Starting phenix.real_space_refine on Fri Jul 19 19:47:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6s_35205/07_2024/8i6s_35205_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6s_35205/07_2024/8i6s_35205.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6s_35205/07_2024/8i6s_35205.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6s_35205/07_2024/8i6s_35205.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6s_35205/07_2024/8i6s_35205_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6s_35205/07_2024/8i6s_35205_neut.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.032 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 20 5.16 5 C 5581 2.51 5 N 1432 2.21 5 O 1600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 131": "OE1" <-> "OE2" Residue "A PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 295": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8641 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2261 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 12, 'TRANS': 288} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 20, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "B" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1680 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 22} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 2316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2316 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 12, 'TRANS': 290} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 20} Unresolved non-hydrogen planarities: 40 Chain: "D" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1679 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 22} Unresolved non-hydrogen planarities: 45 Chain: "E" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 641 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 75} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.18, per 1000 atoms: 0.83 Number of scatterers: 8641 At special positions: 0 Unit cell: (66.066, 78.936, 179.322, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 20 16.00 P 6 15.00 Mg 2 11.99 O 1600 8.00 N 1432 7.00 C 5581 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 1.7 seconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2050 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 9 sheets defined 56.5% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 36 through 54 Processing helix chain 'A' and resid 55 through 69 removed outlier: 3.726A pdb=" N SER A 59 " --> pdb=" O HIS A 55 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 65 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR A 69 " --> pdb=" O VAL A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 81 removed outlier: 3.953A pdb=" N MET A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER A 77 " --> pdb=" O PRO A 73 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 117 removed outlier: 3.573A pdb=" N GLY A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU A 114 " --> pdb=" O GLN A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 142 removed outlier: 3.644A pdb=" N ALA A 133 " --> pdb=" O SER A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 178 removed outlier: 3.715A pdb=" N ARG A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 231 removed outlier: 3.541A pdb=" N ILE A 213 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE A 231 " --> pdb=" O ILE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 244 removed outlier: 4.262A pdb=" N ILE A 238 " --> pdb=" O ARG A 234 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A 241 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A 244 " --> pdb=" O VAL A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 293 removed outlier: 3.547A pdb=" N ARG A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) Proline residue: A 254 - end of helix removed outlier: 3.651A pdb=" N TYR A 257 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR A 262 " --> pdb=" O MET A 258 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP A 271 " --> pdb=" O GLY A 267 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY A 283 " --> pdb=" O ASN A 279 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N SER A 284 " --> pdb=" O TRP A 280 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL A 286 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ASN A 287 " --> pdb=" O GLY A 283 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU A 288 " --> pdb=" O SER A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 332 removed outlier: 3.508A pdb=" N THR A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG A 327 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS A 328 " --> pdb=" O ALA A 324 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU A 332 " --> pdb=" O HIS A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 49 Processing helix chain 'B' and resid 73 through 80 removed outlier: 3.925A pdb=" N LEU B 77 " --> pdb=" O GLN B 73 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLN B 80 " --> pdb=" O PHE B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 101 removed outlier: 3.858A pdb=" N ASN B 99 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE B 100 " --> pdb=" O VAL B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 112 No H-bonds generated for 'chain 'B' and resid 110 through 112' Processing helix chain 'B' and resid 113 through 125 removed outlier: 4.028A pdb=" N LEU B 122 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU B 123 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG B 124 " --> pdb=" O SER B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 removed outlier: 3.694A pdb=" N LEU B 138 " --> pdb=" O PRO B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 153 removed outlier: 4.120A pdb=" N GLN B 144 " --> pdb=" O THR B 140 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA B 151 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 186 removed outlier: 4.690A pdb=" N GLU B 175 " --> pdb=" O ARG B 171 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE B 180 " --> pdb=" O ILE B 176 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU B 181 " --> pdb=" O MET B 177 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP B 182 " --> pdb=" O GLY B 178 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B 186 " --> pdb=" O ASP B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 202 removed outlier: 3.632A pdb=" N ALA B 201 " --> pdb=" O ALA B 198 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG B 202 " --> pdb=" O LEU B 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 198 through 202' Processing helix chain 'C' and resid 34 through 54 Processing helix chain 'C' and resid 55 through 69 removed outlier: 3.632A pdb=" N PHE C 60 " --> pdb=" O PRO C 56 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS C 63 " --> pdb=" O SER C 59 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 65 " --> pdb=" O PHE C 61 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR C 69 " --> pdb=" O VAL C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 84 removed outlier: 3.833A pdb=" N MET C 74 " --> pdb=" O LEU C 70 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU C 84 " --> pdb=" O LEU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.587A pdb=" N ARG C 92 " --> pdb=" O SER C 89 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA C 93 " --> pdb=" O TRP C 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 89 through 93' Processing helix chain 'C' and resid 106 through 119 removed outlier: 3.565A pdb=" N ASP C 111 " --> pdb=" O ASN C 107 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU C 117 " --> pdb=" O ARG C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 removed outlier: 3.912A pdb=" N LEU C 137 " --> pdb=" O ALA C 133 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN C 138 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU C 139 " --> pdb=" O SER C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 173 removed outlier: 3.732A pdb=" N ALA C 173 " --> pdb=" O GLY C 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 170 through 173' Processing helix chain 'C' and resid 174 through 179 removed outlier: 3.610A pdb=" N LEU C 178 " --> pdb=" O LEU C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 196 removed outlier: 4.722A pdb=" N GLU C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG C 196 " --> pdb=" O VAL C 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 191 through 196' Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 202 through 233 removed outlier: 3.536A pdb=" N ILE C 213 " --> pdb=" O PHE C 209 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL C 216 " --> pdb=" O THR C 212 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL C 222 " --> pdb=" O THR C 218 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG C 228 " --> pdb=" O GLY C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 243 removed outlier: 4.510A pdb=" N GLU C 239 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL C 240 " --> pdb=" O ASN C 236 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE C 241 " --> pdb=" O GLU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 292 removed outlier: 3.712A pdb=" N VAL C 251 " --> pdb=" O THR C 247 " (cutoff:3.500A) Proline residue: C 254 - end of helix removed outlier: 3.684A pdb=" N TYR C 257 " --> pdb=" O ARG C 253 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET C 258 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR C 262 " --> pdb=" O MET C 258 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE C 268 " --> pdb=" O LEU C 264 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLY C 283 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N SER C 284 " --> pdb=" O TRP C 280 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL C 285 " --> pdb=" O LEU C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 332 removed outlier: 3.869A pdb=" N ALA C 326 " --> pdb=" O TRP C 322 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ARG C 327 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N HIS C 328 " --> pdb=" O ALA C 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 50 removed outlier: 3.661A pdb=" N ILE D 48 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 49 " --> pdb=" O LEU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 80 removed outlier: 3.927A pdb=" N LEU D 77 " --> pdb=" O GLN D 73 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN D 80 " --> pdb=" O PHE D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 101 Processing helix chain 'D' and resid 101 through 108 removed outlier: 3.742A pdb=" N GLN D 105 " --> pdb=" O ALA D 101 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE D 106 " --> pdb=" O LEU D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 112 No H-bonds generated for 'chain 'D' and resid 110 through 112' Processing helix chain 'D' and resid 113 through 122 removed outlier: 3.574A pdb=" N ARG D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL D 118 " --> pdb=" O ILE D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 153 removed outlier: 4.027A pdb=" N ARG D 145 " --> pdb=" O GLY D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 183 removed outlier: 3.957A pdb=" N SER D 174 " --> pdb=" O PRO D 170 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU D 175 " --> pdb=" O ARG D 171 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU D 181 " --> pdb=" O MET D 177 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP D 182 " --> pdb=" O GLY D 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 114 removed outlier: 3.612A pdb=" N GLN E 96 " --> pdb=" O LYS E 92 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA E 98 " --> pdb=" O LYS E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 163 removed outlier: 3.507A pdb=" N ARG E 148 " --> pdb=" O ILE E 144 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU E 149 " --> pdb=" O ASN E 145 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU E 150 " --> pdb=" O LYS E 146 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR E 158 " --> pdb=" O SER E 154 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN E 161 " --> pdb=" O GLU E 157 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 127 Processing sheet with id=AA2, first strand: chain 'B' and resid 21 through 25 removed outlier: 6.829A pdb=" N VAL B 21 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN B 6 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE B 4 " --> pdb=" O PHE B 23 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 32 through 33 removed outlier: 6.118A pdb=" N PHE B 32 " --> pdb=" O LEU B 208 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 59 through 61 removed outlier: 4.468A pdb=" N LEU B 59 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU B 61 " --> pdb=" O GLN B 64 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN B 64 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 158 through 159 Processing sheet with id=AA6, first strand: chain 'C' and resid 126 through 128 removed outlier: 4.181A pdb=" N GLN C 126 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE C 128 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL C 158 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 4 through 5 removed outlier: 4.016A pdb=" N GLU D 5 " --> pdb=" O LYS D 58 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS D 58 " --> pdb=" O GLU D 5 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU D 61 " --> pdb=" O GLN D 64 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN D 64 " --> pdb=" O LEU D 61 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 190 through 193 removed outlier: 3.882A pdb=" N VAL D 33 " --> pdb=" O ILE D 192 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N LEU D 208 " --> pdb=" O ILE D 30 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N PHE D 32 " --> pdb=" O LEU D 208 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N LEU D 210 " --> pdb=" O PHE D 32 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR D 34 " --> pdb=" O LEU D 210 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 81 through 82 removed outlier: 3.611A pdb=" N GLY D 82 " --> pdb=" O LEU D 158 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 361 hydrogen bonds defined for protein. 1071 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: 2.08 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2048 1.33 - 1.46: 1723 1.46 - 1.58: 4967 1.58 - 1.70: 10 1.70 - 1.83: 38 Bond restraints: 8786 Sorted by residual: bond pdb=" C6 ATP D 301 " pdb=" N6 ATP D 301 " ideal model delta sigma weight residual 1.337 1.449 -0.112 1.10e-02 8.26e+03 1.04e+02 bond pdb=" C6 ATP B 302 " pdb=" N6 ATP B 302 " ideal model delta sigma weight residual 1.337 1.449 -0.112 1.10e-02 8.26e+03 1.03e+02 bond pdb=" C5 ATP B 302 " pdb=" N7 ATP B 302 " ideal model delta sigma weight residual 1.387 1.469 -0.082 1.00e-02 1.00e+04 6.69e+01 bond pdb=" C5 ATP D 301 " pdb=" N7 ATP D 301 " ideal model delta sigma weight residual 1.387 1.468 -0.081 1.00e-02 1.00e+04 6.57e+01 bond pdb=" O5' ATP D 301 " pdb=" PA ATP D 301 " ideal model delta sigma weight residual 1.579 1.650 -0.071 1.10e-02 8.26e+03 4.14e+01 ... (remaining 8781 not shown) Histogram of bond angle deviations from ideal: 97.81 - 105.50: 182 105.50 - 113.18: 4802 113.18 - 120.87: 4183 120.87 - 128.56: 2637 128.56 - 136.24: 82 Bond angle restraints: 11886 Sorted by residual: angle pdb=" PB ATP B 302 " pdb=" O3B ATP B 302 " pdb=" PG ATP B 302 " ideal model delta sigma weight residual 139.87 116.52 23.35 1.00e+00 1.00e+00 5.45e+02 angle pdb=" PB ATP D 301 " pdb=" O3B ATP D 301 " pdb=" PG ATP D 301 " ideal model delta sigma weight residual 139.87 125.37 14.50 1.00e+00 1.00e+00 2.10e+02 angle pdb=" PA ATP B 302 " pdb=" O3A ATP B 302 " pdb=" PB ATP B 302 " ideal model delta sigma weight residual 136.83 122.76 14.07 1.00e+00 1.00e+00 1.98e+02 angle pdb=" O3A ATP B 302 " pdb=" PB ATP B 302 " pdb=" O3B ATP B 302 " ideal model delta sigma weight residual 101.57 116.72 -15.15 1.54e+00 4.24e-01 9.73e+01 angle pdb=" PA ATP D 301 " pdb=" O3A ATP D 301 " pdb=" PB ATP D 301 " ideal model delta sigma weight residual 136.83 127.43 9.40 1.00e+00 1.00e+00 8.84e+01 ... (remaining 11881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4659 17.97 - 35.95: 550 35.95 - 53.92: 125 53.92 - 71.89: 23 71.89 - 89.86: 9 Dihedral angle restraints: 5366 sinusoidal: 2178 harmonic: 3188 Sorted by residual: dihedral pdb=" CA VAL A 192 " pdb=" C VAL A 192 " pdb=" N TRP A 193 " pdb=" CA TRP A 193 " ideal model delta harmonic sigma weight residual 180.00 137.38 42.62 0 5.00e+00 4.00e-02 7.27e+01 dihedral pdb=" CA ASP C 190 " pdb=" C ASP C 190 " pdb=" N LEU C 191 " pdb=" CA LEU C 191 " ideal model delta harmonic sigma weight residual -180.00 -157.62 -22.38 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA LEU A 229 " pdb=" C LEU A 229 " pdb=" N HIS A 230 " pdb=" CA HIS A 230 " ideal model delta harmonic sigma weight residual 180.00 157.90 22.10 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 5363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1133 0.073 - 0.146: 224 0.146 - 0.219: 46 0.219 - 0.292: 5 0.292 - 0.365: 3 Chirality restraints: 1411 Sorted by residual: chirality pdb=" CB ILE B 215 " pdb=" CA ILE B 215 " pdb=" CG1 ILE B 215 " pdb=" CG2 ILE B 215 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CB ILE D 2 " pdb=" CA ILE D 2 " pdb=" CG1 ILE D 2 " pdb=" CG2 ILE D 2 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CB VAL B 125 " pdb=" CA VAL B 125 " pdb=" CG1 VAL B 125 " pdb=" CG2 VAL B 125 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 1408 not shown) Planarity restraints: 1476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 195 " -0.045 2.00e-02 2.50e+03 6.17e-02 5.71e+01 pdb=" CG HIS B 195 " 0.107 2.00e-02 2.50e+03 pdb=" ND1 HIS B 195 " -0.056 2.00e-02 2.50e+03 pdb=" CD2 HIS B 195 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS B 195 " 0.050 2.00e-02 2.50e+03 pdb=" NE2 HIS B 195 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 192 " -0.025 2.00e-02 2.50e+03 4.92e-02 2.42e+01 pdb=" C VAL A 192 " 0.085 2.00e-02 2.50e+03 pdb=" O VAL A 192 " -0.032 2.00e-02 2.50e+03 pdb=" N TRP A 193 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 280 " -0.013 2.00e-02 2.50e+03 1.55e-02 6.01e+00 pdb=" CG TRP C 280 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP C 280 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP C 280 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 280 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 280 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 280 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 280 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 280 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 280 " 0.001 2.00e-02 2.50e+03 ... (remaining 1473 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 84 2.64 - 3.20: 7059 3.20 - 3.77: 13820 3.77 - 4.33: 17569 4.33 - 4.90: 27254 Nonbonded interactions: 65786 Sorted by model distance: nonbonded pdb=" OG1 THR B 140 " pdb="MG MG B 301 " model vdw 2.073 2.170 nonbonded pdb="MG MG B 301 " pdb=" O3A ATP D 301 " model vdw 2.077 2.170 nonbonded pdb=" O1A ATP B 302 " pdb="MG MG B 303 " model vdw 2.133 2.170 nonbonded pdb="MG MG B 301 " pdb=" O2B ATP D 301 " model vdw 2.135 2.170 nonbonded pdb=" O1B ATP B 302 " pdb="MG MG B 303 " model vdw 2.253 2.170 ... (remaining 65781 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 'C' and (resid 35 through 88 or (resid 89 and (name N or name CA or name \ C or name O or name CB )) or resid 90 or (resid 91 through 95 and (name N or nam \ e CA or name C or name O or name CB )) or resid 96 through 122 or (resid 123 and \ (name N or name CA or name C or name O or name CB )) or resid 124 through 164 o \ r (resid 165 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 66 or (resid 167 through 169 and (name N or name CA or name C or name O or name \ CB )) or resid 170 or (resid 171 and (name N or name CA or name C or name O or n \ ame CB )) or resid 172 through 194 or (resid 195 and (name N or name CA or name \ C or name O or name CB )) or resid 196 or (resid 197 through 199 and (name N or \ name CA or name C or name O or name CB )) or resid 200 through 335)) } ncs_group { reference = (chain 'B' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ )) or resid 12 through 222)) selection = (chain 'D' and resid 1 through 222) } 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: 14.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.670 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6010 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 : 0.006 0.112 8786 Z= 0.421 Angle : 1.394 23.352 11886 Z= 0.763 Chirality : 0.063 0.365 1411 Planarity : 0.007 0.062 1476 Dihedral : 16.404 89.863 3316 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.13 % Favored : 95.70 % Rotamer: Outliers : 0.97 % Allowed : 2.48 % Favored : 96.54 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -5.18 (0.17), residues: 1115 helix: -4.23 (0.09), residues: 575 sheet: -0.91 (0.68), residues: 55 loop : -2.52 (0.22), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 280 HIS 0.080 0.004 HIS B 195 PHE 0.039 0.001 PHE D 180 TYR 0.040 0.002 TYR A 250 ARG 0.004 0.000 ARG E 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 120 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.6692 (mmp) cc_final: 0.6455 (mmp) REVERT: A 215 LEU cc_start: 0.6983 (mm) cc_final: 0.5502 (tp) REVERT: B 162 ASP cc_start: 0.7197 (p0) cc_final: 0.6967 (p0) REVERT: C 66 MET cc_start: 0.4364 (tpt) cc_final: 0.3997 (tpt) REVERT: D 154 HIS cc_start: 0.6844 (p-80) cc_final: 0.5443 (t-90) outliers start: 9 outliers final: 9 residues processed: 126 average time/residue: 0.1613 time to fit residues: 30.4772 Evaluate side-chains 85 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.0970 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 64 optimal weight: 0.0170 chunk 100 optimal weight: 0.4980 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS A 230 HIS C 82 ASN ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6007 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8786 Z= 0.155 Angle : 0.629 6.898 11886 Z= 0.319 Chirality : 0.040 0.172 1411 Planarity : 0.004 0.034 1476 Dihedral : 8.531 76.635 1213 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.14 % Favored : 96.68 % Rotamer: Outliers : 0.97 % Allowed : 5.29 % Favored : 93.74 % 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 (0.22), residues: 1115 helix: -1.45 (0.19), residues: 579 sheet: -0.80 (0.71), residues: 53 loop : -2.02 (0.24), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 271 HIS 0.022 0.001 HIS B 195 PHE 0.012 0.001 PHE C 207 TYR 0.007 0.001 TYR A 250 ARG 0.001 0.000 ARG E 111 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 106 time to evaluate : 1.067 Fit side-chains revert: symmetry clash REVERT: A 215 LEU cc_start: 0.7185 (mm) cc_final: 0.5648 (tp) REVERT: A 230 HIS cc_start: 0.5367 (OUTLIER) cc_final: 0.5072 (t70) REVERT: B 51 MET cc_start: 0.2116 (ppp) cc_final: 0.1209 (ptt) REVERT: B 86 GLN cc_start: 0.7783 (mm-40) cc_final: 0.7296 (mm-40) REVERT: B 162 ASP cc_start: 0.7361 (p0) cc_final: 0.6767 (p0) REVERT: C 295 ASP cc_start: 0.7954 (p0) cc_final: 0.7673 (p0) outliers start: 9 outliers final: 8 residues processed: 113 average time/residue: 0.1618 time to fit residues: 27.8706 Evaluate side-chains 85 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.3980 chunk 31 optimal weight: 3.9990 chunk 83 optimal weight: 0.4980 chunk 68 optimal weight: 0.0570 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 89 optimal weight: 0.1980 chunk 34 optimal weight: 0.8980 chunk 81 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN C 230 HIS ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6020 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8786 Z= 0.138 Angle : 0.592 6.614 11886 Z= 0.289 Chirality : 0.040 0.148 1411 Planarity : 0.003 0.030 1476 Dihedral : 8.051 69.083 1213 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.14 % Favored : 96.68 % Rotamer: Outliers : 0.86 % Allowed : 6.59 % Favored : 92.55 % 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: -1.22 (0.24), residues: 1115 helix: -0.01 (0.21), residues: 589 sheet: -0.86 (0.69), residues: 53 loop : -1.81 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 271 HIS 0.016 0.001 HIS B 195 PHE 0.028 0.001 PHE D 180 TYR 0.007 0.001 TYR E 114 ARG 0.001 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 107 time to evaluate : 1.047 Fit side-chains revert: symmetry clash REVERT: A 45 LEU cc_start: 0.9084 (tt) cc_final: 0.8832 (pp) REVERT: A 215 LEU cc_start: 0.7406 (mm) cc_final: 0.5845 (tp) REVERT: B 86 GLN cc_start: 0.7928 (mm-40) cc_final: 0.7430 (mm-40) REVERT: B 162 ASP cc_start: 0.7362 (p0) cc_final: 0.6695 (p0) outliers start: 8 outliers final: 8 residues processed: 112 average time/residue: 0.1624 time to fit residues: 27.8878 Evaluate side-chains 84 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 chunk 107 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 89 optimal weight: 0.0030 chunk 60 optimal weight: 0.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 GLN ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6096 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8786 Z= 0.150 Angle : 0.601 7.103 11886 Z= 0.292 Chirality : 0.040 0.149 1411 Planarity : 0.003 0.030 1476 Dihedral : 7.801 65.346 1213 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.14 % Favored : 96.68 % Rotamer: Outliers : 0.86 % Allowed : 6.26 % Favored : 92.87 % 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: -0.64 (0.25), residues: 1115 helix: 0.52 (0.22), residues: 594 sheet: -0.87 (0.70), residues: 53 loop : -1.59 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 318 HIS 0.018 0.001 HIS B 195 PHE 0.021 0.001 PHE C 53 TYR 0.008 0.001 TYR C 37 ARG 0.001 0.000 ARG E 148 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 101 time to evaluate : 1.076 Fit side-chains revert: symmetry clash REVERT: A 45 LEU cc_start: 0.9128 (tt) cc_final: 0.8887 (pp) REVERT: B 51 MET cc_start: 0.2043 (ppp) cc_final: 0.1604 (ptt) REVERT: B 86 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7577 (mm-40) REVERT: B 162 ASP cc_start: 0.7463 (p0) cc_final: 0.6733 (p0) REVERT: C 53 PHE cc_start: 0.7404 (m-80) cc_final: 0.7159 (m-80) REVERT: D 180 PHE cc_start: 0.8885 (m-10) cc_final: 0.8613 (m-80) outliers start: 8 outliers final: 8 residues processed: 106 average time/residue: 0.1519 time to fit residues: 24.6885 Evaluate side-chains 86 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 78 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.2786 > 50: distance: 39 - 45: 20.285 distance: 40 - 86: 24.501 distance: 45 - 46: 31.543 distance: 46 - 47: 25.076 distance: 46 - 49: 38.029 distance: 47 - 48: 31.862 distance: 47 - 53: 42.433 distance: 49 - 50: 34.811 distance: 50 - 51: 3.398 distance: 50 - 52: 24.627 distance: 53 - 54: 23.112 distance: 54 - 55: 13.495 distance: 54 - 57: 23.592 distance: 55 - 56: 27.359 distance: 55 - 61: 19.775 distance: 57 - 58: 40.371 distance: 58 - 59: 6.935 distance: 58 - 60: 45.196 distance: 61 - 62: 36.485 distance: 62 - 63: 51.112 distance: 63 - 64: 51.848 distance: 63 - 65: 44.637 distance: 65 - 66: 39.676 distance: 66 - 67: 11.767 distance: 67 - 68: 50.198 distance: 67 - 69: 55.553 distance: 69 - 70: 23.870 distance: 70 - 71: 29.297 distance: 70 - 73: 45.479 distance: 71 - 72: 40.701 distance: 71 - 78: 42.387 distance: 73 - 74: 52.652 distance: 75 - 76: 18.998 distance: 75 - 77: 20.917 distance: 78 - 79: 52.698 distance: 79 - 80: 7.297 distance: 79 - 82: 21.160 distance: 80 - 81: 11.959 distance: 80 - 86: 32.863 distance: 82 - 83: 34.022 distance: 83 - 84: 38.742 distance: 83 - 85: 47.062 distance: 86 - 87: 30.282 distance: 87 - 88: 39.884 distance: 87 - 90: 7.576 distance: 88 - 89: 19.447 distance: 88 - 94: 29.673 distance: 90 - 91: 50.915 distance: 91 - 92: 9.420 distance: 91 - 93: 22.035 distance: 94 - 95: 33.581 distance: 96 - 97: 30.019 distance: 96 - 98: 11.476 distance: 98 - 99: 54.013 distance: 99 - 100: 39.418 distance: 99 - 102: 39.139 distance: 100 - 101: 31.422 distance: 100 - 107: 40.976 distance: 102 - 103: 50.462 distance: 103 - 104: 40.753 distance: 104 - 105: 7.636 distance: 105 - 106: 33.425 distance: 107 - 108: 30.451 distance: 108 - 109: 35.269 distance: 108 - 111: 33.975 distance: 109 - 110: 3.865 distance: 109 - 115: 32.767 distance: 111 - 112: 39.839 distance: 111 - 113: 56.806 distance: 112 - 114: 43.225