Starting phenix.real_space_refine on Sun Nov 17 04:24:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpr_34941/11_2024/8hpr_34941.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpr_34941/11_2024/8hpr_34941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpr_34941/11_2024/8hpr_34941.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpr_34941/11_2024/8hpr_34941.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpr_34941/11_2024/8hpr_34941.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpr_34941/11_2024/8hpr_34941.cif" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned 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 33 5.16 5 C 8071 2.51 5 N 2147 2.21 5 O 2386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 86 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12645 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2013 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 14, 'TRANS': 262} Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1848 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 16, 'TRANS': 240} Chain breaks: 1 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 1, 'ARG:plan': 2, 'TRP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "C" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2695 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 345} Chain breaks: 2 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "D" Number of atoms: 2719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2719 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 344} Chain breaks: 2 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "E" Number of atoms: 3283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3283 Classifications: {'peptide': 437} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 405} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "H" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.77, per 1000 atoms: 0.69 Number of scatterers: 12645 At special positions: 0 Unit cell: (82.82, 84.46, 169.74, 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 33 16.00 P 6 15.00 Mg 2 11.99 O 2386 8.00 N 2147 7.00 C 8071 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=0, symmetry=0 Links applied ALPHA1-1 " GLC H 1 " - " GLC H 2 " Time building additional restraints: 3.38 Conformation dependent library (CDL) restraints added in 1.8 seconds 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3154 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 13 sheets defined 56.1% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 23 through 28 Processing helix chain 'A' and resid 28 through 51 removed outlier: 4.478A pdb=" N LEU A 34 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALA A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) Proline residue: A 42 - end of helix Processing helix chain 'A' and resid 67 through 74 Processing helix chain 'A' and resid 76 through 110 removed outlier: 4.059A pdb=" N TRP A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 123 through 128 Processing helix chain 'A' and resid 129 through 142 Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 157 through 160 Processing helix chain 'A' and resid 161 through 191 Proline residue: A 179 - end of helix removed outlier: 3.648A pdb=" N LEU A 184 " --> pdb=" O PHE A 180 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU A 191 " --> pdb=" O ALA A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 203 removed outlier: 3.943A pdb=" N LEU A 197 " --> pdb=" O PRO A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 214 Processing helix chain 'A' and resid 214 through 237 Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 253 through 264 removed outlier: 3.603A pdb=" N TYR A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 292 removed outlier: 4.384A pdb=" N ILE A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 37 removed outlier: 4.263A pdb=" N TRP B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Proline residue: B 27 - end of helix Processing helix chain 'B' and resid 54 through 62 Processing helix chain 'B' and resid 64 through 84 removed outlier: 3.859A pdb=" N GLY B 75 " --> pdb=" O PHE B 71 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 98 removed outlier: 3.977A pdb=" N MET B 90 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 116 Processing helix chain 'B' and resid 117 through 133 removed outlier: 3.644A pdb=" N LEU B 121 " --> pdb=" O PRO B 117 " (cutoff:3.500A) Proline residue: B 124 - end of helix removed outlier: 3.570A pdb=" N ASN B 127 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY B 131 " --> pdb=" O ASN B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 149 removed outlier: 3.855A pdb=" N LEU B 141 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ILE B 143 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Proline residue: B 144 - end of helix Processing helix chain 'B' and resid 154 through 162 Processing helix chain 'B' and resid 165 through 175 removed outlier: 3.653A pdb=" N GLU B 169 " --> pdb=" O PRO B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 187 removed outlier: 4.010A pdb=" N ARG B 184 " --> pdb=" O ALA B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 207 Proline residue: B 193 - end of helix removed outlier: 5.104A pdb=" N THR B 197 " --> pdb=" O PRO B 193 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ALA B 198 " --> pdb=" O GLY B 194 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 217 Processing helix chain 'B' and resid 224 through 231 Processing helix chain 'B' and resid 241 through 263 removed outlier: 3.759A pdb=" N ILE B 254 " --> pdb=" O MET B 250 " (cutoff:3.500A) Proline residue: B 255 - end of helix Processing helix chain 'C' and resid 46 through 55 Processing helix chain 'C' and resid 76 through 81 removed outlier: 3.604A pdb=" N ARG C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP C 81 " --> pdb=" O PRO C 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 76 through 81' Processing helix chain 'C' and resid 96 through 108 Proline residue: C 104 - end of helix Processing helix chain 'C' and resid 111 through 127 Processing helix chain 'C' and resid 135 through 139 Processing helix chain 'C' and resid 141 through 156 removed outlier: 3.729A pdb=" N GLN C 145 " --> pdb=" O GLY C 141 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG C 151 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ALA C 152 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE C 153 " --> pdb=" O MET C 149 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 189 Processing helix chain 'C' and resid 198 through 206 removed outlier: 4.115A pdb=" N ALA C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 229 Processing helix chain 'C' and resid 232 through 239 Processing helix chain 'C' and resid 266 through 274 Processing helix chain 'C' and resid 287 through 291 Processing helix chain 'C' and resid 295 through 297 No H-bonds generated for 'chain 'C' and resid 295 through 297' Processing helix chain 'C' and resid 298 through 303 Processing helix chain 'C' and resid 375 through 377 No H-bonds generated for 'chain 'C' and resid 375 through 377' Processing helix chain 'D' and resid 47 through 55 Processing helix chain 'D' and resid 76 through 81 removed outlier: 3.698A pdb=" N ASP D 81 " --> pdb=" O PRO D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 101 Processing helix chain 'D' and resid 102 through 108 Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 135 through 139 Processing helix chain 'D' and resid 143 through 154 removed outlier: 3.566A pdb=" N ARG D 151 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA D 152 " --> pdb=" O ALA D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 189 removed outlier: 3.863A pdb=" N GLN D 176 " --> pdb=" O LYS D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 206 removed outlier: 3.554A pdb=" N THR D 204 " --> pdb=" O THR D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 229 removed outlier: 3.631A pdb=" N LEU D 226 " --> pdb=" O THR D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 239 Processing helix chain 'D' and resid 266 through 276 Processing helix chain 'D' and resid 287 through 291 Processing helix chain 'D' and resid 295 through 297 No H-bonds generated for 'chain 'D' and resid 295 through 297' Processing helix chain 'D' and resid 298 through 305 Processing helix chain 'D' and resid 373 through 377 Processing helix chain 'E' and resid 40 through 56 removed outlier: 3.806A pdb=" N PHE E 44 " --> pdb=" O GLU E 40 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA E 46 " --> pdb=" O ALA E 42 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY E 56 " --> pdb=" O ASN E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 83 Processing helix chain 'E' and resid 97 through 104 Processing helix chain 'E' and resid 109 through 113 Processing helix chain 'E' and resid 117 through 124 Processing helix chain 'E' and resid 165 through 179 Processing helix chain 'E' and resid 192 through 206 removed outlier: 3.762A pdb=" N PHE E 199 " --> pdb=" O MET E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 243 Processing helix chain 'E' and resid 249 through 253 Processing helix chain 'E' and resid 254 through 264 Processing helix chain 'E' and resid 276 through 286 Processing helix chain 'E' and resid 297 through 301 Processing helix chain 'E' and resid 313 through 326 Processing helix chain 'E' and resid 359 through 371 Processing helix chain 'E' and resid 372 through 384 Processing helix chain 'E' and resid 390 through 394 Processing helix chain 'E' and resid 395 through 402 Processing helix chain 'E' and resid 404 through 414 removed outlier: 3.828A pdb=" N ASN E 414 " --> pdb=" O GLN E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 436 removed outlier: 3.653A pdb=" N VAL E 427 " --> pdb=" O VAL E 423 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU E 435 " --> pdb=" O MET E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 441 Processing helix chain 'E' and resid 442 through 460 removed outlier: 3.659A pdb=" N GLN E 455 " --> pdb=" O THR E 451 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 21 through 31 removed outlier: 6.336A pdb=" N ALA C 23 " --> pdb=" O SER C 12 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N SER C 12 " --> pdb=" O ALA C 23 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LYS C 25 " --> pdb=" O THR C 10 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N THR C 10 " --> pdb=" O LYS C 25 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE C 27 " --> pdb=" O ARG C 8 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL C 9 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N SER C 62 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU C 70 " --> pdb=" O ILE C 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 82 through 85 removed outlier: 6.232A pdb=" N PHE C 36 " --> pdb=" O ARG C 208 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL C 210 " --> pdb=" O PHE C 36 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE C 38 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N MET C 212 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL C 40 " --> pdb=" O MET C 212 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN C 219 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LEU C 213 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N VAL C 217 " --> pdb=" O LEU C 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 261 through 264 Processing sheet with id=AA4, first strand: chain 'C' and resid 292 through 293 removed outlier: 3.965A pdb=" N ILE C 372 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU C 306 " --> pdb=" O ILE C 372 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 314 through 317 removed outlier: 3.967A pdb=" N ILE C 314 " --> pdb=" O HIS C 325 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 21 through 31 removed outlier: 5.917A pdb=" N ALA D 23 " --> pdb=" O SER D 12 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N SER D 12 " --> pdb=" O ALA D 23 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LYS D 25 " --> pdb=" O THR D 10 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR D 10 " --> pdb=" O LYS D 25 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE D 27 " --> pdb=" O ARG D 8 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL D 9 " --> pdb=" O SER D 62 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N SER D 62 " --> pdb=" O VAL D 9 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 82 through 85 removed outlier: 6.649A pdb=" N ALA D 83 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ASP D 163 " --> pdb=" O ALA D 83 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL D 85 " --> pdb=" O ASP D 163 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N PHE D 160 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N VAL D 195 " --> pdb=" O PHE D 160 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N MET D 162 " --> pdb=" O VAL D 195 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N PHE D 36 " --> pdb=" O ARG D 208 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL D 210 " --> pdb=" O PHE D 36 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE D 38 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N MET D 212 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL D 209 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE D 220 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL D 211 " --> pdb=" O GLN D 218 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 261 through 264 removed outlier: 3.910A pdb=" N ILE D 282 " --> pdb=" O ALA D 249 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 292 through 293 removed outlier: 3.863A pdb=" N GLU D 366 " --> pdb=" O ALA D 312 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 314 through 317 removed outlier: 3.998A pdb=" N ILE D 314 " --> pdb=" O HIS D 325 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 60 through 66 removed outlier: 7.361A pdb=" N LEU E 88 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ASN E 33 " --> pdb=" O LEU E 88 " (cutoff:3.500A) removed outlier: 10.857A pdb=" N ASP E 94 " --> pdb=" O PRO E 37 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LEU E 351 " --> pdb=" O PRO E 144 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 135 through 136 removed outlier: 3.695A pdb=" N GLU E 139 " --> pdb=" O TRP E 136 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 185 through 186 690 hydrogen bonds defined for protein. 1947 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.89 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2377 1.32 - 1.45: 2987 1.45 - 1.57: 7465 1.57 - 1.69: 10 1.69 - 1.82: 62 Bond restraints: 12901 Sorted by residual: bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.78e+01 bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.73e+01 bond pdb=" C5 ATP D 501 " pdb=" C6 ATP D 501 " ideal model delta sigma weight residual 1.409 1.483 -0.074 1.00e-02 1.00e+04 5.41e+01 bond pdb=" C5 ATP C 501 " pdb=" C6 ATP C 501 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.37e+01 bond pdb=" C5 GLC H 1 " pdb=" O5 GLC H 1 " ideal model delta sigma weight residual 1.415 1.549 -0.134 2.00e-02 2.50e+03 4.49e+01 ... (remaining 12896 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.87: 17091 3.87 - 7.74: 534 7.74 - 11.61: 8 11.61 - 15.49: 1 15.49 - 19.36: 4 Bond angle restraints: 17638 Sorted by residual: angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 120.51 19.36 1.00e+00 1.00e+00 3.75e+02 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 120.57 19.30 1.00e+00 1.00e+00 3.72e+02 angle pdb=" PA ATP D 501 " pdb=" O3A ATP D 501 " pdb=" PB ATP D 501 " ideal model delta sigma weight residual 136.83 120.56 16.27 1.00e+00 1.00e+00 2.65e+02 angle pdb=" PA ATP C 501 " pdb=" O3A ATP C 501 " pdb=" PB ATP C 501 " ideal model delta sigma weight residual 136.83 120.72 16.11 1.00e+00 1.00e+00 2.59e+02 angle pdb=" C5 ATP C 501 " pdb=" C4 ATP C 501 " pdb=" N3 ATP C 501 " ideal model delta sigma weight residual 126.80 118.67 8.13 1.00e+00 1.00e+00 6.61e+01 ... (remaining 17633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.83: 7440 24.83 - 49.66: 280 49.66 - 74.49: 23 74.49 - 99.32: 12 99.32 - 124.15: 2 Dihedral angle restraints: 7757 sinusoidal: 2875 harmonic: 4882 Sorted by residual: dihedral pdb=" CA GLU A 58 " pdb=" C GLU A 58 " pdb=" N PRO A 59 " pdb=" CA PRO A 59 " ideal model delta harmonic sigma weight residual -180.00 -150.86 -29.14 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA GLU D 130 " pdb=" C GLU D 130 " pdb=" N LEU D 131 " pdb=" CA LEU D 131 " ideal model delta harmonic sigma weight residual 180.00 151.18 28.82 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA LYS D 322 " pdb=" C LYS D 322 " pdb=" N TYR D 323 " pdb=" CA TYR D 323 " ideal model delta harmonic sigma weight residual 180.00 151.58 28.42 0 5.00e+00 4.00e-02 3.23e+01 ... (remaining 7754 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1148 0.070 - 0.140: 670 0.140 - 0.210: 218 0.210 - 0.280: 50 0.280 - 0.350: 15 Chirality restraints: 2101 Sorted by residual: chirality pdb=" C1 GLC H 1 " pdb=" C2 GLC H 1 " pdb=" O5 GLC H 1 " pdb=" O1 GLC H 2 " both_signs ideal model delta sigma weight residual False 2.40 2.29 0.11 2.00e-02 2.50e+03 2.81e+01 chirality pdb=" CA TYR D 89 " pdb=" N TYR D 89 " pdb=" C TYR D 89 " pdb=" CB TYR D 89 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CA PHE B 161 " pdb=" N PHE B 161 " pdb=" C PHE B 161 " pdb=" CB PHE B 161 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.96e+00 ... (remaining 2098 not shown) Planarity restraints: 2269 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 97 " 0.161 2.00e-02 2.50e+03 9.03e-02 2.04e+02 pdb=" CG TRP E 97 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 TRP E 97 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TRP E 97 " -0.072 2.00e-02 2.50e+03 pdb=" NE1 TRP E 97 " -0.070 2.00e-02 2.50e+03 pdb=" CE2 TRP E 97 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP E 97 " -0.133 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 97 " 0.103 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 97 " -0.047 2.00e-02 2.50e+03 pdb=" CH2 TRP E 97 " 0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 153 " 0.121 2.00e-02 2.50e+03 6.04e-02 9.12e+01 pdb=" CG TRP E 153 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP E 153 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 TRP E 153 " -0.046 2.00e-02 2.50e+03 pdb=" NE1 TRP E 153 " -0.036 2.00e-02 2.50e+03 pdb=" CE2 TRP E 153 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP E 153 " -0.072 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 153 " 0.079 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 153 " -0.036 2.00e-02 2.50e+03 pdb=" CH2 TRP E 153 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 35 " 0.103 2.00e-02 2.50e+03 5.99e-02 7.18e+01 pdb=" CG TYR E 35 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR E 35 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR E 35 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR E 35 " -0.045 2.00e-02 2.50e+03 pdb=" CE2 TYR E 35 " -0.036 2.00e-02 2.50e+03 pdb=" CZ TYR E 35 " -0.020 2.00e-02 2.50e+03 pdb=" OH TYR E 35 " 0.103 2.00e-02 2.50e+03 ... (remaining 2266 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 505 2.74 - 3.28: 13782 3.28 - 3.82: 19862 3.82 - 4.36: 25503 4.36 - 4.90: 41089 Nonbonded interactions: 100741 Sorted by model distance: nonbonded pdb=" O GLY D 46 " pdb=" SD MET D 212 " model vdw 2.201 3.400 nonbonded pdb=" OE1 GLN C 87 " pdb="MG MG C 502 " model vdw 2.222 2.170 nonbonded pdb=" O1G ATP D 501 " pdb="MG MG D 502 " model vdw 2.230 2.170 nonbonded pdb=" OG SER D 48 " pdb="MG MG D 502 " model vdw 2.241 2.170 nonbonded pdb=" NE2 GLN C 87 " pdb="MG MG C 502 " model vdw 2.256 2.250 ... (remaining 100736 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 'C' and (resid 2 through 83 or (resid 84 and (name N or name CA or name C \ or name O or name CB )) or resid 85 through 97 or (resid 98 and (name N or name \ CA or name C or name O or name CB )) or resid 99 through 273 or (resid 274 thro \ ugh 278 and (name N or name CA or name C or name O or name CB )) or resid 279 th \ rough 327 or resid 352 through 388 or (resid 389 and (name N or name CA or name \ C or name O or name CB )) or resid 390 through 391 or resid 501 through 502)) selection = (chain 'D' and (resid 2 through 20 or (resid 21 through 23 and (name N or name C \ A or name C or name O or name CB )) or resid 24 through 81 or (resid 82 through \ 84 and (name N or name CA or name C or name O or name CB )) or resid 85 through \ 108 or (resid 109 and (name N or name CA or name C or name O or name CB )) or re \ sid 110 through 118 or (resid 119 through 120 and (name N or name CA or name C o \ r name O or name CB )) or resid 121 through 123 or (resid 124 through 125 and (n \ ame N or name CA or name C or name O or name CB )) or resid 126 through 130 or ( \ resid 131 through 132 and (name N or name CA or name C or name O or name CB )) o \ r resid 133 through 143 or (resid 144 and (name N or name CA or name C or name O \ or name CB )) or resid 145 through 179 or (resid 180 and (name N or name CA or \ name C or name O or name CB )) or resid 181 through 232 or (resid 233 and (name \ N or name CA or name C or name O or name CB )) or resid 234 through 356 or (resi \ d 357 through 358 and (name N or name CA or name C or name O or name CB )) or re \ sid 359 or (resid 360 and (name N or name CA or name C or name O or name CB )) o \ r resid 361 through 377 or (resid 378 and (name N or name CA or name C or name O \ or name CB )) or resid 379 through 386 or (resid 387 and (name N or name CA or \ name C or name O or name CB )) or resid 388 through 391 or resid 501 through 502 \ )) } 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: 3.590 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: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 31.990 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 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 : 0.012 0.134 12901 Z= 0.812 Angle : 1.778 19.356 17638 Z= 1.213 Chirality : 0.096 0.350 2101 Planarity : 0.013 0.113 2269 Dihedral : 13.559 124.146 4603 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.43 % Favored : 94.51 % Rotamer: Outliers : 0.64 % Allowed : 6.65 % Favored : 92.71 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 3.19 % 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: -2.19 (0.18), residues: 1676 helix: -1.74 (0.15), residues: 813 sheet: -0.56 (0.43), residues: 133 loop : -1.06 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.161 0.022 TRP E 97 HIS 0.013 0.003 HIS D 290 PHE 0.080 0.012 PHE D 234 TYR 0.106 0.018 TYR B 23 ARG 0.016 0.001 ARG D 80 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 395 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8793 (t80) cc_final: 0.8157 (t80) REVERT: A 137 TRP cc_start: 0.8796 (m100) cc_final: 0.8560 (m100) REVERT: A 147 TYR cc_start: 0.8611 (p90) cc_final: 0.8345 (p90) REVERT: A 180 PHE cc_start: 0.8658 (t80) cc_final: 0.8358 (t80) REVERT: A 195 ASP cc_start: 0.8221 (m-30) cc_final: 0.7993 (m-30) REVERT: A 219 ILE cc_start: 0.8959 (mt) cc_final: 0.8693 (pt) REVERT: A 233 ASP cc_start: 0.8351 (t70) cc_final: 0.8126 (t0) REVERT: A 255 SER cc_start: 0.9476 (m) cc_final: 0.9043 (t) REVERT: A 291 LYS cc_start: 0.8660 (tppp) cc_final: 0.8295 (tttt) REVERT: B 25 LEU cc_start: 0.7742 (mt) cc_final: 0.7502 (mm) REVERT: B 175 ASP cc_start: 0.7731 (m-30) cc_final: 0.7390 (m-30) REVERT: B 260 VAL cc_start: 0.8362 (t) cc_final: 0.8144 (p) REVERT: C 13 TYR cc_start: 0.8247 (m-80) cc_final: 0.7786 (m-10) REVERT: C 51 LEU cc_start: 0.9141 (tp) cc_final: 0.8493 (tp) REVERT: C 87 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8353 (tt0) REVERT: C 149 MET cc_start: 0.8817 (ttt) cc_final: 0.8590 (ttp) REVERT: C 172 LYS cc_start: 0.8968 (ttpp) cc_final: 0.8762 (ttmm) REVERT: C 244 MET cc_start: 0.6770 (ttm) cc_final: 0.6569 (tpt) REVERT: D 92 TYR cc_start: 0.8017 (m-80) cc_final: 0.7766 (m-10) REVERT: D 197 HIS cc_start: 0.8575 (m170) cc_final: 0.8235 (m-70) REVERT: D 198 ASP cc_start: 0.8036 (t0) cc_final: 0.7686 (t0) REVERT: D 244 MET cc_start: 0.5617 (ttm) cc_final: 0.5377 (tpp) REVERT: D 281 ASN cc_start: 0.7478 (m-40) cc_final: 0.7113 (m110) REVERT: E 315 GLU cc_start: 0.9454 (mt-10) cc_final: 0.9215 (pp20) REVERT: E 322 ASP cc_start: 0.8902 (m-30) cc_final: 0.8684 (p0) outliers start: 8 outliers final: 3 residues processed: 400 average time/residue: 0.2876 time to fit residues: 158.4744 Evaluate side-chains 262 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 258 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain E residue 148 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 97 optimal weight: 0.0170 chunk 151 optimal weight: 10.0000 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN B 17 ASN ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 HIS C 219 GLN C 290 HIS D 99 GLN D 199 GLN E 49 ASN E 359 HIS E 375 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12901 Z= 0.233 Angle : 0.765 8.695 17638 Z= 0.400 Chirality : 0.048 0.203 2101 Planarity : 0.005 0.047 2269 Dihedral : 8.487 62.285 1927 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.04 % Allowed : 14.09 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: -0.65 (0.20), residues: 1676 helix: -0.04 (0.17), residues: 828 sheet: -0.61 (0.39), residues: 156 loop : -0.70 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 12 HIS 0.009 0.002 HIS D 290 PHE 0.022 0.002 PHE B 161 TYR 0.023 0.002 TYR C 194 ARG 0.006 0.001 ARG D 8 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 290 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8614 (t80) cc_final: 0.8333 (t80) REVERT: A 137 TRP cc_start: 0.8746 (m100) cc_final: 0.8483 (m100) REVERT: A 233 ASP cc_start: 0.8268 (t70) cc_final: 0.8019 (t0) REVERT: A 267 ASN cc_start: 0.8589 (t0) cc_final: 0.8327 (t0) REVERT: C 81 ASP cc_start: 0.5962 (t0) cc_final: 0.5637 (m-30) REVERT: C 184 LEU cc_start: 0.9214 (tp) cc_final: 0.8816 (tp) REVERT: D 198 ASP cc_start: 0.8130 (t0) cc_final: 0.7811 (t0) REVERT: E 275 TYR cc_start: 0.5587 (m-10) cc_final: 0.5188 (m-10) REVERT: E 315 GLU cc_start: 0.9480 (mt-10) cc_final: 0.9216 (pp20) outliers start: 38 outliers final: 20 residues processed: 307 average time/residue: 0.2508 time to fit residues: 111.1683 Evaluate side-chains 250 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 230 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 247 PHE Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 254 ASP Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 379 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 84 optimal weight: 0.1980 chunk 47 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 151 optimal weight: 0.0670 chunk 164 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 150 optimal weight: 8.9990 chunk 51 optimal weight: 0.4980 chunk 121 optimal weight: 7.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 ASN ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 GLN D 199 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12901 Z= 0.222 Angle : 0.681 8.146 17638 Z= 0.352 Chirality : 0.046 0.208 2101 Planarity : 0.005 0.050 2269 Dihedral : 8.150 66.207 1921 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.20 % Allowed : 16.01 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: -0.31 (0.20), residues: 1676 helix: 0.31 (0.18), residues: 828 sheet: -0.56 (0.37), residues: 177 loop : -0.60 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 273 HIS 0.009 0.001 HIS C 325 PHE 0.023 0.002 PHE B 161 TYR 0.023 0.002 TYR C 194 ARG 0.006 0.001 ARG E 64 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 236 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8504 (t80) cc_final: 0.8005 (t80) REVERT: A 137 TRP cc_start: 0.8726 (m100) cc_final: 0.8496 (m100) REVERT: A 147 TYR cc_start: 0.8487 (p90) cc_final: 0.8175 (p90) REVERT: A 233 ASP cc_start: 0.8350 (t70) cc_final: 0.8068 (t0) REVERT: B 61 PHE cc_start: 0.8678 (m-80) cc_final: 0.7957 (m-80) REVERT: B 128 MET cc_start: 0.8744 (mmt) cc_final: 0.8337 (ttm) REVERT: C 186 ASP cc_start: 0.7875 (p0) cc_final: 0.7580 (m-30) REVERT: C 257 ARG cc_start: 0.9441 (mtt180) cc_final: 0.9104 (ptp90) REVERT: C 361 ARG cc_start: 0.7947 (mtt180) cc_final: 0.7212 (mmm160) REVERT: D 198 ASP cc_start: 0.8202 (t0) cc_final: 0.7855 (t0) REVERT: D 361 ARG cc_start: 0.7188 (mmm160) cc_final: 0.6945 (mmm160) REVERT: E 131 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8559 (mt) outliers start: 40 outliers final: 27 residues processed: 258 average time/residue: 0.2506 time to fit residues: 93.1802 Evaluate side-chains 236 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 208 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 247 PHE Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 387 ASN Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 254 ASP Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 379 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 150 optimal weight: 0.0670 chunk 114 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 102 optimal weight: 0.0980 chunk 152 optimal weight: 6.9990 chunk 161 optimal weight: 0.9980 chunk 79 optimal weight: 0.2980 chunk 144 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 ASN ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 GLN D 290 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12901 Z= 0.185 Angle : 0.644 8.191 17638 Z= 0.330 Chirality : 0.045 0.215 2101 Planarity : 0.005 0.051 2269 Dihedral : 7.320 69.768 1918 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.44 % Allowed : 16.41 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: -0.21 (0.21), residues: 1676 helix: 0.47 (0.18), residues: 826 sheet: -0.47 (0.38), residues: 167 loop : -0.68 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 30 HIS 0.008 0.001 HIS D 290 PHE 0.023 0.001 PHE B 161 TYR 0.016 0.001 TYR C 194 ARG 0.005 0.001 ARG E 64 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 235 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8420 (t80) cc_final: 0.8015 (t80) REVERT: A 147 TYR cc_start: 0.8532 (p90) cc_final: 0.8213 (p90) REVERT: A 233 ASP cc_start: 0.8363 (t70) cc_final: 0.8031 (t0) REVERT: B 61 PHE cc_start: 0.8692 (m-80) cc_final: 0.8025 (m-80) REVERT: B 128 MET cc_start: 0.8587 (mmt) cc_final: 0.8218 (mtp) REVERT: C 53 MET cc_start: 0.8711 (mtm) cc_final: 0.8379 (mtm) REVERT: D 198 ASP cc_start: 0.8231 (t0) cc_final: 0.7882 (t0) REVERT: E 91 MET cc_start: 0.8531 (ptp) cc_final: 0.8307 (ptp) REVERT: E 315 GLU cc_start: 0.9484 (mt-10) cc_final: 0.9206 (pp20) outliers start: 43 outliers final: 26 residues processed: 258 average time/residue: 0.2628 time to fit residues: 99.7223 Evaluate side-chains 230 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 204 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 289 TYR Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 247 PHE Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 387 ASN Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 169 MET Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 254 ASP Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 346 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 134 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 82 optimal weight: 0.0000 chunk 144 optimal weight: 0.8980 chunk 40 optimal weight: 0.0980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN B 99 GLN ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12901 Z= 0.178 Angle : 0.642 10.048 17638 Z= 0.322 Chirality : 0.045 0.208 2101 Planarity : 0.005 0.049 2269 Dihedral : 6.913 69.866 1918 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.20 % Allowed : 17.85 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: -0.00 (0.21), residues: 1676 helix: 0.58 (0.18), residues: 827 sheet: 0.06 (0.43), residues: 137 loop : -0.60 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 30 HIS 0.004 0.001 HIS D 290 PHE 0.022 0.001 PHE B 161 TYR 0.014 0.001 TYR C 194 ARG 0.005 0.000 ARG D 361 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 233 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8390 (t80) cc_final: 0.8056 (t80) REVERT: A 98 PHE cc_start: 0.8264 (t80) cc_final: 0.7918 (t80) REVERT: A 219 ILE cc_start: 0.8784 (mm) cc_final: 0.8454 (mt) REVERT: A 229 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.7366 (t80) REVERT: A 233 ASP cc_start: 0.8414 (t70) cc_final: 0.7946 (t0) REVERT: B 61 PHE cc_start: 0.8651 (m-80) cc_final: 0.7967 (m-80) REVERT: B 128 MET cc_start: 0.8494 (mmt) cc_final: 0.8151 (mtp) REVERT: C 53 MET cc_start: 0.8717 (mtm) cc_final: 0.8379 (mtm) REVERT: C 89 TYR cc_start: 0.8957 (p90) cc_final: 0.8718 (p90) REVERT: C 186 ASP cc_start: 0.7216 (m-30) cc_final: 0.6900 (p0) REVERT: C 244 MET cc_start: 0.6097 (tpt) cc_final: 0.5011 (tpp) REVERT: D 198 ASP cc_start: 0.8203 (t0) cc_final: 0.7855 (t0) REVERT: D 361 ARG cc_start: 0.7147 (mmm160) cc_final: 0.6845 (mmm160) REVERT: E 91 MET cc_start: 0.8567 (ptp) cc_final: 0.8300 (ptp) REVERT: E 286 LYS cc_start: 0.9308 (mmmt) cc_final: 0.8870 (mtmm) REVERT: E 315 GLU cc_start: 0.9490 (mt-10) cc_final: 0.9208 (pp20) outliers start: 40 outliers final: 29 residues processed: 255 average time/residue: 0.2504 time to fit residues: 92.5831 Evaluate side-chains 241 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 211 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 289 TYR Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 176 GLN Chi-restraints excluded: chain D residue 247 PHE Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 379 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 54 optimal weight: 9.9990 chunk 145 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 94 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 13 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12901 Z= 0.214 Angle : 0.630 8.361 17638 Z= 0.320 Chirality : 0.045 0.231 2101 Planarity : 0.005 0.048 2269 Dihedral : 6.601 73.298 1918 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.68 % Allowed : 17.93 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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 (0.21), residues: 1676 helix: 0.72 (0.19), residues: 826 sheet: -0.10 (0.44), residues: 138 loop : -0.62 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 30 HIS 0.003 0.001 HIS D 290 PHE 0.030 0.002 PHE C 238 TYR 0.025 0.002 TYR E 378 ARG 0.004 0.000 ARG B 221 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 215 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8493 (t80) cc_final: 0.8083 (t80) REVERT: A 219 ILE cc_start: 0.8805 (mm) cc_final: 0.8413 (mt) REVERT: A 230 ARG cc_start: 0.8306 (tpt170) cc_final: 0.8082 (tpt170) REVERT: A 233 ASP cc_start: 0.8483 (t70) cc_final: 0.7981 (t0) REVERT: B 61 PHE cc_start: 0.8674 (m-80) cc_final: 0.8009 (m-80) REVERT: B 128 MET cc_start: 0.8452 (mmt) cc_final: 0.8106 (mtp) REVERT: C 13 TYR cc_start: 0.8410 (m-10) cc_final: 0.8071 (m-10) REVERT: C 53 MET cc_start: 0.8754 (mtm) cc_final: 0.8404 (mtm) REVERT: C 186 ASP cc_start: 0.7232 (m-30) cc_final: 0.6890 (p0) REVERT: C 244 MET cc_start: 0.5979 (tpt) cc_final: 0.3922 (tpt) REVERT: D 198 ASP cc_start: 0.8250 (t0) cc_final: 0.7899 (t0) REVERT: D 361 ARG cc_start: 0.7276 (mmm160) cc_final: 0.6992 (mmm160) REVERT: E 91 MET cc_start: 0.8586 (ptp) cc_final: 0.8184 (ptp) REVERT: E 286 LYS cc_start: 0.9286 (mmmt) cc_final: 0.8869 (mtmm) REVERT: E 315 GLU cc_start: 0.9494 (mt-10) cc_final: 0.9214 (pp20) outliers start: 46 outliers final: 37 residues processed: 237 average time/residue: 0.2648 time to fit residues: 91.9129 Evaluate side-chains 241 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 204 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 254 ASP Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 367 ILE Chi-restraints excluded: chain E residue 379 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 155 optimal weight: 0.2980 chunk 18 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 160 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 GLN D 199 GLN ** E 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12901 Z= 0.199 Angle : 0.633 9.310 17638 Z= 0.321 Chirality : 0.045 0.198 2101 Planarity : 0.005 0.049 2269 Dihedral : 6.398 72.132 1918 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.68 % Allowed : 18.33 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: 0.07 (0.21), residues: 1676 helix: 0.75 (0.19), residues: 828 sheet: 0.09 (0.44), residues: 142 loop : -0.72 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 30 HIS 0.003 0.001 HIS D 290 PHE 0.027 0.002 PHE C 234 TYR 0.016 0.001 TYR E 378 ARG 0.003 0.000 ARG A 230 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 227 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8506 (t80) cc_final: 0.8135 (t80) REVERT: A 219 ILE cc_start: 0.8811 (mm) cc_final: 0.8416 (mt) REVERT: A 229 PHE cc_start: 0.8166 (OUTLIER) cc_final: 0.7561 (t80) REVERT: A 233 ASP cc_start: 0.8514 (t70) cc_final: 0.7989 (t0) REVERT: B 61 PHE cc_start: 0.8679 (m-80) cc_final: 0.8008 (m-80) REVERT: B 128 MET cc_start: 0.8431 (mmt) cc_final: 0.8091 (mtp) REVERT: B 209 ASP cc_start: 0.7621 (t70) cc_final: 0.7333 (t0) REVERT: C 13 TYR cc_start: 0.8349 (m-10) cc_final: 0.7943 (m-10) REVERT: C 53 MET cc_start: 0.8750 (mtm) cc_final: 0.8374 (mtm) REVERT: C 186 ASP cc_start: 0.7219 (m-30) cc_final: 0.6993 (p0) REVERT: C 244 MET cc_start: 0.5933 (tpt) cc_final: 0.3884 (tpt) REVERT: D 198 ASP cc_start: 0.8209 (t0) cc_final: 0.7849 (t0) REVERT: D 361 ARG cc_start: 0.7330 (mmm160) cc_final: 0.7059 (mmm160) REVERT: E 41 GLU cc_start: 0.7316 (tm-30) cc_final: 0.6748 (tm-30) REVERT: E 100 GLU cc_start: 0.7717 (tp30) cc_final: 0.7483 (tp30) REVERT: E 286 LYS cc_start: 0.9308 (mmmt) cc_final: 0.8912 (mtmm) REVERT: E 315 GLU cc_start: 0.9487 (mt-10) cc_final: 0.9203 (pp20) outliers start: 46 outliers final: 35 residues processed: 251 average time/residue: 0.2611 time to fit residues: 94.1606 Evaluate side-chains 252 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 216 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 367 ILE Chi-restraints excluded: chain E residue 370 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 99 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 96 optimal weight: 0.0170 chunk 48 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 126 optimal weight: 10.0000 chunk 146 optimal weight: 0.5980 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 HIS D 99 GLN D 176 GLN D 199 GLN ** E 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12901 Z= 0.192 Angle : 0.638 10.001 17638 Z= 0.323 Chirality : 0.045 0.274 2101 Planarity : 0.005 0.049 2269 Dihedral : 6.168 71.385 1918 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.60 % Allowed : 19.06 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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 (0.21), residues: 1676 helix: 0.79 (0.19), residues: 829 sheet: 0.10 (0.42), residues: 151 loop : -0.65 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 30 HIS 0.006 0.001 HIS D 94 PHE 0.033 0.002 PHE A 83 TYR 0.016 0.001 TYR C 194 ARG 0.007 0.000 ARG D 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 225 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8506 (t80) cc_final: 0.8132 (t80) REVERT: A 219 ILE cc_start: 0.8790 (mm) cc_final: 0.8399 (mt) REVERT: A 233 ASP cc_start: 0.8518 (t70) cc_final: 0.7995 (t0) REVERT: A 292 ILE cc_start: 0.8451 (mm) cc_final: 0.8241 (tt) REVERT: B 61 PHE cc_start: 0.8667 (m-80) cc_final: 0.8006 (m-80) REVERT: B 128 MET cc_start: 0.8354 (mmt) cc_final: 0.8014 (mtp) REVERT: B 209 ASP cc_start: 0.7523 (t70) cc_final: 0.7181 (t0) REVERT: C 13 TYR cc_start: 0.8344 (m-10) cc_final: 0.7959 (m-10) REVERT: C 53 MET cc_start: 0.8717 (mtm) cc_final: 0.8341 (mtm) REVERT: C 244 MET cc_start: 0.5864 (tpt) cc_final: 0.5405 (tpt) REVERT: D 198 ASP cc_start: 0.8227 (t0) cc_final: 0.7854 (t0) REVERT: D 361 ARG cc_start: 0.7360 (mmm160) cc_final: 0.7034 (mmm160) REVERT: E 286 LYS cc_start: 0.9285 (mmmt) cc_final: 0.8910 (mtmm) REVERT: E 315 GLU cc_start: 0.9472 (mt-10) cc_final: 0.9203 (pp20) outliers start: 45 outliers final: 35 residues processed: 247 average time/residue: 0.2395 time to fit residues: 86.0989 Evaluate side-chains 246 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 211 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 367 ILE Chi-restraints excluded: chain E residue 370 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 154 optimal weight: 1.9990 chunk 140 optimal weight: 0.0870 chunk 149 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 65 optimal weight: 0.5980 chunk 117 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 chunk 98 optimal weight: 0.1980 chunk 158 optimal weight: 0.8980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 GLN E 301 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12901 Z= 0.178 Angle : 0.673 18.741 17638 Z= 0.334 Chirality : 0.047 0.568 2101 Planarity : 0.005 0.049 2269 Dihedral : 6.061 71.683 1918 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.80 % Allowed : 19.94 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: 0.18 (0.21), residues: 1676 helix: 0.79 (0.19), residues: 835 sheet: 0.22 (0.42), residues: 151 loop : -0.65 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP B 30 HIS 0.003 0.001 HIS D 290 PHE 0.024 0.002 PHE C 238 TYR 0.016 0.001 TYR E 177 ARG 0.006 0.000 ARG D 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 231 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8449 (t80) cc_final: 0.7995 (t80) REVERT: A 219 ILE cc_start: 0.8755 (mm) cc_final: 0.8362 (mt) REVERT: A 233 ASP cc_start: 0.8500 (t70) cc_final: 0.8050 (t0) REVERT: B 61 PHE cc_start: 0.8675 (m-80) cc_final: 0.8009 (m-80) REVERT: B 128 MET cc_start: 0.8311 (mmt) cc_final: 0.7989 (mtp) REVERT: C 13 TYR cc_start: 0.8361 (m-10) cc_final: 0.8069 (m-10) REVERT: C 203 MET cc_start: 0.8968 (tpp) cc_final: 0.8642 (tpt) REVERT: C 244 MET cc_start: 0.5698 (tpt) cc_final: 0.5275 (tpt) REVERT: C 269 MET cc_start: 0.8678 (mtp) cc_final: 0.8470 (ptp) REVERT: C 353 ILE cc_start: 0.9073 (mm) cc_final: 0.8527 (tp) REVERT: D 198 ASP cc_start: 0.8253 (t0) cc_final: 0.7896 (t0) REVERT: D 268 HIS cc_start: 0.9217 (m-70) cc_final: 0.8765 (m90) REVERT: D 361 ARG cc_start: 0.7377 (mmm160) cc_final: 0.7045 (mmm160) REVERT: E 41 GLU cc_start: 0.7336 (tm-30) cc_final: 0.6831 (tm-30) REVERT: E 286 LYS cc_start: 0.9274 (mmmt) cc_final: 0.8930 (mtmm) REVERT: E 315 GLU cc_start: 0.9468 (mt-10) cc_final: 0.9204 (pp20) outliers start: 35 outliers final: 30 residues processed: 248 average time/residue: 0.2563 time to fit residues: 91.3100 Evaluate side-chains 247 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 217 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 301 GLN Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 367 ILE Chi-restraints excluded: chain E residue 370 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 96 optimal weight: 0.6980 chunk 75 optimal weight: 0.2980 chunk 110 optimal weight: 0.3980 chunk 166 optimal weight: 0.6980 chunk 153 optimal weight: 4.9990 chunk 132 optimal weight: 0.0040 chunk 13 optimal weight: 0.0870 chunk 102 optimal weight: 1.9990 chunk 81 optimal weight: 0.0270 chunk 105 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 overall best weight: 0.1628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 176 GLN C 219 GLN E 200 ASN E 301 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12901 Z= 0.170 Angle : 0.676 17.847 17638 Z= 0.333 Chirality : 0.046 0.512 2101 Planarity : 0.005 0.050 2269 Dihedral : 6.034 72.090 1918 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.32 % Allowed : 20.50 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.16 (0.21), residues: 1676 helix: 0.77 (0.19), residues: 835 sheet: 0.28 (0.42), residues: 151 loop : -0.66 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 30 HIS 0.003 0.001 HIS D 290 PHE 0.024 0.001 PHE C 238 TYR 0.017 0.001 TYR E 177 ARG 0.007 0.000 ARG D 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 232 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8451 (t80) cc_final: 0.8085 (t80) REVERT: A 49 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8898 (mp) REVERT: A 134 SER cc_start: 0.8593 (t) cc_final: 0.8147 (p) REVERT: A 219 ILE cc_start: 0.8722 (mm) cc_final: 0.8335 (mt) REVERT: A 233 ASP cc_start: 0.8473 (t70) cc_final: 0.7984 (t0) REVERT: B 61 PHE cc_start: 0.8660 (m-80) cc_final: 0.7987 (m-80) REVERT: B 128 MET cc_start: 0.8266 (mmt) cc_final: 0.7867 (ttp) REVERT: C 13 TYR cc_start: 0.8348 (m-10) cc_final: 0.8025 (m-10) REVERT: C 244 MET cc_start: 0.5638 (tpt) cc_final: 0.5277 (tpt) REVERT: C 269 MET cc_start: 0.8684 (mtp) cc_final: 0.8457 (ptp) REVERT: C 353 ILE cc_start: 0.9077 (mm) cc_final: 0.8567 (tp) REVERT: D 198 ASP cc_start: 0.8288 (t0) cc_final: 0.7916 (t0) REVERT: D 268 HIS cc_start: 0.9177 (m-70) cc_final: 0.8769 (m90) REVERT: D 361 ARG cc_start: 0.7469 (mmm160) cc_final: 0.7141 (mmm160) REVERT: E 35 TYR cc_start: 0.7674 (m-80) cc_final: 0.7427 (m-80) REVERT: E 41 GLU cc_start: 0.7352 (tm-30) cc_final: 0.6910 (tm-30) REVERT: E 286 LYS cc_start: 0.9265 (mmmt) cc_final: 0.8942 (mtmm) REVERT: E 315 GLU cc_start: 0.9460 (mt-10) cc_final: 0.9201 (pp20) outliers start: 29 outliers final: 24 residues processed: 246 average time/residue: 0.2421 time to fit residues: 87.1078 Evaluate side-chains 244 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 219 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 254 ASP Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 370 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 40 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 19 optimal weight: 0.2980 chunk 36 optimal weight: 5.9990 chunk 132 optimal weight: 0.0770 chunk 55 optimal weight: 0.0970 chunk 136 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 0.1980 chunk 116 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.2936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.132543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.099532 restraints weight = 31411.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.103004 restraints weight = 17334.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.105274 restraints weight = 11953.425| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.142 12901 Z= 0.223 Angle : 0.880 59.139 17638 Z= 0.494 Chirality : 0.048 0.672 2101 Planarity : 0.005 0.070 2269 Dihedral : 6.069 72.065 1918 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.40 % Favored : 96.54 % Rotamer: Outliers : 2.24 % Allowed : 20.74 % Favored : 77.02 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.14 (0.21), residues: 1676 helix: 0.75 (0.19), residues: 834 sheet: 0.28 (0.42), residues: 151 loop : -0.67 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 30 HIS 0.003 0.001 HIS D 290 PHE 0.023 0.001 PHE C 238 TYR 0.013 0.001 TYR E 177 ARG 0.005 0.000 ARG D 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3056.77 seconds wall clock time: 57 minutes 8.68 seconds (3428.68 seconds total)