Starting phenix.real_space_refine (version: dev) on Mon Feb 20 16:32:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f2d_4173/02_2023/6f2d_4173.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f2d_4173/02_2023/6f2d_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_4173/02_2023/6f2d_4173.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f2d_4173/02_2023/6f2d_4173.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f2d_4173/02_2023/6f2d_4173.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f2d_4173/02_2023/6f2d_4173.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 12541 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1575 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 15, 'TRANS': 187} Chain: "B" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1575 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 15, 'TRANS': 187} Chain: "C" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1575 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 15, 'TRANS': 187} Chain: "D" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1575 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 15, 'TRANS': 187} Chain: "E" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1575 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 15, 'TRANS': 187} Chain: "F" Number of atoms: 1986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1986 Classifications: {'peptide': 258} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 240} Chain: "G" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "H" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "I" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "J" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Time building chain proxies: 7.08, per 1000 atoms: 0.56 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: 5.82 Conformation dependent library (CDL) restraints added in 1.9 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: 0.43 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: 3.08 Time building geometry restraints manager: 6.22 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 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. 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 4.990 Check model and map are aligned: 0.200 Process input model: 34.260 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.120 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 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 % 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 *********************** 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 : 1.705 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 outliers start: 7 outliers final: 3 residues processed: 454 average time/residue: 0.2719 time to fit residues: 169.4186 Evaluate side-chains 234 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 231 time to evaluate : 1.616 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1054 time to fit residues: 2.6472 ------------------------------------------------------------------------------- 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: 1.9990 chunk 118 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 80 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 74 optimal weight: 0.5980 chunk 91 optimal weight: 20.0000 chunk 142 optimal weight: 0.5980 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 F 165 ASN F 242 HIS F 262 ASN J 39 GLN ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 12820 Z= 0.250 Angle : 0.885 9.119 17476 Z= 0.440 Chirality : 0.047 0.253 2189 Planarity : 0.007 0.074 2130 Dihedral : 7.278 29.890 1695 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.83 % Favored : 90.74 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.19), residues: 1609 helix: -1.11 (0.14), residues: 1202 sheet: None (None), residues: 0 loop : -3.95 (0.26), residues: 407 *********************** 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 362 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 361 time to evaluate : 1.524 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 outliers start: 1 outliers final: 1 residues processed: 362 average time/residue: 0.2398 time to fit residues: 124.5845 Evaluate side-chains 237 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 236 time to evaluate : 1.498 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1064 time to fit residues: 2.1478 ------------------------------------------------------------------------------- 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: 9.9990 chunk 44 optimal weight: 0.0270 chunk 118 optimal weight: 6.9990 chunk 97 optimal weight: 20.0000 chunk 39 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 154 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.8040 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 12820 Z= 0.218 Angle : 0.812 11.015 17476 Z= 0.398 Chirality : 0.045 0.249 2189 Planarity : 0.007 0.078 2130 Dihedral : 6.725 27.398 1695 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.68 % Allowed : 8.27 % Favored : 91.05 % Rotamer Outliers : 0.07 % 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: -1.30 (0.20), residues: 1609 helix: 0.11 (0.15), residues: 1206 sheet: None (None), residues: 0 loop : -3.82 (0.27), residues: 403 *********************** 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 322 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 321 time to evaluate : 1.410 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 outliers start: 1 outliers final: 0 residues processed: 322 average time/residue: 0.2368 time to fit residues: 109.5871 Evaluate side-chains 228 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.509 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9928 ------------------------------------------------------------------------------- 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: 2.9990 chunk 107 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 68 optimal weight: 0.1980 chunk 95 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 151 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 40 optimal weight: 20.0000 chunk 126 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.5288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 12820 Z= 0.213 Angle : 0.771 8.691 17476 Z= 0.380 Chirality : 0.044 0.159 2189 Planarity : 0.006 0.068 2130 Dihedral : 6.400 27.773 1695 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.75 % Allowed : 7.83 % Favored : 91.42 % Rotamer Outliers : 0.07 % 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: -0.80 (0.21), residues: 1609 helix: 0.47 (0.15), residues: 1197 sheet: None (None), residues: 0 loop : -3.53 (0.27), residues: 412 *********************** 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 301 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 300 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 301 average time/residue: 0.2265 time to fit residues: 99.5720 Evaluate side-chains 226 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 1.445 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7625 ------------------------------------------------------------------------------- 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: 10.0000 chunk 2 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 129 optimal weight: 8.9990 chunk 104 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN ** C 233 GLN ** 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: 0.7130 moved from start: 0.5685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 12820 Z= 0.204 Angle : 0.762 8.546 17476 Z= 0.371 Chirality : 0.043 0.172 2189 Planarity : 0.006 0.065 2130 Dihedral : 6.187 26.880 1695 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.75 % Allowed : 7.46 % Favored : 91.80 % Rotamer Outliers : 0.15 % 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: -0.34 (0.21), residues: 1609 helix: 0.81 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -3.25 (0.28), residues: 425 *********************** 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 299 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 297 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 298 average time/residue: 0.2195 time to fit residues: 96.6617 Evaluate side-chains 234 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 1.524 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9452 ------------------------------------------------------------------------------- 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: 10.0000 chunk 89 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 126 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 12 optimal weight: 8.9990 chunk 50 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.5904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 12820 Z= 0.222 Angle : 0.769 8.914 17476 Z= 0.373 Chirality : 0.044 0.180 2189 Planarity : 0.006 0.076 2130 Dihedral : 5.991 25.880 1695 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.81 % Allowed : 7.02 % Favored : 92.17 % Rotamer Outliers : 0.00 % 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: -0.02 (0.21), residues: 1609 helix: 0.99 (0.15), residues: 1187 sheet: None (None), residues: 0 loop : -2.98 (0.29), residues: 422 *********************** 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 289 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 289 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.2221 time to fit residues: 95.5533 Evaluate side-chains 224 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 1.502 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0093 ------------------------------------------------------------------------------- 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: 0.3980 chunk 86 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.6239 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= 0.196 Angle : 0.767 9.653 17476 Z= 0.369 Chirality : 0.043 0.171 2189 Planarity : 0.006 0.069 2130 Dihedral : 5.814 26.204 1695 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.33 % Favored : 91.98 % Rotamer Outliers : 0.00 % 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: 0.07 (0.21), residues: 1609 helix: 1.02 (0.15), residues: 1201 sheet: None (None), residues: 0 loop : -2.98 (0.30), residues: 408 *********************** 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 300 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.2368 time to fit residues: 102.6518 Evaluate side-chains 226 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 1.495 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0010 ------------------------------------------------------------------------------- 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: 2.9990 chunk 90 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 137 optimal weight: 8.9990 chunk 144 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 GLN ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 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: 0.7191 moved from start: 0.6181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 12820 Z= 0.294 Angle : 0.825 9.645 17476 Z= 0.400 Chirality : 0.046 0.184 2189 Planarity : 0.007 0.075 2130 Dihedral : 5.950 25.933 1695 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.96 % Favored : 91.36 % Rotamer Outliers : 0.00 % 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: -0.08 (0.21), residues: 1609 helix: 0.92 (0.15), residues: 1196 sheet: None (None), residues: 0 loop : -2.98 (0.30), residues: 413 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.2402 time to fit residues: 95.3305 Evaluate side-chains 208 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 1.520 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0798 ------------------------------------------------------------------------------- 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: 1.9990 chunk 141 optimal weight: 5.9990 chunk 144 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 110 optimal weight: 0.0670 chunk 43 optimal weight: 0.4980 chunk 127 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 140 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.6500 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= 0.199 Angle : 0.787 9.717 17476 Z= 0.379 Chirality : 0.043 0.187 2189 Planarity : 0.006 0.072 2130 Dihedral : 5.726 26.115 1695 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.27 % Favored : 92.04 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.21), residues: 1609 helix: 1.07 (0.15), residues: 1192 sheet: None (None), residues: 0 loop : -3.14 (0.30), residues: 417 *********************** 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 276 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.2419 time to fit residues: 98.5425 Evaluate side-chains 208 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 1.568 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0730 ------------------------------------------------------------------------------- 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: 6.9990 chunk 91 optimal weight: 8.9990 chunk 70 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 156 optimal weight: 10.0000 chunk 143 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 12 optimal weight: 0.0770 chunk 96 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN F 143 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.6735 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= 0.193 Angle : 0.788 10.499 17476 Z= 0.379 Chirality : 0.044 0.262 2189 Planarity : 0.006 0.069 2130 Dihedral : 5.645 25.738 1695 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.46 % Favored : 91.86 % Rotamer Outliers : 0.00 % 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: 0.13 (0.22), residues: 1609 helix: 1.09 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : -3.04 (0.31), residues: 409 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.2254 time to fit residues: 88.7672 Evaluate side-chains 203 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.508 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9987 ------------------------------------------------------------------------------- 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: 1.9990 chunk 38 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 0.1980 chunk 109 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN F 143 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.089363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.074244 restraints weight = 43830.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.076161 restraints weight = 27071.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.077499 restraints weight = 19054.743| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.6875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 12820 Z= 0.209 Angle : 0.808 12.343 17476 Z= 0.387 Chirality : 0.044 0.288 2189 Planarity : 0.006 0.071 2130 Dihedral : 5.521 24.993 1695 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.40 % Favored : 91.98 % Rotamer Outliers : 0.00 % 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: 0.19 (0.22), residues: 1609 helix: 1.15 (0.15), residues: 1201 sheet: None (None), residues: 0 loop : -3.08 (0.30), residues: 408 =============================================================================== Job complete usr+sys time: 2526.69 seconds wall clock time: 46 minutes 28.11 seconds (2788.11 seconds total)