Starting phenix.real_space_refine on Fri Mar 15 18:54:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r69_4733/03_2024/6r69_4733.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r69_4733/03_2024/6r69_4733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r69_4733/03_2024/6r69_4733.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r69_4733/03_2024/6r69_4733.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r69_4733/03_2024/6r69_4733.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r69_4733/03_2024/6r69_4733.pdb" } resolution = 3.65 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= -0.000 sd= 0.002 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 "A GLU 125": "OE1" <-> "OE2" Residue "A PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 106": "OD1" <-> "OD2" Residue "D ASP 111": "OD1" <-> "OD2" Residue "D GLU 144": "OE1" <-> "OE2" Residue "D PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 125": "OE1" <-> "OE2" Residue "E ASP 128": "OD1" <-> "OD2" Residue "E ASP 197": "OD1" <-> "OD2" Residue "E ASP 230": "OD1" <-> "OD2" Residue "E TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 241": "OE1" <-> "OE2" Residue "F ASP 253": "OD1" <-> "OD2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 46": "OE1" <-> "OE2" Residue "I TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 75": "OD1" <-> "OD2" Residue "J PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s 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: 6.76, per 1000 atoms: 0.54 Number of scatterers: 12541 At special positions: 0 Unit cell: (105.4, 101.15, 130.9, 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: 5.16 Conformation dependent library (CDL) restraints added in 2.3 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: 73 helices and 0 sheets defined 81.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 43 through 61 removed outlier: 3.714A pdb=" N PHE A 47 " --> pdb=" O GLN A 43 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 51 " --> pdb=" O PHE A 47 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR A 52 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 3.654A 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 66 through 77 Processing helix chain 'A' and resid 87 through 101 removed outlier: 3.637A 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 119 removed outlier: 3.957A pdb=" N GLU A 118 " --> pdb=" O GLN A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 140 Proline residue: A 133 - end of helix removed outlier: 3.556A pdb=" N ARG A 140 " --> pdb=" O ALA A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 154 removed outlier: 3.806A pdb=" N LEU A 147 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 208 Proline residue: A 172 - end of helix removed outlier: 3.874A pdb=" N GLN A 184 " --> pdb=" O LYS A 180 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR A 188 " --> pdb=" O GLN A 184 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ILE A 191 " --> pdb=" O PHE A 187 " (cutoff:3.500A) Proline residue: A 192 - end of helix removed outlier: 3.525A pdb=" N LEU A 207 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 228 removed outlier: 3.767A pdb=" N LEU A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Proline residue: A 220 - end of helix removed outlier: 4.348A pdb=" N PHE A 226 " --> pdb=" O LYS A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 245 removed outlier: 3.628A pdb=" N LEU A 234 " --> pdb=" O ASP A 230 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TYR A 244 " --> pdb=" O ALA A 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 63 Proline residue: B 55 - end of helix removed outlier: 3.964A pdb=" N LEU B 59 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER B 63 " --> pdb=" O LEU B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 77 removed outlier: 3.765A pdb=" N ALA B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 119 removed outlier: 3.598A pdb=" N GLY B 91 " --> pdb=" O GLN B 87 " (cutoff:3.500A) Proline residue: B 103 - end of helix removed outlier: 4.825A pdb=" N GLN B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Proline residue: B 115 - end of helix removed outlier: 3.811A pdb=" N GLU B 118 " --> pdb=" O GLN B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 142 Proline residue: B 133 - end of helix removed outlier: 3.688A pdb=" N GLN B 141 " --> pdb=" O PHE B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 153 removed outlier: 3.803A pdb=" N LEU B 147 " --> pdb=" O ARG B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 165 Processing helix chain 'B' and resid 166 through 205 Proline residue: B 172 - end of helix removed outlier: 4.127A pdb=" N ILE B 191 " --> pdb=" O PHE B 187 " (cutoff:3.500A) Proline residue: B 192 - end of helix Processing helix chain 'B' and resid 217 through 229 removed outlier: 4.061A pdb=" N PHE B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE B 226 " --> pdb=" O LYS B 222 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 245 removed outlier: 3.620A pdb=" N LEU B 234 " --> pdb=" O ASP B 230 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL B 236 " --> pdb=" O TRP B 232 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE B 243 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N TYR B 244 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER B 245 " --> pdb=" O GLN B 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 62 removed outlier: 3.743A pdb=" N ILE C 48 " --> pdb=" O THR C 44 " (cutoff:3.500A) Proline residue: C 55 - end of helix removed outlier: 3.755A pdb=" N THR C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 75 removed outlier: 3.879A pdb=" N ILE C 68 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE C 69 " --> pdb=" O THR C 65 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL C 70 " --> pdb=" O ARG C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 101 Processing helix chain 'C' and resid 101 through 117 removed outlier: 4.766A pdb=" N GLN C 114 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Proline residue: C 115 - end of helix Processing helix chain 'C' and resid 123 through 140 removed outlier: 4.063A pdb=" N LEU C 127 " --> pdb=" O MET C 123 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLY C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN C 132 " --> pdb=" O ASP C 128 " (cutoff:3.500A) Proline residue: C 133 - end of helix removed outlier: 3.555A pdb=" N ALA C 136 " --> pdb=" O GLN C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 154 removed outlier: 3.956A pdb=" N LEU C 147 " --> pdb=" O ARG C 143 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA C 154 " --> pdb=" O PHE C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 190 removed outlier: 3.665A pdb=" N LEU C 170 " --> pdb=" O PRO C 166 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 171 " --> pdb=" O MET C 167 " (cutoff:3.500A) Proline residue: C 172 - end of helix removed outlier: 3.609A pdb=" N PHE C 190 " --> pdb=" O GLY C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 208 Processing helix chain 'C' and resid 213 through 216 Processing helix chain 'C' and resid 217 through 228 removed outlier: 4.269A pdb=" N PHE C 221 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE C 226 " --> pdb=" O LYS C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 245 removed outlier: 3.614A pdb=" N LEU C 234 " --> pdb=" O ASP C 230 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU C 235 " --> pdb=" O GLY C 231 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 236 " --> pdb=" O TRP C 232 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N PHE C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N TYR C 244 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER C 245 " --> pdb=" O GLN C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 62 removed outlier: 3.675A pdb=" N ILE D 48 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR D 52 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N PHE D 53 " --> pdb=" O THR D 49 " (cutoff:3.500A) Proline residue: D 55 - end of helix removed outlier: 3.994A pdb=" N THR D 62 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 75 Processing helix chain 'D' and resid 87 through 112 Proline residue: D 103 - end of helix Processing helix chain 'D' and resid 114 through 118 Processing helix chain 'D' and resid 127 through 140 Proline residue: D 133 - end of helix Processing helix chain 'D' and resid 143 through 153 removed outlier: 3.637A pdb=" N LEU D 147 " --> pdb=" O ARG D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 190 removed outlier: 3.701A pdb=" N LEU D 171 " --> pdb=" O MET D 167 " (cutoff:3.500A) Proline residue: D 172 - end of helix Processing helix chain 'D' and resid 190 through 208 Processing helix chain 'D' and resid 213 through 228 removed outlier: 3.543A pdb=" N ILE D 217 " --> pdb=" O PRO D 213 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LEU D 219 " --> pdb=" O ALA D 215 " (cutoff:3.500A) Proline residue: D 220 - end of helix Processing helix chain 'D' and resid 232 through 245 removed outlier: 3.522A pdb=" N VAL D 236 " --> pdb=" O TRP D 232 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA D 240 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N PHE D 243 " --> pdb=" O LEU D 239 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TYR D 244 " --> pdb=" O ALA D 240 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER D 245 " --> pdb=" O GLN D 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 63 removed outlier: 4.414A pdb=" N ILE E 48 " --> pdb=" O THR E 44 " (cutoff:3.500A) Proline residue: E 55 - end of helix removed outlier: 3.847A pdb=" N THR E 62 " --> pdb=" O LEU E 58 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER E 63 " --> pdb=" O LEU E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 77 removed outlier: 3.809A pdb=" N VAL E 70 " --> pdb=" O ARG E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 117 removed outlier: 4.234A pdb=" N ALA E 93 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR E 97 " --> pdb=" O ALA E 93 " (cutoff:3.500A) Proline residue: E 103 - end of helix removed outlier: 4.593A pdb=" N GLN E 114 " --> pdb=" O VAL E 110 " (cutoff:3.500A) Proline residue: E 115 - end of helix Processing helix chain 'E' and resid 124 through 140 Proline residue: E 133 - end of helix Processing helix chain 'E' and resid 143 through 155 removed outlier: 3.949A pdb=" N LEU E 147 " --> pdb=" O ARG E 143 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA E 148 " --> pdb=" O GLU E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 208 removed outlier: 3.509A pdb=" N LEU E 170 " --> pdb=" O PRO E 166 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU E 171 " --> pdb=" O MET E 167 " (cutoff:3.500A) Proline residue: E 172 - end of helix removed outlier: 3.730A pdb=" N ILE E 191 " --> pdb=" O PHE E 187 " (cutoff:3.500A) Proline residue: E 192 - end of helix removed outlier: 3.589A pdb=" N LEU E 207 " --> pdb=" O VAL E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 228 removed outlier: 4.564A pdb=" N PHE E 221 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS E 222 " --> pdb=" O ALA E 218 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU E 223 " --> pdb=" O LEU E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 245 removed outlier: 3.861A pdb=" N LEU E 234 " --> pdb=" O ASP E 230 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE E 243 " --> pdb=" O LEU E 239 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR E 244 " --> pdb=" O ALA E 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 14 removed outlier: 4.248A pdb=" N LEU F 10 " --> pdb=" O SER F 6 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR F 11 " --> pdb=" O GLU F 7 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TRP F 12 " --> pdb=" O GLN F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 29 Processing helix chain 'F' and resid 44 through 55 removed outlier: 3.834A pdb=" N ILE F 48 " --> pdb=" O LEU F 44 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL F 53 " --> pdb=" O MET F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 89 removed outlier: 3.662A pdb=" N MET F 75 " --> pdb=" O LEU F 71 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN F 76 " --> pdb=" O TRP F 72 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN F 77 " --> pdb=" O LEU F 73 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE F 78 " --> pdb=" O ALA F 74 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU F 79 " --> pdb=" O MET F 75 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN F 89 " --> pdb=" O GLY F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 104 removed outlier: 4.063A pdb=" N VAL F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE F 101 " --> pdb=" O THR F 97 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE F 102 " --> pdb=" O ALA F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 141 removed outlier: 3.808A pdb=" N MET F 131 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE F 137 " --> pdb=" O ALA F 133 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU F 138 " --> pdb=" O MET F 134 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE F 140 " --> pdb=" O LEU F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 157 removed outlier: 3.535A pdb=" N HIS F 155 " --> pdb=" O VAL F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 176 removed outlier: 4.297A pdb=" N GLY F 176 " --> pdb=" O LEU F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 206 removed outlier: 4.097A pdb=" N LEU F 181 " --> pdb=" O GLY F 177 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA F 187 " --> pdb=" O GLY F 183 " (cutoff:3.500A) Proline residue: F 189 - end of helix removed outlier: 3.658A pdb=" N GLY F 202 " --> pdb=" O ASN F 198 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU F 204 " --> pdb=" O ALA F 200 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN F 205 " --> pdb=" O LEU F 201 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG F 206 " --> pdb=" O GLY F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 212 removed outlier: 3.641A pdb=" N LEU F 211 " --> pdb=" O ALA F 208 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER F 212 " --> pdb=" O PRO F 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 208 through 212' Processing helix chain 'F' and resid 216 through 232 removed outlier: 4.197A pdb=" N THR F 223 " --> pdb=" O PRO F 219 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET F 229 " --> pdb=" O GLY F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 261 removed outlier: 3.573A pdb=" N PHE F 239 " --> pdb=" O LEU F 235 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU F 241 " --> pdb=" O ALA F 237 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N HIS F 242 " --> pdb=" O PRO F 238 " (cutoff:3.500A) removed outlier: 3.941A 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 40 removed outlier: 3.585A pdb=" N MET G 7 " --> pdb=" O PRO G 3 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY G 10 " --> pdb=" O VAL G 6 " (cutoff:3.500A) Proline residue: G 23 - end of helix Processing helix chain 'G' and resid 50 through 66 removed outlier: 3.782A pdb=" N VAL G 58 " --> pdb=" O LYS G 54 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE G 63 " --> pdb=" O PHE G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 89 removed outlier: 3.997A pdb=" N LEU G 73 " --> pdb=" O MET G 69 " (cutoff:3.500A) Proline residue: G 85 - end of helix removed outlier: 3.693A pdb=" N ILE G 88 " --> pdb=" O LEU G 84 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY G 89 " --> pdb=" O PRO G 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 40 Proline residue: H 23 - end of helix removed outlier: 3.705A pdb=" N LEU H 38 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA H 40 " --> pdb=" O SER H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 66 removed outlier: 3.631A pdb=" N VAL H 58 " --> pdb=" O LYS H 54 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE H 63 " --> pdb=" O PHE H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 84 removed outlier: 4.083A pdb=" N LEU H 73 " --> pdb=" O MET H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 87 No H-bonds generated for 'chain 'H' and resid 85 through 87' Processing helix chain 'I' and resid 2 through 39 Proline residue: I 23 - end of helix Processing helix chain 'I' and resid 50 through 66 removed outlier: 3.531A pdb=" N VAL I 58 " --> pdb=" O LYS I 54 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE I 63 " --> pdb=" O PHE I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 88 Proline residue: I 85 - end of helix removed outlier: 4.104A pdb=" N ILE I 88 " --> pdb=" O LEU I 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 38 removed outlier: 4.157A pdb=" N GLY J 10 " --> pdb=" O VAL J 6 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS J 15 " --> pdb=" O THR J 11 " (cutoff:3.500A) Proline residue: J 23 - end of helix removed outlier: 3.701A pdb=" N LEU J 38 " --> pdb=" O ILE J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 66 removed outlier: 4.011A pdb=" N LYS J 54 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE J 63 " --> pdb=" O PHE J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 88 removed outlier: 3.815A pdb=" N LEU J 73 " --> pdb=" O MET J 69 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG J 78 " --> pdb=" O LEU J 74 " (cutoff:3.500A) Proline residue: J 85 - end of helix removed outlier: 3.619A pdb=" N ILE J 88 " --> pdb=" O LEU J 84 " (cutoff:3.500A) 788 hydrogen bonds defined for protein. 2349 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: 3.47 Time building geometry restraints manager: 5.54 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: 3717 1.34 - 1.46: 1593 1.46 - 1.57: 7313 1.57 - 1.69: 0 1.69 - 1.81: 197 Bond restraints: 12820 Sorted by residual: bond pdb=" N PHE F 140 " pdb=" CA PHE F 140 " ideal model delta sigma weight residual 1.468 1.451 0.018 1.24e-02 6.50e+03 2.00e+00 bond pdb=" CG1 ILE B 68 " pdb=" CD1 ILE B 68 " ideal model delta sigma weight residual 1.513 1.461 0.052 3.90e-02 6.57e+02 1.76e+00 bond pdb=" C GLU I 46 " pdb=" O GLU I 46 " ideal model delta sigma weight residual 1.234 1.245 -0.011 8.30e-03 1.45e+04 1.72e+00 bond pdb=" N GLU J 46 " pdb=" CA GLU J 46 " ideal model delta sigma weight residual 1.468 1.452 0.016 1.24e-02 6.50e+03 1.71e+00 bond pdb=" CB TRP C 232 " pdb=" CG TRP C 232 " ideal model delta sigma weight residual 1.498 1.458 0.040 3.10e-02 1.04e+03 1.64e+00 ... (remaining 12815 not shown) Histogram of bond angle deviations from ideal: 97.93 - 105.15: 429 105.15 - 112.36: 6767 112.36 - 119.58: 4115 119.58 - 126.80: 6019 126.80 - 134.02: 146 Bond angle restraints: 17476 Sorted by residual: angle pdb=" C THR J 42 " pdb=" N GLN J 43 " pdb=" CA GLN J 43 " ideal model delta sigma weight residual 120.38 126.95 -6.57 1.46e+00 4.69e-01 2.02e+01 angle pdb=" CA LEU F 150 " pdb=" CB LEU F 150 " pdb=" CG LEU F 150 " ideal model delta sigma weight residual 116.30 101.67 14.63 3.50e+00 8.16e-02 1.75e+01 angle pdb=" C ILE F 159 " pdb=" N GLY F 160 " pdb=" CA GLY F 160 " ideal model delta sigma weight residual 121.41 113.52 7.89 1.96e+00 2.60e-01 1.62e+01 angle pdb=" N PHE B 64 " pdb=" CA PHE B 64 " pdb=" CB PHE B 64 " ideal model delta sigma weight residual 114.27 107.74 6.53 1.64e+00 3.72e-01 1.58e+01 angle pdb=" N PHE D 64 " pdb=" CA PHE D 64 " pdb=" CB PHE D 64 " ideal model delta sigma weight residual 114.17 110.02 4.15 1.14e+00 7.69e-01 1.33e+01 ... (remaining 17471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 6847 17.38 - 34.75: 745 34.75 - 52.13: 114 52.13 - 69.50: 16 69.50 - 86.88: 9 Dihedral angle restraints: 7731 sinusoidal: 2988 harmonic: 4743 Sorted by residual: dihedral pdb=" CA ALA I 41 " pdb=" C ALA I 41 " pdb=" N THR I 42 " pdb=" CA THR I 42 " ideal model delta harmonic sigma weight residual -180.00 -140.71 -39.29 0 5.00e+00 4.00e-02 6.17e+01 dihedral pdb=" CA ALA G 41 " pdb=" C ALA G 41 " pdb=" N THR G 42 " pdb=" CA THR G 42 " ideal model delta harmonic sigma weight residual -180.00 -141.80 -38.20 0 5.00e+00 4.00e-02 5.84e+01 dihedral pdb=" CA LEU F 211 " pdb=" C LEU F 211 " pdb=" N SER F 212 " pdb=" CA SER F 212 " ideal model delta harmonic sigma weight residual 180.00 142.14 37.86 0 5.00e+00 4.00e-02 5.73e+01 ... (remaining 7728 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1309 0.035 - 0.070: 610 0.070 - 0.105: 222 0.105 - 0.140: 39 0.140 - 0.175: 9 Chirality restraints: 2189 Sorted by residual: chirality pdb=" CA PRO G 67 " pdb=" N PRO G 67 " pdb=" C PRO G 67 " pdb=" CB PRO G 67 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.66e-01 chirality pdb=" CG LEU D 223 " pdb=" CB LEU D 223 " pdb=" CD1 LEU D 223 " pdb=" CD2 LEU D 223 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.12e-01 chirality pdb=" CA PRO E 81 " pdb=" N PRO E 81 " pdb=" C PRO E 81 " pdb=" CB PRO E 81 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.00e-01 ... (remaining 2186 not shown) Planarity restraints: 2130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 84 " 0.051 5.00e-02 4.00e+02 7.82e-02 9.79e+00 pdb=" N PRO C 85 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO C 85 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 85 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 213 " 0.047 5.00e-02 4.00e+02 7.13e-02 8.13e+00 pdb=" N PRO D 214 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO D 214 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 214 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 84 " 0.046 5.00e-02 4.00e+02 7.04e-02 7.93e+00 pdb=" N PRO D 85 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO D 85 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 85 " 0.039 5.00e-02 4.00e+02 ... (remaining 2127 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1146 2.73 - 3.27: 13976 3.27 - 3.82: 19782 3.82 - 4.36: 23427 4.36 - 4.90: 39753 Nonbonded interactions: 98084 Sorted by model distance: nonbonded pdb=" OE1 GLU G 46 " pdb=" OG SER H 50 " model vdw 2.191 2.440 nonbonded pdb=" O ALA D 131 " pdb=" N ARG D 135 " model vdw 2.195 2.520 nonbonded pdb=" OG1 THR D 65 " pdb=" OE1 GLU D 178 " model vdw 2.199 2.440 nonbonded pdb=" O ALA F 83 " pdb=" OG1 THR F 87 " model vdw 2.201 2.440 nonbonded pdb=" O MET C 138 " pdb=" OG1 THR C 142 " model vdw 2.203 2.440 ... (remaining 98079 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: 1.330 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: 5.710 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 35.500 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.080 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 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 : 0.005 0.052 12820 Z= 0.348 Angle : 0.896 14.628 17476 Z= 0.506 Chirality : 0.045 0.175 2189 Planarity : 0.007 0.078 2130 Dihedral : 14.420 86.876 4637 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.82 % Favored : 89.81 % Rotamer: Outliers : 0.15 % Allowed : 5.38 % Favored : 94.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -3.99 (0.18), residues: 1609 helix: -1.98 (0.12), residues: 1203 sheet: None (None), residues: 0 loop : -4.27 (0.27), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 68 HIS 0.003 0.001 HIS F 14 PHE 0.030 0.002 PHE B 64 TYR 0.013 0.001 TYR A 113 ARG 0.007 0.001 ARG B 66 *********************** 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 388 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 386 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 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 224 MET cc_start: 0.7711 (ptm) cc_final: 0.7419 (ptt) REVERT: B 47 PHE cc_start: 0.7840 (t80) cc_final: 0.7616 (t80) REVERT: C 60 MET cc_start: 0.8002 (mmp) cc_final: 0.7786 (mmt) outliers start: 2 outliers final: 0 residues processed: 387 average time/residue: 0.2521 time to fit residues: 136.6071 Evaluate side-chains 250 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 2.9990 chunk 118 optimal weight: 0.0370 chunk 66 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 80 optimal weight: 20.0000 chunk 63 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 74 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 142 optimal weight: 6.9990 overall best weight: 2.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN B 241 GLN C 76 ASN C 184 GLN C 241 GLN D 76 ASN D 87 GLN E 76 ASN F 105 GLN ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 HIS F 165 ASN F 249 ASN ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 ASN I 71 ASN J 39 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12820 Z= 0.278 Angle : 0.805 10.674 17476 Z= 0.396 Chirality : 0.045 0.171 2189 Planarity : 0.007 0.076 2130 Dihedral : 6.168 40.988 1695 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.89 % Favored : 90.99 % Rotamer: Outliers : 2.40 % Allowed : 15.92 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -1.85 (0.21), residues: 1609 helix: -0.46 (0.15), residues: 1241 sheet: None (None), residues: 0 loop : -3.63 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 232 HIS 0.005 0.001 HIS F 14 PHE 0.038 0.002 PHE B 64 TYR 0.014 0.002 TYR D 174 ARG 0.007 0.001 ARG E 152 *********************** 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 311 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 278 time to evaluate : 1.624 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: A 129 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8228 (tttm) REVERT: A 163 GLU cc_start: 0.7415 (tp30) cc_final: 0.7000 (mm-30) REVERT: C 123 MET cc_start: 0.7145 (tmm) cc_final: 0.6924 (tmm) REVERT: E 86 ASN cc_start: 0.7286 (OUTLIER) cc_final: 0.7052 (p0) REVERT: E 160 GLN cc_start: 0.8033 (pm20) cc_final: 0.7362 (pp30) REVERT: F 33 LEU cc_start: 0.3869 (mp) cc_final: 0.3499 (mt) REVERT: F 210 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7915 (pt0) REVERT: I 45 ASN cc_start: 0.6377 (OUTLIER) cc_final: 0.5779 (t0) REVERT: J 7 MET cc_start: 0.7843 (tpp) cc_final: 0.7611 (tpp) outliers start: 33 outliers final: 11 residues processed: 298 average time/residue: 0.2443 time to fit residues: 104.1191 Evaluate side-chains 248 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 233 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 210 GLN Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain I residue 45 ASN Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 84 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 79 optimal weight: 7.9990 chunk 44 optimal weight: 0.0050 chunk 118 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 142 optimal weight: 6.9990 chunk 154 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN E 119 GLN ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12820 Z= 0.212 Angle : 0.787 12.164 17476 Z= 0.377 Chirality : 0.045 0.352 2189 Planarity : 0.007 0.071 2130 Dihedral : 5.879 42.217 1695 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.02 % Favored : 91.86 % Rotamer: Outliers : 2.91 % Allowed : 17.81 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -1.12 (0.21), residues: 1609 helix: 0.12 (0.15), residues: 1234 sheet: None (None), residues: 0 loop : -3.54 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 232 HIS 0.004 0.001 HIS F 14 PHE 0.034 0.001 PHE B 64 TYR 0.027 0.002 TYR D 174 ARG 0.008 0.001 ARG C 140 *********************** 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 316 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 276 time to evaluate : 1.432 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: symmetry clash REVERT: A 180 LYS cc_start: 0.7323 (mttp) cc_final: 0.7090 (mttp) REVERT: B 211 MET cc_start: 0.7010 (mmp) cc_final: 0.6750 (mmp) REVERT: C 123 MET cc_start: 0.6998 (tmm) cc_final: 0.6459 (tmm) REVERT: D 123 MET cc_start: 0.7903 (mpp) cc_final: 0.6777 (ptm) REVERT: E 160 GLN cc_start: 0.7982 (pm20) cc_final: 0.7309 (pp30) REVERT: G 34 ILE cc_start: 0.8797 (tp) cc_final: 0.8595 (tt) REVERT: H 1 MET cc_start: 0.6090 (mmt) cc_final: 0.5746 (mmt) outliers start: 40 outliers final: 15 residues processed: 303 average time/residue: 0.2238 time to fit residues: 98.9487 Evaluate side-chains 251 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 236 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 84 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 141 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 68 optimal weight: 20.0000 chunk 95 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 chunk 151 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 40 optimal weight: 20.0000 chunk 126 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 GLN C 76 ASN C 160 GLN ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 HIS ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12820 Z= 0.233 Angle : 0.775 10.823 17476 Z= 0.375 Chirality : 0.044 0.185 2189 Planarity : 0.006 0.072 2130 Dihedral : 5.736 41.776 1695 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.70 % Favored : 91.24 % Rotamer: Outliers : 2.83 % Allowed : 19.99 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.71 (0.22), residues: 1609 helix: 0.42 (0.15), residues: 1232 sheet: None (None), residues: 0 loop : -3.38 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 232 HIS 0.005 0.001 HIS F 14 PHE 0.034 0.001 PHE B 64 TYR 0.024 0.002 TYR J 76 ARG 0.006 0.001 ARG C 152 *********************** 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 294 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 255 time to evaluate : 1.503 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: C 123 MET cc_start: 0.6953 (tmm) cc_final: 0.6407 (tmm) REVERT: E 160 GLN cc_start: 0.8054 (pm20) cc_final: 0.7347 (pp30) outliers start: 39 outliers final: 17 residues processed: 281 average time/residue: 0.2389 time to fit residues: 98.0897 Evaluate side-chains 251 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 234 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 52 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 86 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 chunk 129 optimal weight: 0.0020 chunk 104 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 GLN C 76 ASN ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12820 Z= 0.185 Angle : 0.777 11.982 17476 Z= 0.369 Chirality : 0.043 0.239 2189 Planarity : 0.006 0.071 2130 Dihedral : 5.585 41.515 1695 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.52 % Favored : 92.42 % Rotamer: Outliers : 2.91 % Allowed : 20.86 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.45 (0.22), residues: 1609 helix: 0.62 (0.15), residues: 1240 sheet: None (None), residues: 0 loop : -3.43 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 232 HIS 0.005 0.001 HIS F 14 PHE 0.030 0.001 PHE B 64 TYR 0.025 0.002 TYR D 174 ARG 0.006 0.001 ARG A 75 *********************** 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 305 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 265 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7194 (ptp-170) REVERT: C 123 MET cc_start: 0.6871 (tmm) cc_final: 0.6428 (tmm) REVERT: D 123 MET cc_start: 0.7729 (mpp) cc_final: 0.7057 (ttt) REVERT: D 209 MET cc_start: 0.6493 (mmp) cc_final: 0.6080 (mmt) REVERT: F 75 MET cc_start: 0.7276 (mpp) cc_final: 0.6992 (ptp) REVERT: J 83 ASN cc_start: 0.8286 (t0) cc_final: 0.8079 (t0) outliers start: 40 outliers final: 16 residues processed: 294 average time/residue: 0.2318 time to fit residues: 98.6036 Evaluate side-chains 256 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 239 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 56 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 136 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 151 optimal weight: 0.3980 chunk 126 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12820 Z= 0.200 Angle : 0.797 12.187 17476 Z= 0.377 Chirality : 0.044 0.201 2189 Planarity : 0.006 0.072 2130 Dihedral : 5.451 40.493 1695 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.14 % Favored : 91.80 % Rotamer: Outliers : 2.40 % Allowed : 22.09 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.26 (0.22), residues: 1609 helix: 0.71 (0.15), residues: 1249 sheet: None (None), residues: 0 loop : -3.31 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 232 HIS 0.004 0.001 HIS F 14 PHE 0.051 0.001 PHE C 95 TYR 0.022 0.002 TYR C 174 ARG 0.007 0.001 ARG A 75 *********************** 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 286 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 253 time to evaluate : 1.500 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: A 66 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7191 (ptp-170) REVERT: C 101 MET cc_start: 0.7731 (mpp) cc_final: 0.7435 (mpp) REVERT: C 123 MET cc_start: 0.6814 (tmm) cc_final: 0.6416 (tmm) REVERT: D 123 MET cc_start: 0.7482 (mpp) cc_final: 0.6457 (ttt) REVERT: E 209 MET cc_start: 0.6851 (mpp) cc_final: 0.6514 (mpp) REVERT: F 75 MET cc_start: 0.7396 (mpp) cc_final: 0.7142 (ptp) REVERT: J 47 MET cc_start: 0.6737 (pmm) cc_final: 0.6381 (ppp) REVERT: J 83 ASN cc_start: 0.8247 (t0) cc_final: 0.7991 (t0) outliers start: 33 outliers final: 21 residues processed: 273 average time/residue: 0.2206 time to fit residues: 88.4612 Evaluate side-chains 261 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 239 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 59 PHE Chi-restraints excluded: chain J residue 36 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 17 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 151 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 92 optimal weight: 0.0020 chunk 69 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12820 Z= 0.199 Angle : 0.805 12.425 17476 Z= 0.378 Chirality : 0.044 0.188 2189 Planarity : 0.006 0.072 2130 Dihedral : 5.331 39.923 1695 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.52 % Favored : 92.42 % Rotamer: Outliers : 2.18 % Allowed : 23.76 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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 (0.22), residues: 1609 helix: 0.83 (0.15), residues: 1252 sheet: None (None), residues: 0 loop : -3.20 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 232 HIS 0.005 0.001 HIS F 14 PHE 0.036 0.001 PHE C 95 TYR 0.021 0.001 TYR C 174 ARG 0.006 0.000 ARG A 75 *********************** 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 291 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 261 time to evaluate : 1.118 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 66 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7387 (ptp-170) REVERT: B 210 MET cc_start: 0.7579 (mpp) cc_final: 0.7162 (mtt) REVERT: C 101 MET cc_start: 0.7813 (mpp) cc_final: 0.7345 (mpp) REVERT: C 123 MET cc_start: 0.6735 (tmm) cc_final: 0.6351 (tmm) REVERT: D 123 MET cc_start: 0.7460 (mpp) cc_final: 0.6491 (ttt) REVERT: E 160 GLN cc_start: 0.8046 (pm20) cc_final: 0.7659 (pp30) REVERT: E 209 MET cc_start: 0.6745 (mpp) cc_final: 0.6454 (mpp) REVERT: J 47 MET cc_start: 0.6709 (pmm) cc_final: 0.6474 (ppp) REVERT: J 83 ASN cc_start: 0.8218 (t0) cc_final: 0.7981 (t0) outliers start: 30 outliers final: 20 residues processed: 279 average time/residue: 0.1910 time to fit residues: 78.6420 Evaluate side-chains 264 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 243 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 36 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 60 optimal weight: 20.0000 chunk 90 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 29 optimal weight: 0.1980 chunk 96 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 137 optimal weight: 6.9990 chunk 144 optimal weight: 0.0070 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN C 184 GLN D 87 GLN H 39 GLN ** I 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12820 Z= 0.200 Angle : 0.824 12.861 17476 Z= 0.387 Chirality : 0.045 0.361 2189 Planarity : 0.006 0.074 2130 Dihedral : 5.261 38.791 1695 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 2.11 % Allowed : 23.76 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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 (0.22), residues: 1609 helix: 0.92 (0.15), residues: 1254 sheet: None (None), residues: 0 loop : -3.12 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 232 HIS 0.009 0.001 HIS F 14 PHE 0.033 0.001 PHE C 95 TYR 0.020 0.001 TYR C 174 ARG 0.006 0.000 ARG F 96 *********************** 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: 29 poor density : 268 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7404 (ptp-170) REVERT: A 86 ASN cc_start: 0.5379 (OUTLIER) cc_final: 0.5068 (t0) REVERT: C 101 MET cc_start: 0.7862 (mpp) cc_final: 0.7528 (mpp) REVERT: C 123 MET cc_start: 0.6660 (tmm) cc_final: 0.6279 (tmm) REVERT: C 210 MET cc_start: 0.7576 (pmm) cc_final: 0.7288 (pmm) REVERT: D 123 MET cc_start: 0.7389 (mpp) cc_final: 0.6457 (ttt) REVERT: E 209 MET cc_start: 0.6710 (mpp) cc_final: 0.6472 (mpp) REVERT: J 47 MET cc_start: 0.6627 (pmm) cc_final: 0.6424 (ppp) REVERT: J 83 ASN cc_start: 0.8232 (t0) cc_final: 0.7969 (t0) outliers start: 29 outliers final: 17 residues processed: 289 average time/residue: 0.2249 time to fit residues: 95.8729 Evaluate side-chains 269 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 250 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 36 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 144 optimal weight: 0.0970 chunk 84 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 43 optimal weight: 0.0870 chunk 127 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 92 optimal weight: 0.0070 overall best weight: 0.3374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 GLN H 39 GLN ** I 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.5181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12820 Z= 0.205 Angle : 0.872 12.157 17476 Z= 0.404 Chirality : 0.047 0.378 2189 Planarity : 0.006 0.073 2130 Dihedral : 5.260 38.748 1695 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 1.67 % Allowed : 25.15 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.01 (0.22), residues: 1609 helix: 0.84 (0.15), residues: 1259 sheet: None (None), residues: 0 loop : -3.03 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 232 HIS 0.007 0.001 HIS F 14 PHE 0.031 0.001 PHE F 17 TYR 0.019 0.001 TYR C 174 ARG 0.007 0.001 ARG F 96 *********************** 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 279 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 256 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7405 (ptp-170) REVERT: A 86 ASN cc_start: 0.5577 (OUTLIER) cc_final: 0.5236 (t0) REVERT: A 209 MET cc_start: 0.6290 (mmp) cc_final: 0.5640 (mmp) REVERT: C 123 MET cc_start: 0.6648 (tmm) cc_final: 0.6291 (tmm) REVERT: D 123 MET cc_start: 0.7335 (mpp) cc_final: 0.6440 (ttt) REVERT: E 209 MET cc_start: 0.6700 (mpp) cc_final: 0.6479 (mpp) REVERT: J 83 ASN cc_start: 0.8178 (t0) cc_final: 0.7884 (t0) outliers start: 23 outliers final: 16 residues processed: 274 average time/residue: 0.2188 time to fit residues: 89.2203 Evaluate side-chains 255 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 237 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 36 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 149 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 70 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 GLN H 39 GLN ** I 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.5149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12820 Z= 0.239 Angle : 0.878 12.879 17476 Z= 0.408 Chirality : 0.047 0.373 2189 Planarity : 0.006 0.074 2130 Dihedral : 5.203 37.334 1695 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.14 % Favored : 91.80 % Rotamer: Outliers : 1.82 % Allowed : 25.73 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 0.06 (0.22), residues: 1609 helix: 0.87 (0.15), residues: 1270 sheet: None (None), residues: 0 loop : -3.14 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 232 HIS 0.006 0.001 HIS F 14 PHE 0.033 0.001 PHE B 64 TYR 0.022 0.001 TYR H 76 ARG 0.007 0.001 ARG A 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 266 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 241 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7455 (ptp-170) REVERT: A 86 ASN cc_start: 0.5574 (OUTLIER) cc_final: 0.5284 (t0) REVERT: C 123 MET cc_start: 0.6597 (tmm) cc_final: 0.6260 (tmm) REVERT: D 123 MET cc_start: 0.7368 (mpp) cc_final: 0.6414 (ttt) REVERT: E 205 MET cc_start: 0.7846 (tpt) cc_final: 0.7624 (tpp) REVERT: E 209 MET cc_start: 0.6737 (mpp) cc_final: 0.6496 (mpp) REVERT: J 83 ASN cc_start: 0.8202 (t0) cc_final: 0.7922 (t0) outliers start: 25 outliers final: 20 residues processed: 259 average time/residue: 0.2145 time to fit residues: 83.2451 Evaluate side-chains 258 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 236 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 207 MET Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 36 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 chunk 114 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 52 optimal weight: 0.3980 chunk 128 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 109 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.079092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.064070 restraints weight = 47245.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.066084 restraints weight = 26165.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.067447 restraints weight = 17618.542| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.5331 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= 0.213 Angle : 0.876 13.399 17476 Z= 0.407 Chirality : 0.047 0.374 2189 Planarity : 0.006 0.073 2130 Dihedral : 5.175 38.058 1695 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.27 % Favored : 92.67 % Rotamer: Outliers : 1.60 % Allowed : 25.58 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 0.12 (0.22), residues: 1609 helix: 0.93 (0.15), residues: 1252 sheet: None (None), residues: 0 loop : -2.98 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP B 232 HIS 0.006 0.001 HIS F 14 PHE 0.031 0.001 PHE B 64 TYR 0.033 0.001 TYR B 174 ARG 0.007 0.001 ARG F 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2630.17 seconds wall clock time: 48 minutes 35.78 seconds (2915.78 seconds total)