Starting phenix.real_space_refine on Fri Nov 15 11:24:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6s_35205/11_2024/8i6s_35205.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6s_35205/11_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_35205/11_2024/8i6s_35205.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6s_35205/11_2024/8i6s_35205.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6s_35205/11_2024/8i6s_35205.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6s_35205/11_2024/8i6s_35205.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. Time to flip 6 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 9.04, per 1000 atoms: 1.05 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 - 3.00 Amino acid : True - 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: 2.35 Conformation dependent library (CDL) restraints added in 1.1 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: 0.94 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: 2.24 Time building geometry restraints manager: 2.69 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: 0.00 - 4.67: 11671 4.67 - 9.34: 180 9.34 - 14.01: 29 14.01 - 18.68: 5 18.68 - 23.35: 1 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 Time spend for trying shortcut: 0.00 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: 10.350 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: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 26.500 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 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:2.890 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.340 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 1.044 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: 0.1647 time to fit residues: 31.2690 Evaluate side-chains 85 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 1.072 ------------------------------------------------------------------------------- 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: 40.0000 chunk 84 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 87 optimal weight: 9.9990 chunk 33 optimal weight: 0.0970 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 0.0170 chunk 100 optimal weight: 0.7980 overall best weight: 0.4216 ------------------------------------------------------------------------------- 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 ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6015 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8786 Z= 0.158 Angle : 0.644 7.140 11886 Z= 0.324 Chirality : 0.041 0.187 1411 Planarity : 0.004 0.034 1476 Dihedral : 8.352 72.386 1213 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.32 % Favored : 96.50 % Rotamer: Outliers : 1.08 % Allowed : 5.18 % 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: -2.62 (0.22), residues: 1115 helix: -1.52 (0.18), residues: 585 sheet: -0.85 (0.71), residues: 53 loop : -1.99 (0.25), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 271 HIS 0.021 0.001 HIS B 195 PHE 0.011 0.001 PHE B 85 TYR 0.007 0.001 TYR A 250 ARG 0.002 0.000 ARG E 148 *********************** 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 116 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.9013 (tt) cc_final: 0.8784 (pp) REVERT: B 162 ASP cc_start: 0.7342 (p0) cc_final: 0.6859 (p0) REVERT: C 295 ASP cc_start: 0.7930 (p0) cc_final: 0.7676 (p0) outliers start: 10 outliers final: 9 residues processed: 113 average time/residue: 0.1679 time to fit residues: 28.6530 Evaluate side-chains 86 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 1.290 ------------------------------------------------------------------------------- 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: 0.8980 chunk 31 optimal weight: 0.1980 chunk 83 optimal weight: 0.5980 chunk 68 optimal weight: 0.3980 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 89 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6048 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8786 Z= 0.141 Angle : 0.608 7.339 11886 Z= 0.298 Chirality : 0.041 0.157 1411 Planarity : 0.003 0.032 1476 Dihedral : 7.741 60.320 1213 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.32 % Favored : 96.50 % Rotamer: Outliers : 0.97 % Allowed : 6.70 % Favored : 92.33 % 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: -1.35 (0.24), residues: 1115 helix: -0.14 (0.21), residues: 581 sheet: -0.94 (0.69), residues: 53 loop : -1.80 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 271 HIS 0.019 0.001 HIS B 195 PHE 0.010 0.001 PHE C 207 TYR 0.009 0.001 TYR C 37 ARG 0.001 0.000 ARG E 148 *********************** 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 to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.6819 (mm) cc_final: 0.6605 (mt) REVERT: B 51 MET cc_start: 0.1971 (ppp) cc_final: 0.1223 (ptt) REVERT: B 86 GLN cc_start: 0.7763 (mm-40) cc_final: 0.7317 (mm-40) REVERT: B 162 ASP cc_start: 0.7443 (p0) cc_final: 0.6924 (p0) REVERT: C 295 ASP cc_start: 0.7952 (p0) cc_final: 0.7614 (p0) REVERT: D 180 PHE cc_start: 0.8903 (m-10) cc_final: 0.8639 (m-80) outliers start: 9 outliers final: 9 residues processed: 112 average time/residue: 0.1617 time to fit residues: 27.5917 Evaluate side-chains 85 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 1.047 ------------------------------------------------------------------------------- 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: 2.9990 chunk 52 optimal weight: 6.9990 chunk 11 optimal weight: 0.3980 chunk 48 optimal weight: 0.0050 chunk 67 optimal weight: 6.9990 chunk 101 optimal weight: 0.0010 chunk 107 optimal weight: 5.9990 chunk 96 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.4000 ------------------------------------------------------------------------------- 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 D 154 HIS ** 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: 0.6034 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8786 Z= 0.135 Angle : 0.602 7.120 11886 Z= 0.291 Chirality : 0.041 0.152 1411 Planarity : 0.003 0.031 1476 Dihedral : 7.379 59.219 1213 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.50 % Favored : 96.41 % Rotamer: Outliers : 0.86 % Allowed : 5.62 % Favored : 93.52 % 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: -0.77 (0.25), residues: 1115 helix: 0.45 (0.22), residues: 585 sheet: -0.87 (0.70), residues: 53 loop : -1.67 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 271 HIS 0.018 0.001 HIS B 195 PHE 0.007 0.001 PHE C 207 TYR 0.010 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 114 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 1.116 Fit side-chains revert: symmetry clash REVERT: B 51 MET cc_start: 0.1974 (ppp) cc_final: 0.1351 (ptt) REVERT: B 162 ASP cc_start: 0.7353 (p0) cc_final: 0.6798 (p0) REVERT: C 295 ASP cc_start: 0.8023 (p0) cc_final: 0.7672 (p0) REVERT: D 180 PHE cc_start: 0.8858 (m-10) cc_final: 0.8565 (m-80) outliers start: 8 outliers final: 8 residues processed: 111 average time/residue: 0.1617 time to fit residues: 27.4437 Evaluate side-chains 89 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS A 282 ASN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 HIS ** 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: 0.6145 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8786 Z= 0.167 Angle : 0.629 8.257 11886 Z= 0.308 Chirality : 0.042 0.149 1411 Planarity : 0.003 0.032 1476 Dihedral : 6.797 58.794 1213 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.59 % Favored : 96.32 % Rotamer: Outliers : 0.86 % Allowed : 4.43 % Favored : 94.71 % 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: -0.51 (0.25), residues: 1115 helix: 0.64 (0.22), residues: 590 sheet: -1.09 (0.63), residues: 63 loop : -1.50 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 318 HIS 0.012 0.001 HIS B 195 PHE 0.009 0.001 PHE C 255 TYR 0.010 0.001 TYR C 37 ARG 0.001 0.000 ARG E 148 *********************** REFINEMENT MACRO_CYCLE 5 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 108 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 162 ASP cc_start: 0.7453 (p0) cc_final: 0.6884 (p0) REVERT: C 295 ASP cc_start: 0.8006 (p0) cc_final: 0.7637 (p0) REVERT: D 180 PHE cc_start: 0.8988 (m-10) cc_final: 0.8690 (m-80) outliers start: 8 outliers final: 8 residues processed: 105 average time/residue: 0.1636 time to fit residues: 26.1772 Evaluate side-chains 83 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 103 optimal weight: 8.9990 chunk 12 optimal weight: 0.0060 chunk 61 optimal weight: 6.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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** B 167 ASN C 230 HIS ** D 154 HIS ** 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: 0.6105 moved from start: 0.2852 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= 0.146 Angle : 0.622 7.843 11886 Z= 0.299 Chirality : 0.041 0.167 1411 Planarity : 0.003 0.031 1476 Dihedral : 6.745 58.799 1213 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.50 % Favored : 96.41 % Rotamer: Outliers : 0.86 % Allowed : 4.21 % Favored : 94.92 % 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: -0.30 (0.26), residues: 1115 helix: 0.86 (0.23), residues: 585 sheet: -1.21 (0.63), residues: 63 loop : -1.41 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 271 HIS 0.024 0.002 HIS B 195 PHE 0.025 0.001 PHE C 53 TYR 0.010 0.001 TYR C 37 ARG 0.001 0.000 ARG E 148 *********************** REFINEMENT MACRO_CYCLE 6 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 108 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 1.081 Fit side-chains REVERT: B 162 ASP cc_start: 0.7443 (p0) cc_final: 0.6863 (p0) REVERT: C 38 LEU cc_start: 0.7959 (tp) cc_final: 0.7656 (tp) REVERT: C 295 ASP cc_start: 0.7978 (p0) cc_final: 0.7618 (p0) REVERT: D 180 PHE cc_start: 0.8999 (m-10) cc_final: 0.8656 (m-80) outliers start: 8 outliers final: 8 residues processed: 105 average time/residue: 0.1610 time to fit residues: 25.9866 Evaluate side-chains 85 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 66 optimal weight: 0.6980 chunk 65 optimal weight: 0.0770 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 0.0060 chunk 63 optimal weight: 0.0170 chunk 32 optimal weight: 1.9990 overall best weight: 0.3594 ------------------------------------------------------------------------------- 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 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6076 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8786 Z= 0.139 Angle : 0.621 7.711 11886 Z= 0.296 Chirality : 0.041 0.170 1411 Planarity : 0.003 0.031 1476 Dihedral : 6.603 60.004 1213 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.50 % Favored : 96.41 % Rotamer: Outliers : 1.08 % Allowed : 4.00 % Favored : 94.92 % 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: -0.15 (0.26), residues: 1115 helix: 0.97 (0.23), residues: 586 sheet: -1.15 (0.64), residues: 63 loop : -1.33 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 271 HIS 0.013 0.001 HIS B 195 PHE 0.009 0.001 PHE C 207 TYR 0.009 0.001 TYR C 37 ARG 0.001 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 7 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 111 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.9102 (tt) cc_final: 0.8886 (pp) REVERT: B 162 ASP cc_start: 0.7406 (p0) cc_final: 0.6836 (p0) REVERT: C 295 ASP cc_start: 0.7956 (p0) cc_final: 0.7598 (p0) REVERT: D 180 PHE cc_start: 0.8972 (m-10) cc_final: 0.8704 (m-80) outliers start: 10 outliers final: 10 residues processed: 108 average time/residue: 0.1570 time to fit residues: 26.2277 Evaluate side-chains 87 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 0.1980 chunk 72 optimal weight: 0.0020 chunk 52 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 chunk 99 optimal weight: 0.0870 overall best weight: 0.3966 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6058 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8786 Z= 0.138 Angle : 0.619 7.998 11886 Z= 0.294 Chirality : 0.042 0.161 1411 Planarity : 0.003 0.032 1476 Dihedral : 6.555 60.631 1213 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.50 % Favored : 96.41 % Rotamer: Outliers : 1.19 % Allowed : 3.24 % Favored : 95.57 % 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: -0.04 (0.26), residues: 1115 helix: 1.09 (0.23), residues: 586 sheet: -1.07 (0.66), residues: 63 loop : -1.32 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 271 HIS 0.011 0.001 HIS B 195 PHE 0.008 0.001 PHE C 207 TYR 0.018 0.001 TYR E 143 ARG 0.001 0.000 ARG E 148 *********************** REFINEMENT MACRO_CYCLE 8 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 to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: A 45 LEU cc_start: 0.9139 (tt) cc_final: 0.8905 (pp) REVERT: B 162 ASP cc_start: 0.7401 (p0) cc_final: 0.6844 (p0) REVERT: C 82 ASN cc_start: 0.3954 (OUTLIER) cc_final: 0.3726 (t0) REVERT: C 295 ASP cc_start: 0.7965 (p0) cc_final: 0.7619 (p0) REVERT: D 180 PHE cc_start: 0.8937 (m-10) cc_final: 0.8672 (m-80) outliers start: 11 outliers final: 10 residues processed: 112 average time/residue: 0.1611 time to fit residues: 27.5022 Evaluate side-chains 87 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 0.0270 chunk 78 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 94 optimal weight: 0.4980 chunk 99 optimal weight: 0.8980 chunk 65 optimal weight: 20.0000 chunk 105 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6099 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8786 Z= 0.151 Angle : 0.644 8.345 11886 Z= 0.306 Chirality : 0.042 0.162 1411 Planarity : 0.003 0.032 1476 Dihedral : 6.697 61.680 1213 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.96 % Rotamer: Outliers : 1.08 % Allowed : 2.70 % Favored : 96.22 % 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: 0.05 (0.26), residues: 1115 helix: 1.17 (0.23), residues: 585 sheet: -1.11 (0.65), residues: 63 loop : -1.28 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 271 HIS 0.027 0.001 HIS B 195 PHE 0.009 0.001 PHE A 99 TYR 0.010 0.001 TYR C 37 ARG 0.002 0.000 ARG E 148 *********************** REFINEMENT MACRO_CYCLE 9 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 108 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 1.064 Fit side-chains REVERT: B 162 ASP cc_start: 0.7418 (p0) cc_final: 0.6887 (p0) REVERT: C 38 LEU cc_start: 0.7979 (tp) cc_final: 0.7667 (tp) REVERT: C 295 ASP cc_start: 0.7953 (p0) cc_final: 0.7607 (p0) REVERT: D 180 PHE cc_start: 0.8894 (m-10) cc_final: 0.8638 (m-80) outliers start: 10 outliers final: 10 residues processed: 105 average time/residue: 0.1645 time to fit residues: 26.3780 Evaluate side-chains 85 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 8.9990 chunk 73 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 0.0770 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 93 optimal weight: 0.3980 chunk 26 optimal weight: 0.9990 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN C 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6094 moved from start: 0.3322 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= 0.151 Angle : 0.652 8.680 11886 Z= 0.310 Chirality : 0.042 0.152 1411 Planarity : 0.003 0.032 1476 Dihedral : 6.645 59.355 1213 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.59 % Favored : 96.32 % Rotamer: Outliers : 1.08 % Allowed : 2.16 % Favored : 96.76 % 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: 0.08 (0.26), residues: 1115 helix: 1.22 (0.23), residues: 586 sheet: -1.18 (0.62), residues: 70 loop : -1.28 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 271 HIS 0.023 0.001 HIS B 195 PHE 0.031 0.001 PHE C 53 TYR 0.009 0.001 TYR C 37 ARG 0.002 0.000 ARG E 148 ********************** REFINEMENT MACRO_CYCLE 10 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 108 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 1.028 Fit side-chains REVERT: B 162 ASP cc_start: 0.7454 (p0) cc_final: 0.6909 (p0) REVERT: C 295 ASP cc_start: 0.7947 (p0) cc_final: 0.7595 (p0) REVERT: D 180 PHE cc_start: 0.8866 (m-10) cc_final: 0.8662 (m-80) outliers start: 10 outliers final: 10 residues processed: 105 average time/residue: 0.1584 time to fit residues: 25.4943 Evaluate side-chains 85 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 88 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 chunk 16 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 5 optimal weight: 0.0870 chunk 63 optimal weight: 2.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.095849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.079029 restraints weight = 53423.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.080543 restraints weight = 38949.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.081672 restraints weight = 31029.377| |-----------------------------------------------------------------------------| r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6237 moved from start: 0.3404 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= 0.147 Angle : 0.649 8.586 11886 Z= 0.307 Chirality : 0.042 0.153 1411 Planarity : 0.003 0.032 1476 Dihedral : 6.553 59.176 1213 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.96 % Rotamer: Outliers : 1.08 % Allowed : 2.38 % Favored : 96.54 % 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: 0.17 (0.27), residues: 1115 helix: 1.31 (0.23), residues: 585 sheet: -1.26 (0.61), residues: 70 loop : -1.23 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 271 HIS 0.020 0.001 HIS B 195 PHE 0.007 0.001 PHE A 99 TYR 0.009 0.001 TYR C 37 ARG 0.002 0.000 ARG E 148 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2020.33 seconds wall clock time: 37 minutes 40.41 seconds (2260.41 seconds total)