Starting phenix.real_space_refine on Mon Jul 22 02:52:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wm8_37645/07_2024/8wm8_37645.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wm8_37645/07_2024/8wm8_37645.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wm8_37645/07_2024/8wm8_37645.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wm8_37645/07_2024/8wm8_37645.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wm8_37645/07_2024/8wm8_37645.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wm8_37645/07_2024/8wm8_37645.cif" } resolution = 3.54 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= 0.001 sd= 0.073 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: 5 Type Number sf(0) Gaussians S 25 5.16 5 C 5396 2.51 5 N 1374 2.21 5 O 1459 1.98 5 H 8522 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 215": "OD1" <-> "OD2" Residue "D TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 72": "OD1" <-> "OD2" Residue "B ASP 120": "OD1" <-> "OD2" Residue "B ASP 175": "OD1" <-> "OD2" Residue "B TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 264": "OD1" <-> "OD2" Residue "A PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 8": "OD1" <-> "OD2" Residue "C PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 16776 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 4116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 4116 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 17, 'TRANS': 241} Chain: "B" Number of atoms: 4198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 4198 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 17, 'TRANS': 247} Chain: "A" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 4170 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 17, 'TRANS': 245} Chain: "C" Number of atoms: 4288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 4288 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 11, 'TRANS': 256} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'NO3': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.38, per 1000 atoms: 0.44 Number of scatterers: 16776 At special positions: 0 Unit cell: (81.32, 118.77, 95.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 25 16.00 O 1459 8.00 N 1374 7.00 C 5396 6.00 H 8522 1.00 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: 12.72 Conformation dependent library (CDL) restraints added in 2.0 seconds 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 4 sheets defined 56.6% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'D' and resid 62 through 71 Processing helix chain 'D' and resid 83 through 86 Processing helix chain 'D' and resid 100 through 104 removed outlier: 3.852A pdb=" N CYS D 103 " --> pdb=" O GLN D 100 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LEU D 104 " --> pdb=" O ASN D 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 100 through 104' Processing helix chain 'D' and resid 109 through 119 removed outlier: 4.008A pdb=" N ALA D 117 " --> pdb=" O ASN D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 140 removed outlier: 3.710A pdb=" N ALA D 132 " --> pdb=" O ALA D 128 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG D 135 " --> pdb=" O ARG D 131 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET D 140 " --> pdb=" O GLU D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 170 removed outlier: 3.663A pdb=" N GLN D 160 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ARG D 161 " --> pdb=" O GLY D 157 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL D 162 " --> pdb=" O MET D 158 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE D 170 " --> pdb=" O ARG D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 204 removed outlier: 3.548A pdb=" N GLU D 191 " --> pdb=" O ILE D 187 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN D 193 " --> pdb=" O LYS D 189 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU D 194 " --> pdb=" O GLU D 190 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN D 198 " --> pdb=" O GLU D 194 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS D 203 " --> pdb=" O ILE D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 221 Processing helix chain 'D' and resid 256 through 271 removed outlier: 3.769A pdb=" N ASP D 260 " --> pdb=" O PRO D 256 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 23 removed outlier: 3.643A pdb=" N ASN B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TRP B 23 " --> pdb=" O ASN B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 44 removed outlier: 3.553A pdb=" N LEU B 30 " --> pdb=" O VAL B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 61 through 67 removed outlier: 3.686A pdb=" N PHE B 65 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 66 " --> pdb=" O TRP B 62 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE B 67 " --> pdb=" O ASP B 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 61 through 67' Processing helix chain 'B' and resid 80 through 94 removed outlier: 3.832A pdb=" N SER B 87 " --> pdb=" O GLN B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 111 removed outlier: 3.823A pdb=" N ILE B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE B 104 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU B 105 " --> pdb=" O ALA B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 129 removed outlier: 4.034A pdb=" N ALA B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Proline residue: B 121 - end of helix removed outlier: 4.340A pdb=" N VAL B 125 " --> pdb=" O PRO B 121 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU B 126 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR B 128 " --> pdb=" O GLN B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 133 Processing helix chain 'B' and resid 134 through 142 Processing helix chain 'B' and resid 145 through 155 removed outlier: 3.664A pdb=" N ILE B 150 " --> pdb=" O ASN B 146 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N PHE B 151 " --> pdb=" O PRO B 147 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 171 removed outlier: 3.871A pdb=" N ASN B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR B 166 " --> pdb=" O LEU B 162 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL B 167 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY B 168 " --> pdb=" O ASN B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 183 removed outlier: 3.620A pdb=" N ILE B 177 " --> pdb=" O PRO B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 195 Processing helix chain 'B' and resid 195 through 208 Proline residue: B 201 - end of helix Processing helix chain 'B' and resid 208 through 219 removed outlier: 3.804A pdb=" N GLY B 212 " --> pdb=" O ARG B 208 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU B 213 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER B 214 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 240 removed outlier: 3.610A pdb=" N ASN B 239 " --> pdb=" O TRP B 235 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR B 240 " --> pdb=" O ASP B 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 235 through 240' Processing helix chain 'B' and resid 244 through 275 removed outlier: 3.950A pdb=" N GLU B 248 " --> pdb=" O THR B 244 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE B 249 " --> pdb=" O ASN B 245 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU B 253 " --> pdb=" O ILE B 249 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY B 268 " --> pdb=" O ASP B 264 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS B 273 " --> pdb=" O PHE B 269 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL B 274 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL B 275 " --> pdb=" O ALA B 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 25 Processing helix chain 'A' and resid 26 through 44 Processing helix chain 'A' and resid 53 through 60 Processing helix chain 'A' and resid 83 through 88 Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 96 through 109 removed outlier: 3.530A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE A 104 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 133 Processing helix chain 'A' and resid 134 through 143 Processing helix chain 'A' and resid 144 through 157 Processing helix chain 'A' and resid 158 through 171 removed outlier: 4.024A pdb=" N ASN A 164 " --> pdb=" O PRO A 160 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 182 removed outlier: 3.549A pdb=" N ILE A 177 " --> pdb=" O PRO A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 199 through 214 removed outlier: 3.569A pdb=" N THR A 205 " --> pdb=" O PRO A 201 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLY A 212 " --> pdb=" O ARG A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 221 Processing helix chain 'A' and resid 221 through 226 removed outlier: 3.736A pdb=" N VAL A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 removed outlier: 3.562A pdb=" N LEU A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA A 252 " --> pdb=" O GLU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 275 removed outlier: 3.697A pdb=" N VAL A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.534A pdb=" N ILE C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'C' and resid 94 through 105 removed outlier: 3.507A pdb=" N VAL C 99 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 100 " --> pdb=" O ARG C 96 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 123 removed outlier: 3.745A pdb=" N ALA C 117 " --> pdb=" O GLY C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 155 removed outlier: 3.805A pdb=" N ARG C 146 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL C 147 " --> pdb=" O MET C 143 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA C 148 " --> pdb=" O LYS C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 186 removed outlier: 3.825A pdb=" N GLU C 179 " --> pdb=" O GLY C 175 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLN C 180 " --> pdb=" O SER C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 203 removed outlier: 3.837A pdb=" N ALA C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 238 removed outlier: 3.831A pdb=" N VAL C 238 " --> pdb=" O ARG C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 269 removed outlier: 4.187A pdb=" N TYR C 244 " --> pdb=" O HIS C 240 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU C 249 " --> pdb=" O ASN C 245 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA C 268 " --> pdb=" O GLN C 264 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 37 through 47 removed outlier: 6.433A pdb=" N LYS D 28 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ASP D 41 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL D 26 " --> pdb=" O ASP D 41 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE D 43 " --> pdb=" O GLU D 24 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU D 24 " --> pdb=" O ILE D 43 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU D 45 " --> pdb=" O VAL D 22 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N VAL D 22 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLU D 24 " --> pdb=" O VAL D 80 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL D 80 " --> pdb=" O GLU D 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 97 through 98 removed outlier: 3.518A pdb=" N LEU D 208 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N VAL D 225 " --> pdb=" O PHE D 52 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N CYS D 54 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 23 through 25 removed outlier: 6.529A pdb=" N ARG C 12 " --> pdb=" O ALA C 24 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N HIS C 9 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY C 65 " --> pdb=" O HIS C 9 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 161 through 162 removed outlier: 7.129A pdb=" N LEU C 162 " --> pdb=" O VAL C 195 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N SER C 39 " --> pdb=" O VAL C 210 " (cutoff:3.500A) 318 hydrogen bonds defined for protein. 927 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: 5.41 Time building geometry restraints manager: 13.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8514 1.03 - 1.23: 9 1.23 - 1.42: 3400 1.42 - 1.62: 4997 1.62 - 1.81: 42 Bond restraints: 16962 Sorted by residual: bond pdb=" N NO3 A 301 " pdb=" O3 NO3 A 301 " ideal model delta sigma weight residual 1.237 1.264 -0.027 2.00e-02 2.50e+03 1.84e+00 bond pdb=" N NO3 A 301 " pdb=" O2 NO3 A 301 " ideal model delta sigma weight residual 1.237 1.264 -0.027 2.00e-02 2.50e+03 1.80e+00 bond pdb=" N NO3 A 301 " pdb=" O1 NO3 A 301 " ideal model delta sigma weight residual 1.237 1.263 -0.026 2.00e-02 2.50e+03 1.73e+00 bond pdb=" C ILE B 209 " pdb=" O ILE B 209 " ideal model delta sigma weight residual 1.241 1.228 0.013 1.19e-02 7.06e+03 1.28e+00 bond pdb=" C GLY D 35 " pdb=" N PRO D 36 " ideal model delta sigma weight residual 1.333 1.343 -0.010 1.01e-02 9.80e+03 9.72e-01 ... (remaining 16957 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.15: 428 107.15 - 113.86: 20739 113.86 - 120.58: 5468 120.58 - 127.29: 4135 127.29 - 134.01: 108 Bond angle restraints: 30878 Sorted by residual: angle pdb=" N SER A 96 " pdb=" CA SER A 96 " pdb=" C SER A 96 " ideal model delta sigma weight residual 113.41 107.47 5.94 1.22e+00 6.72e-01 2.37e+01 angle pdb=" N ASN A 117 " pdb=" CA ASN A 117 " pdb=" C ASN A 117 " ideal model delta sigma weight residual 114.62 109.17 5.45 1.14e+00 7.69e-01 2.28e+01 angle pdb=" N VAL C 106 " pdb=" CA VAL C 106 " pdb=" C VAL C 106 " ideal model delta sigma weight residual 111.62 108.23 3.39 7.90e-01 1.60e+00 1.84e+01 angle pdb=" N ASP D 178 " pdb=" CA ASP D 178 " pdb=" C ASP D 178 " ideal model delta sigma weight residual 110.41 106.28 4.13 1.23e+00 6.61e-01 1.13e+01 angle pdb=" CA ASN A 117 " pdb=" C ASN A 117 " pdb=" N ALA A 118 " ideal model delta sigma weight residual 119.71 116.30 3.41 1.17e+00 7.31e-01 8.47e+00 ... (remaining 30873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 7061 17.96 - 35.92: 570 35.92 - 53.88: 221 53.88 - 71.84: 37 71.84 - 89.80: 16 Dihedral angle restraints: 7905 sinusoidal: 4361 harmonic: 3544 Sorted by residual: dihedral pdb=" CA TRP A 235 " pdb=" C TRP A 235 " pdb=" N ASP A 236 " pdb=" CA ASP A 236 " ideal model delta harmonic sigma weight residual 180.00 155.45 24.55 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA SER A 157 " pdb=" C SER A 157 " pdb=" N ILE A 158 " pdb=" CA ILE A 158 " ideal model delta harmonic sigma weight residual 180.00 157.86 22.14 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA TRP A 23 " pdb=" C TRP A 23 " pdb=" N LYS A 24 " pdb=" CA LYS A 24 " ideal model delta harmonic sigma weight residual 180.00 160.16 19.84 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 7902 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 851 0.030 - 0.059: 303 0.059 - 0.089: 118 0.089 - 0.118: 62 0.118 - 0.148: 13 Chirality restraints: 1347 Sorted by residual: chirality pdb=" CA ILE B 172 " pdb=" N ILE B 172 " pdb=" C ILE B 172 " pdb=" CB ILE B 172 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA ILE A 172 " pdb=" N ILE A 172 " pdb=" C ILE A 172 " pdb=" CB ILE A 172 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA ILE D 241 " pdb=" N ILE D 241 " pdb=" C ILE D 241 " pdb=" CB ILE D 241 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 ... (remaining 1344 not shown) Planarity restraints: 2447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 112 " 0.030 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO A 113 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 113 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 113 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 146 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO B 147 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 147 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 147 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 245 " 0.026 5.00e-02 4.00e+02 3.90e-02 2.44e+00 pdb=" N PRO D 246 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 246 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 246 " 0.022 5.00e-02 4.00e+02 ... (remaining 2444 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 795 2.18 - 2.78: 34458 2.78 - 3.39: 46449 3.39 - 3.99: 59381 3.99 - 4.60: 92618 Nonbonded interactions: 233701 Sorted by model distance: nonbonded pdb=" O PRO A 160 " pdb="HD21 ASN A 164 " model vdw 1.572 1.850 nonbonded pdb=" OD1 ASP D 267 " pdb="HD21 ASN D 271 " model vdw 1.592 1.850 nonbonded pdb=" O PHE D 219 " pdb="HH11 ARG D 247 " model vdw 1.614 1.850 nonbonded pdb=" OD1 ASN D 263 " pdb=" HH TYR C 244 " model vdw 1.650 1.850 nonbonded pdb=" OD1 ASP C 8 " pdb=" HD1 HIS C 9 " model vdw 1.675 1.850 ... (remaining 233696 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' and resid 15 through 277) selection = (chain 'B' and ((resid 15 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 16 through 277)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.230 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 53.060 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 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 : 0.002 0.044 8440 Z= 0.155 Angle : 0.581 5.941 11494 Z= 0.328 Chirality : 0.040 0.148 1347 Planarity : 0.004 0.046 1458 Dihedral : 14.853 89.805 3077 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.51 (0.26), residues: 1047 helix: -1.14 (0.24), residues: 517 sheet: -2.40 (0.66), residues: 66 loop : -2.07 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 159 HIS 0.002 0.001 HIS C 240 PHE 0.015 0.001 PHE D 20 TYR 0.011 0.001 TYR D 102 ARG 0.004 0.000 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 ASP cc_start: 0.7786 (t0) cc_final: 0.7582 (t0) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.3660 time to fit residues: 97.0252 Evaluate side-chains 150 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 0.4980 chunk 26 optimal weight: 0.0980 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 19 ASN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8440 Z= 0.229 Angle : 0.639 6.446 11494 Z= 0.332 Chirality : 0.042 0.145 1347 Planarity : 0.005 0.044 1458 Dihedral : 5.179 24.951 1122 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.26 % Favored : 92.65 % Rotamer: Outliers : 0.78 % Allowed : 9.14 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.61 (0.25), residues: 1047 helix: -1.12 (0.22), residues: 528 sheet: -2.66 (0.62), residues: 65 loop : -2.25 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 159 HIS 0.003 0.001 HIS D 137 PHE 0.012 0.001 PHE A 151 TYR 0.018 0.002 TYR A 116 ARG 0.002 0.000 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 163 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 GLN cc_start: 0.6954 (mp-120) cc_final: 0.6741 (mp10) REVERT: A 236 ASP cc_start: 0.7801 (t0) cc_final: 0.7507 (t0) outliers start: 7 outliers final: 5 residues processed: 166 average time/residue: 0.3516 time to fit residues: 85.3688 Evaluate side-chains 157 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 152 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 203 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 25 optimal weight: 0.0050 chunk 93 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 92 optimal weight: 0.3980 chunk 31 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 19 ASN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8440 Z= 0.169 Angle : 0.575 6.134 11494 Z= 0.298 Chirality : 0.041 0.151 1347 Planarity : 0.005 0.046 1458 Dihedral : 5.047 24.457 1122 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.88 % Favored : 93.03 % Rotamer: Outliers : 1.00 % Allowed : 10.59 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.41 (0.26), residues: 1047 helix: -0.98 (0.22), residues: 541 sheet: -2.46 (0.65), residues: 60 loop : -2.18 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 159 HIS 0.006 0.001 HIS D 137 PHE 0.020 0.001 PHE A 154 TYR 0.010 0.001 TYR D 102 ARG 0.002 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 158 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 TYR cc_start: 0.8063 (t80) cc_final: 0.7845 (t80) REVERT: A 144 GLN cc_start: 0.6901 (mp-120) cc_final: 0.6670 (mp10) REVERT: A 236 ASP cc_start: 0.7785 (t0) cc_final: 0.7491 (t0) outliers start: 9 outliers final: 7 residues processed: 160 average time/residue: 0.3248 time to fit residues: 77.5439 Evaluate side-chains 156 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 149 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 203 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 49 optimal weight: 0.4980 chunk 89 optimal weight: 3.9990 chunk 26 optimal weight: 0.0020 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 19 ASN D 137 HIS ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8440 Z= 0.195 Angle : 0.569 6.345 11494 Z= 0.294 Chirality : 0.041 0.148 1347 Planarity : 0.004 0.045 1458 Dihedral : 5.047 24.507 1122 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.35 % Favored : 92.55 % Rotamer: Outliers : 1.00 % Allowed : 12.37 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.40 (0.26), residues: 1047 helix: -0.92 (0.22), residues: 541 sheet: -2.57 (0.63), residues: 60 loop : -2.23 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 159 HIS 0.004 0.001 HIS D 137 PHE 0.013 0.001 PHE A 95 TYR 0.018 0.001 TYR A 116 ARG 0.003 0.000 ARG C 234 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 159 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 TYR cc_start: 0.8063 (t80) cc_final: 0.7819 (t80) REVERT: A 144 GLN cc_start: 0.6930 (mp-120) cc_final: 0.6729 (mp10) REVERT: A 156 THR cc_start: 0.8748 (t) cc_final: 0.8541 (t) REVERT: A 236 ASP cc_start: 0.7818 (t0) cc_final: 0.7532 (t0) outliers start: 9 outliers final: 8 residues processed: 162 average time/residue: 0.3461 time to fit residues: 83.3568 Evaluate side-chains 157 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 149 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 203 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 8440 Z= 0.292 Angle : 0.609 6.875 11494 Z= 0.317 Chirality : 0.042 0.146 1347 Planarity : 0.005 0.045 1458 Dihedral : 5.251 25.399 1122 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.88 % Favored : 91.02 % Rotamer: Outliers : 1.23 % Allowed : 13.82 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.58 (0.25), residues: 1047 helix: -1.07 (0.22), residues: 548 sheet: -2.80 (0.56), residues: 71 loop : -2.27 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 159 HIS 0.003 0.001 HIS C 197 PHE 0.021 0.001 PHE A 95 TYR 0.016 0.001 TYR B 176 ARG 0.004 0.000 ARG C 234 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 150 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 TYR cc_start: 0.8098 (t80) cc_final: 0.7822 (t80) REVERT: A 144 GLN cc_start: 0.7096 (mp-120) cc_final: 0.6869 (mp10) REVERT: A 236 ASP cc_start: 0.7939 (t0) cc_final: 0.7688 (t0) outliers start: 11 outliers final: 9 residues processed: 152 average time/residue: 0.3562 time to fit residues: 81.1095 Evaluate side-chains 156 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 147 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 203 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 52 optimal weight: 0.0980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8440 Z= 0.212 Angle : 0.579 6.525 11494 Z= 0.300 Chirality : 0.041 0.151 1347 Planarity : 0.005 0.044 1458 Dihedral : 5.183 26.231 1122 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.74 % Favored : 92.17 % Rotamer: Outliers : 1.11 % Allowed : 15.27 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.47 (0.25), residues: 1047 helix: -0.96 (0.22), residues: 548 sheet: -2.79 (0.57), residues: 71 loop : -2.23 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 159 HIS 0.004 0.001 HIS C 197 PHE 0.022 0.001 PHE A 154 TYR 0.014 0.001 TYR D 102 ARG 0.004 0.000 ARG C 234 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 149 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 TYR cc_start: 0.8051 (t80) cc_final: 0.7814 (t80) REVERT: A 144 GLN cc_start: 0.7025 (mp-120) cc_final: 0.6782 (mp10) REVERT: A 236 ASP cc_start: 0.7851 (t0) cc_final: 0.7584 (t0) outliers start: 10 outliers final: 10 residues processed: 153 average time/residue: 0.3375 time to fit residues: 76.1472 Evaluate side-chains 154 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 144 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 203 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 0.0980 chunk 11 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 72 optimal weight: 0.2980 chunk 83 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 62 optimal weight: 0.0670 chunk 60 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8440 Z= 0.161 Angle : 0.558 6.200 11494 Z= 0.286 Chirality : 0.041 0.148 1347 Planarity : 0.004 0.044 1458 Dihedral : 5.040 25.356 1122 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.07 % Favored : 92.84 % Rotamer: Outliers : 1.11 % Allowed : 15.72 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.26 (0.26), residues: 1047 helix: -0.77 (0.23), residues: 543 sheet: -2.64 (0.59), residues: 70 loop : -2.16 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 159 HIS 0.002 0.001 HIS C 122 PHE 0.015 0.001 PHE D 273 TYR 0.014 0.001 TYR D 102 ARG 0.005 0.000 ARG C 234 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 155 time to evaluate : 1.224 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: D 115 TYR cc_start: 0.8015 (t80) cc_final: 0.7805 (t80) REVERT: A 144 GLN cc_start: 0.6865 (mp-120) cc_final: 0.6629 (mp10) REVERT: A 236 ASP cc_start: 0.7816 (t0) cc_final: 0.7556 (t0) outliers start: 10 outliers final: 10 residues processed: 158 average time/residue: 0.3469 time to fit residues: 81.5731 Evaluate side-chains 160 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 150 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 203 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8440 Z= 0.272 Angle : 0.601 7.031 11494 Z= 0.311 Chirality : 0.042 0.146 1347 Planarity : 0.005 0.044 1458 Dihedral : 5.182 25.737 1122 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.31 % Favored : 91.60 % Rotamer: Outliers : 1.34 % Allowed : 16.61 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.38 (0.25), residues: 1047 helix: -0.84 (0.22), residues: 548 sheet: -2.78 (0.57), residues: 71 loop : -2.26 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 159 HIS 0.006 0.001 HIS C 197 PHE 0.021 0.001 PHE A 154 TYR 0.016 0.001 TYR B 176 ARG 0.004 0.000 ARG C 234 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 149 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 TYR cc_start: 0.8076 (t80) cc_final: 0.7811 (t80) REVERT: A 144 GLN cc_start: 0.7157 (mp-120) cc_final: 0.6913 (mp10) REVERT: A 236 ASP cc_start: 0.7883 (t0) cc_final: 0.7631 (t0) outliers start: 12 outliers final: 11 residues processed: 155 average time/residue: 0.3351 time to fit residues: 77.0117 Evaluate side-chains 160 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 149 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 203 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8440 Z= 0.200 Angle : 0.579 7.134 11494 Z= 0.297 Chirality : 0.042 0.150 1347 Planarity : 0.005 0.044 1458 Dihedral : 5.123 25.683 1122 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.83 % Favored : 92.07 % Rotamer: Outliers : 1.45 % Allowed : 16.50 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.24 (0.26), residues: 1047 helix: -0.73 (0.22), residues: 548 sheet: -2.70 (0.58), residues: 71 loop : -2.19 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 159 HIS 0.006 0.001 HIS D 137 PHE 0.021 0.001 PHE A 154 TYR 0.014 0.001 TYR D 102 ARG 0.005 0.000 ARG C 234 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 150 time to evaluate : 2.148 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: D 115 TYR cc_start: 0.8034 (t80) cc_final: 0.7803 (t80) REVERT: B 75 GLU cc_start: 0.7560 (pm20) cc_final: 0.7355 (pm20) REVERT: A 144 GLN cc_start: 0.7003 (mp-120) cc_final: 0.6776 (mp10) REVERT: A 236 ASP cc_start: 0.7828 (t0) cc_final: 0.7568 (t0) outliers start: 13 outliers final: 13 residues processed: 156 average time/residue: 0.3530 time to fit residues: 82.0818 Evaluate side-chains 160 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 147 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 203 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 102 optimal weight: 0.1980 chunk 94 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8440 Z= 0.179 Angle : 0.574 7.120 11494 Z= 0.294 Chirality : 0.042 0.185 1347 Planarity : 0.004 0.044 1458 Dihedral : 5.052 25.193 1122 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.35 % Favored : 92.55 % Rotamer: Outliers : 1.34 % Allowed : 17.28 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.10 (0.26), residues: 1047 helix: -0.60 (0.23), residues: 545 sheet: -2.63 (0.58), residues: 71 loop : -2.13 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 159 HIS 0.005 0.001 HIS D 137 PHE 0.022 0.001 PHE A 154 TYR 0.014 0.001 TYR D 102 ARG 0.005 0.000 ARG C 234 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 151 time to evaluate : 1.300 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: D 115 TYR cc_start: 0.8046 (t80) cc_final: 0.7824 (t80) REVERT: A 144 GLN cc_start: 0.6964 (mp-120) cc_final: 0.6733 (mp10) REVERT: A 236 ASP cc_start: 0.7812 (t0) cc_final: 0.7548 (t0) outliers start: 12 outliers final: 12 residues processed: 157 average time/residue: 0.3420 time to fit residues: 79.2671 Evaluate side-chains 160 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 148 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 203 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 0.2980 chunk 75 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 22 optimal weight: 0.1980 chunk 81 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 160 GLN ** 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 = 0.3789 r_free = 0.3789 target = 0.150122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.116675 restraints weight = 34543.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.122537 restraints weight = 16021.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.126272 restraints weight = 9997.389| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8440 Z= 0.178 Angle : 0.572 7.045 11494 Z= 0.292 Chirality : 0.041 0.150 1347 Planarity : 0.004 0.045 1458 Dihedral : 5.008 24.998 1122 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.35 % Favored : 92.55 % Rotamer: Outliers : 1.34 % Allowed : 17.28 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.99 (0.26), residues: 1047 helix: -0.49 (0.23), residues: 552 sheet: -2.59 (0.59), residues: 71 loop : -2.14 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 159 HIS 0.005 0.001 HIS D 137 PHE 0.021 0.001 PHE A 154 TYR 0.013 0.001 TYR D 102 ARG 0.005 0.000 ARG C 234 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3676.55 seconds wall clock time: 64 minutes 36.37 seconds (3876.37 seconds total)