cc_start: 0.8538 (tpt) cc_final: 0.8325 (tpt) REVERT: G 15 LYS cc_start: 0.8735 (mttt) cc_final: 0.8215 (tmtt) REVERT: G 87 ILE cc_start: 0.7650 (mm) cc_final: 0.7432 (mt) REVERT: I 1 MET cc_start: 0.7916 (ptp) cc_final: 0.7509 (pmm) REVERT: I 29 LEU cc_start: 0.8107 (mm) cc_final: 0.7637 (mt) REVERT: J 7 MET cc_start: 0.8261 (tpp) cc_final: 0.7886 (tpp) REVERT: J 47 MET cc_start: 0.7344 (ptt) cc_final: 0.7027 (pmm) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.2104 time to fit residues: 91.8952 Evaluate side-chains 234 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 60 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 74 optimal weight: 0.0060 chunk 14 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 chunk 144 optimal weight: 0.9980 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 HIS ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.6257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12820 Z= 0.189 Angle : 0.756 9.499 17476 Z= 0.362 Chirality : 0.042 0.217 2189 Planarity : 0.006 0.067 2130 Dihedral : 5.695 26.775 1695 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.46 % Favored : 91.86 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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: 0.31 (0.22), residues: 1609 helix: 1.19 (0.15), residues: 1199 sheet: None (None), residues: 0 loop : -2.85 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 72 HIS 0.008 0.002 HIS F 14 PHE 0.040 0.001 PHE D 64 TYR 0.022 0.001 TYR C 174 ARG 0.005 0.001 ARG E 140 *********************** 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 297 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 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: A 60 MET cc_start: 0.9171 (mmm) cc_final: 0.8690 (mpp) REVERT: A 87 GLN cc_start: 0.8260 (mp10) cc_final: 0.7568 (pm20) REVERT: A 139 LEU cc_start: 0.9153 (tp) cc_final: 0.8899 (pp) REVERT: A 178 GLU cc_start: 0.9096 (tp30) cc_final: 0.8749 (tp30) REVERT: A 205 MET cc_start: 0.8460 (mmt) cc_final: 0.8015 (tpt) REVERT: A 209 MET cc_start: 0.7515 (mmp) cc_final: 0.7288 (mmp) REVERT: A 211 MET cc_start: 0.8469 (mmm) cc_final: 0.8229 (mmm) REVERT: B 95 PHE cc_start: 0.8202 (m-10) cc_final: 0.7603 (m-80) REVERT: B 125 GLU cc_start: 0.8471 (mm-30) cc_final: 0.7458 (mm-30) REVERT: B 128 ASP cc_start: 0.8917 (m-30) cc_final: 0.8603 (t70) REVERT: B 129 LYS cc_start: 0.8759 (tttm) cc_final: 0.8481 (mtmt) REVERT: B 209 MET cc_start: 0.8217 (mtp) cc_final: 0.7928 (mtm) REVERT: C 114 GLN cc_start: 0.8249 (tt0) cc_final: 0.7767 (tm-30) REVERT: C 134 LEU cc_start: 0.9466 (tp) cc_final: 0.9222 (tp) REVERT: C 138 MET cc_start: 0.8942 (mtt) cc_final: 0.8619 (mtt) REVERT: C 168 ARG cc_start: 0.8087 (ptt90) cc_final: 0.7387 (ptp-170) REVERT: C 209 MET cc_start: 0.8011 (mmp) cc_final: 0.7627 (mmm) REVERT: C 230 ASP cc_start: 0.8455 (t0) cc_final: 0.8002 (t0) REVERT: D 113 TYR cc_start: 0.8143 (m-10) cc_final: 0.7912 (t80) REVERT: D 167 MET cc_start: 0.8409 (ptm) cc_final: 0.8141 (pmm) REVERT: D 209 MET cc_start: 0.7953 (mmp) cc_final: 0.7732 (mmp) REVERT: D 210 MET cc_start: 0.6198 (pmm) cc_final: 0.5760 (pmm) REVERT: E 163 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7335 (pm20) REVERT: F 17 PHE cc_start: 0.8601 (t80) cc_final: 0.8318 (t80) REVERT: F 22 ARG cc_start: 0.7950 (mtt180) cc_final: 0.7565 (ttt90) REVERT: F 36 ARG cc_start: 0.6920 (mtt-85) cc_final: 0.6151 (mpt180) REVERT: F 49 MET cc_start: 0.8170 (mmt) cc_final: 0.7940 (mmt) REVERT: F 101 PHE cc_start: 0.8567 (m-80) cc_final: 0.7783 (m-80) REVERT: F 185 MET cc_start: 0.7579 (mmm) cc_final: 0.7274 (mtt) REVERT: G 8 MET cc_start: 0.8522 (tpt) cc_final: 0.8282 (tpt) REVERT: G 15 LYS cc_start: 0.8733 (mttt) cc_final: 0.8238 (tmtt) REVERT: G 87 ILE cc_start: 0.7628 (mm) cc_final: 0.7323 (mt) REVERT: I 1 MET cc_start: 0.7912 (ptp) cc_final: 0.7529 (pmm) REVERT: I 29 LEU cc_start: 0.8112 (mm) cc_final: 0.7647 (mt) REVERT: J 7 MET cc_start: 0.8298 (tpp) cc_final: 0.7891 (tpp) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.2277 time to fit residues: 97.8195 Evaluate side-chains 227 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 8.9990 chunk 141 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 84 optimal weight: 0.0470 chunk 61 optimal weight: 8.9990 chunk 110 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 127 optimal weight: 7.9990 chunk 133 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 overall best weight: 1.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN C 141 GLN D 76 ASN F 14 HIS ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.6416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12820 Z= 0.207 Angle : 0.779 10.794 17476 Z= 0.373 Chirality : 0.043 0.202 2189 Planarity : 0.006 0.068 2130 Dihedral : 5.641 26.634 1695 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.21 % Favored : 92.11 % Rotamer: Outliers : 0.07 % Allowed : 0.87 % Favored : 99.06 % 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: 0.32 (0.22), residues: 1609 helix: 1.20 (0.15), residues: 1197 sheet: None (None), residues: 0 loop : -2.83 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 72 HIS 0.008 0.001 HIS F 14 PHE 0.045 0.002 PHE D 64 TYR 0.022 0.002 TYR C 244 ARG 0.010 0.001 ARG E 140 *********************** 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 291 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 290 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.9145 (mmm) cc_final: 0.8759 (mpp) REVERT: A 61 MET cc_start: 0.8796 (tpp) cc_final: 0.8124 (mtm) REVERT: A 87 GLN cc_start: 0.8306 (mp10) cc_final: 0.7996 (mp10) REVERT: A 139 LEU cc_start: 0.9141 (tp) cc_final: 0.8895 (pp) REVERT: A 205 MET cc_start: 0.8448 (mmt) cc_final: 0.8021 (tpt) REVERT: A 211 MET cc_start: 0.8500 (mmm) cc_final: 0.8266 (mmm) REVERT: B 60 MET cc_start: 0.8766 (mmm) cc_final: 0.8116 (mpp) REVERT: B 125 GLU cc_start: 0.8410 (mm-30) cc_final: 0.7379 (mm-30) REVERT: B 128 ASP cc_start: 0.8898 (m-30) cc_final: 0.8576 (t70) REVERT: B 129 LYS cc_start: 0.8739 (tttm) cc_final: 0.8454 (mtmt) REVERT: B 209 MET cc_start: 0.8210 (mtp) cc_final: 0.7971 (mtm) REVERT: C 60 MET cc_start: 0.8900 (tpp) cc_final: 0.8036 (tpp) REVERT: C 114 GLN cc_start: 0.8210 (tt0) cc_final: 0.7719 (tm-30) REVERT: C 138 MET cc_start: 0.8986 (mtt) cc_final: 0.8588 (mtt) REVERT: C 168 ARG cc_start: 0.8075 (ptt90) cc_final: 0.7389 (ptp-170) REVERT: C 209 MET cc_start: 0.8038 (mmp) cc_final: 0.7716 (mmm) REVERT: C 230 ASP cc_start: 0.8384 (t0) cc_final: 0.8015 (t0) REVERT: D 113 TYR cc_start: 0.8140 (m-10) cc_final: 0.7903 (t80) REVERT: D 167 MET cc_start: 0.8410 (ptm) cc_final: 0.8168 (pmm) REVERT: D 209 MET cc_start: 0.8050 (mmp) cc_final: 0.7803 (mmp) REVERT: D 210 MET cc_start: 0.6128 (pmm) cc_final: 0.5824 (pmm) REVERT: E 163 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7355 (pm20) REVERT: E 230 ASP cc_start: 0.8062 (t0) cc_final: 0.7673 (t0) REVERT: F 22 ARG cc_start: 0.7977 (mtt180) cc_final: 0.7624 (ttt90) REVERT: F 36 ARG cc_start: 0.6996 (mtt-85) cc_final: 0.6299 (mpt180) REVERT: F 49 MET cc_start: 0.8160 (mmt) cc_final: 0.7917 (mmt) REVERT: F 152 ASP cc_start: 0.9159 (m-30) cc_final: 0.8959 (m-30) REVERT: F 185 MET cc_start: 0.7571 (mmm) cc_final: 0.7209 (mtt) REVERT: G 8 MET cc_start: 0.8889 (tpt) cc_final: 0.8515 (tpt) REVERT: G 15 LYS cc_start: 0.8742 (mttt) cc_final: 0.8266 (tmtt) REVERT: I 1 MET cc_start: 0.7894 (ptp) cc_final: 0.7575 (pmm) REVERT: I 29 LEU cc_start: 0.8118 (mm) cc_final: 0.7817 (mm) REVERT: J 7 MET cc_start: 0.8285 (tpp) cc_final: 0.7862 (tpp) outliers start: 1 outliers final: 0 residues processed: 290 average time/residue: 0.2242 time to fit residues: 94.2522 Evaluate side-chains 224 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 149 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN E 76 ASN E 132 GLN F 14 HIS ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 HIS ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.6321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12820 Z= 0.291 Angle : 0.840 10.699 17476 Z= 0.405 Chirality : 0.046 0.230 2189 Planarity : 0.007 0.072 2130 Dihedral : 5.828 27.701 1695 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.81 % Allowed : 7.96 % Favored : 91.24 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.14 (0.21), residues: 1609 helix: 1.07 (0.15), residues: 1191 sheet: None (None), residues: 0 loop : -2.86 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP F 72 HIS 0.008 0.002 HIS F 14 PHE 0.047 0.002 PHE D 64 TYR 0.022 0.002 TYR C 174 ARG 0.011 0.001 ARG D 75 ********************** 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 275 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.9135 (mmm) cc_final: 0.8732 (mpp) REVERT: A 61 MET cc_start: 0.8822 (tpp) cc_final: 0.8115 (ttm) REVERT: A 87 GLN cc_start: 0.8400 (mp10) cc_final: 0.8086 (mp10) REVERT: A 205 MET cc_start: 0.8545 (mmt) cc_final: 0.8119 (tpt) REVERT: A 210 MET cc_start: 0.8334 (mtp) cc_final: 0.7835 (ttm) REVERT: A 211 MET cc_start: 0.8332 (mmm) cc_final: 0.8022 (mmm) REVERT: B 60 MET cc_start: 0.8809 (mmm) cc_final: 0.8193 (mpp) REVERT: B 125 GLU cc_start: 0.8463 (mm-30) cc_final: 0.7332 (mm-30) REVERT: B 128 ASP cc_start: 0.8943 (m-30) cc_final: 0.8554 (t70) REVERT: B 129 LYS cc_start: 0.8705 (tttm) cc_final: 0.8439 (mtmt) REVERT: B 209 MET cc_start: 0.8244 (mtp) cc_final: 0.8033 (mtm) REVERT: C 114 GLN cc_start: 0.8222 (tt0) cc_final: 0.7794 (tm-30) REVERT: C 134 LEU cc_start: 0.9441 (tp) cc_final: 0.9200 (tp) REVERT: C 138 MET cc_start: 0.9088 (mtt) cc_final: 0.8673 (mtt) REVERT: C 168 ARG cc_start: 0.8363 (ptt90) cc_final: 0.7705 (ptp-170) REVERT: C 209 MET cc_start: 0.8386 (mmp) cc_final: 0.7598 (mmm) REVERT: C 230 ASP cc_start: 0.8344 (t0) cc_final: 0.7998 (t0) REVERT: D 61 MET cc_start: 0.8515 (ptm) cc_final: 0.8089 (ppp) REVERT: D 209 MET cc_start: 0.8032 (mmp) cc_final: 0.7686 (mmp) REVERT: D 210 MET cc_start: 0.5946 (pmm) cc_final: 0.5582 (pmm) REVERT: E 163 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7422 (pm20) REVERT: E 230 ASP cc_start: 0.8222 (t0) cc_final: 0.7892 (t0) REVERT: F 22 ARG cc_start: 0.8122 (mtt180) cc_final: 0.7517 (ttt90) REVERT: F 36 ARG cc_start: 0.7157 (mtt-85) cc_final: 0.6491 (mpt180) REVERT: F 185 MET cc_start: 0.7594 (mmm) cc_final: 0.7123 (mtt) REVERT: G 8 MET cc_start: 0.8834 (tpt) cc_final: 0.8600 (tpt) REVERT: G 15 LYS cc_start: 0.8832 (mttt) cc_final: 0.8366 (tmtt) REVERT: H 47 MET cc_start: 0.7828 (ptt) cc_final: 0.7373 (ppp) REVERT: I 1 MET cc_start: 0.7817 (ptp) cc_final: 0.7609 (pmm) REVERT: J 7 MET cc_start: 0.8379 (tpp) cc_final: 0.7831 (tpp) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.2156 time to fit residues: 86.8386 Evaluate side-chains 213 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 128 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.088581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.074009 restraints weight = 43949.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.075872 restraints weight = 26625.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.077219 restraints weight = 18702.110| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.6599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12820 Z= 0.206 Angle : 0.793 9.994 17476 Z= 0.381 Chirality : 0.044 0.289 2189 Planarity : 0.006 0.068 2130 Dihedral : 5.675 25.877 1695 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.52 % Favored : 91.86 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.25 (0.22), residues: 1609 helix: 1.14 (0.15), residues: 1198 sheet: None (None), residues: 0 loop : -2.82 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 72 HIS 0.002 0.001 HIS F 143 PHE 0.044 0.002 PHE D 64 TYR 0.020 0.002 TYR C 174 ARG 0.007 0.001 ARG B 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2628.77 seconds wall clock time: 48 minutes 30.74 seconds (2910.74 seconds total)