Starting phenix.real_space_refine on Wed Feb 14 15:01:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arl_11886/02_2024/7arl_11886_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arl_11886/02_2024/7arl_11886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arl_11886/02_2024/7arl_11886.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arl_11886/02_2024/7arl_11886.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arl_11886/02_2024/7arl_11886_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7arl_11886/02_2024/7arl_11886_updated.pdb" } resolution = 3.2 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 56 atoms to isotropic. 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 4 5.49 5 Mg 2 5.21 5 S 48 5.16 5 C 6040 2.51 5 N 1651 2.21 5 O 1722 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 53": "NH1" <-> "NH2" Residue "C ASP 88": "OD1" <-> "OD2" Residue "C ASP 136": "OD1" <-> "OD2" Residue "C GLU 148": "OE1" <-> "OE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 206": "OE1" <-> "OE2" Residue "C ASP 227": "OD1" <-> "OD2" Residue "C GLU 228": "OE1" <-> "OE2" Residue "C GLU 242": "OE1" <-> "OE2" Residue "C ASP 251": "OD1" <-> "OD2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 394": "OE1" <-> "OE2" Residue "C ARG 397": "NH1" <-> "NH2" Residue "E ARG 18": "NH1" <-> "NH2" Residue "E ARG 19": "NH1" <-> "NH2" Residue "E ARG 58": "NH1" <-> "NH2" Residue "E GLU 69": "OE1" <-> "OE2" Residue "E ASP 72": "OD1" <-> "OD2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "E ARG 111": "NH1" <-> "NH2" Residue "E ARG 125": "NH1" <-> "NH2" Residue "E ARG 139": "NH1" <-> "NH2" Residue "E GLU 145": "OE1" <-> "OE2" Residue "E ARG 184": "NH1" <-> "NH2" Residue "E ARG 239": "NH1" <-> "NH2" Residue "E GLU 243": "OE1" <-> "OE2" Residue "E ASP 301": "OD1" <-> "OD2" Residue "E TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 406": "OD1" <-> "OD2" Residue "F ASP 9": "OD1" <-> "OD2" Residue "F ASP 23": "OD1" <-> "OD2" Residue "F PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 59": "OD1" <-> "OD2" Residue "F GLU 83": "OE1" <-> "OE2" Residue "F PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 101": "OD1" <-> "OD2" Residue "F PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 151": "NH1" <-> "NH2" Residue "F GLU 190": "OE1" <-> "OE2" Residue "D ASP 23": "OD1" <-> "OD2" Residue "D PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 59": "OD1" <-> "OD2" Residue "D ARG 151": "NH1" <-> "NH2" Residue "D GLU 190": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9467 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 2969 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 20, 'TRANS': 371} Chain breaks: 1 Chain: "E" Number of atoms: 3159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3159 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 14, 'TRANS': 394} Chain: "F" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1545 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 8, 'TRANS': 214} Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 198 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 6, 'ARG:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 105 Chain: "D" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1609 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 8, 'TRANS': 213} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 5, 'ASN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 52 Chain: "V" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 73 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'Z41': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.72, per 1000 atoms: 0.60 Number of scatterers: 9467 At special positions: 0 Unit cell: (83.148, 90.246, 148.044, 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 48 16.00 P 4 15.00 Mg 2 11.99 O 1722 8.00 N 1651 7.00 C 6040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.49 Conformation dependent library (CDL) restraints added in 1.9 seconds 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2298 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 11 sheets defined 34.6% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'C' and resid 6 through 11 removed outlier: 4.270A pdb=" N GLY C 10 " --> pdb=" O ALA C 6 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N LEU C 11 " --> pdb=" O LEU C 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 6 through 11' Processing helix chain 'C' and resid 21 through 27 removed outlier: 3.621A pdb=" N PHE C 25 " --> pdb=" O ARG C 21 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL C 26 " --> pdb=" O PHE C 22 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER C 27 " --> pdb=" O GLY C 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 21 through 27' Processing helix chain 'C' and resid 29 through 58 removed outlier: 3.508A pdb=" N GLY C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY C 37 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR C 43 " --> pdb=" O MET C 39 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N VAL C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL C 47 " --> pdb=" O THR C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 154 removed outlier: 3.914A pdb=" N GLN C 153 " --> pdb=" O GLN C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 198 No H-bonds generated for 'chain 'C' and resid 196 through 198' Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 257 through 292 removed outlier: 3.691A pdb=" N ARG C 261 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ILE C 274 " --> pdb=" O LEU C 270 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C 288 " --> pdb=" O THR C 284 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N MET C 289 " --> pdb=" O SER C 285 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N MET C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU C 292 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.804A pdb=" N ALA C 298 " --> pdb=" O GLN C 294 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE C 299 " --> pdb=" O GLY C 295 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C 300 " --> pdb=" O GLU C 296 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN C 301 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 294 through 303' Processing helix chain 'C' and resid 307 through 310 No H-bonds generated for 'chain 'C' and resid 307 through 310' Processing helix chain 'C' and resid 313 through 338 removed outlier: 3.870A pdb=" N GLN C 317 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA C 321 " --> pdb=" O GLN C 317 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLY C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE C 324 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA C 337 " --> pdb=" O GLY C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 378 removed outlier: 4.009A pdb=" N ILE C 366 " --> pdb=" O PRO C 362 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL C 367 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU C 377 " --> pdb=" O MET C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 389 removed outlier: 3.758A pdb=" N ALA C 388 " --> pdb=" O SER C 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 24 No H-bonds generated for 'chain 'E' and resid 22 through 24' Processing helix chain 'E' and resid 26 through 34 removed outlier: 3.676A pdb=" N ILE E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 58 removed outlier: 4.051A pdb=" N MET E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN E 56 " --> pdb=" O GLU E 52 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 86 No H-bonds generated for 'chain 'E' and resid 83 through 86' Processing helix chain 'E' and resid 130 through 132 No H-bonds generated for 'chain 'E' and resid 130 through 132' Processing helix chain 'E' and resid 152 through 158 removed outlier: 3.863A pdb=" N ALA E 157 " --> pdb=" O GLY E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 211 No H-bonds generated for 'chain 'E' and resid 208 through 211' Processing helix chain 'E' and resid 255 through 258 No H-bonds generated for 'chain 'E' and resid 255 through 258' Processing helix chain 'E' and resid 260 through 267 removed outlier: 3.603A pdb=" N GLN E 266 " --> pdb=" O TYR E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 283 removed outlier: 3.590A pdb=" N LEU E 278 " --> pdb=" O LEU E 274 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL E 279 " --> pdb=" O ALA E 275 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL E 282 " --> pdb=" O LEU E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 289 Processing helix chain 'E' and resid 293 through 296 No H-bonds generated for 'chain 'E' and resid 293 through 296' Processing helix chain 'E' and resid 299 through 308 removed outlier: 4.042A pdb=" N ALA E 303 " --> pdb=" O SER E 299 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL E 304 " --> pdb=" O GLY E 300 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU E 305 " --> pdb=" O ASP E 301 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU E 308 " --> pdb=" O VAL E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 315 No H-bonds generated for 'chain 'E' and resid 312 through 315' Processing helix chain 'E' and resid 318 through 343 removed outlier: 4.045A pdb=" N ALA E 326 " --> pdb=" O TYR E 322 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY E 330 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY E 334 " --> pdb=" O GLY E 330 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE E 337 " --> pdb=" O CYS E 333 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL E 340 " --> pdb=" O ILE E 336 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL E 341 " --> pdb=" O ILE E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 352 removed outlier: 3.710A pdb=" N GLU E 350 " --> pdb=" O THR E 346 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TRP E 351 " --> pdb=" O PRO E 347 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE E 352 " --> pdb=" O ILE E 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 346 through 352' Processing helix chain 'E' and resid 378 through 403 removed outlier: 3.564A pdb=" N VAL E 385 " --> pdb=" O PHE E 381 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR E 386 " --> pdb=" O TYR E 382 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER E 391 " --> pdb=" O ALA E 387 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU E 393 " --> pdb=" O LEU E 389 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA E 394 " --> pdb=" O LEU E 390 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR E 397 " --> pdb=" O LEU E 393 " (cutoff:3.500A) Proline residue: E 398 - end of helix removed outlier: 3.722A pdb=" N ARG E 401 " --> pdb=" O TYR E 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 56 Processing helix chain 'F' and resid 78 through 87 removed outlier: 3.932A pdb=" N ALA F 82 " --> pdb=" O SER F 78 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU F 83 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU F 84 " --> pdb=" O ALA F 80 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG F 85 " --> pdb=" O LYS F 81 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN F 87 " --> pdb=" O GLU F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 108 removed outlier: 3.750A pdb=" N VAL F 108 " --> pdb=" O ALA F 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 104 through 108' Processing helix chain 'F' and resid 110 through 114 removed outlier: 3.550A pdb=" N ILE F 114 " --> pdb=" O MET F 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 110 through 114' Processing helix chain 'F' and resid 119 through 131 removed outlier: 4.098A pdb=" N ASN F 123 " --> pdb=" O PRO F 119 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER F 124 " --> pdb=" O ALA F 120 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU F 130 " --> pdb=" O ALA F 126 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS F 131 " --> pdb=" O LEU F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 160 removed outlier: 3.576A pdb=" N VAL F 154 " --> pdb=" O GLU F 150 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA F 155 " --> pdb=" O ARG F 151 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA F 157 " --> pdb=" O ARG F 153 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA F 159 " --> pdb=" O ALA F 155 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU F 160 " --> pdb=" O ILE F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 194 removed outlier: 3.997A pdb=" N PHE F 185 " --> pdb=" O ALA F 181 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN F 192 " --> pdb=" O LEU F 188 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG F 193 " --> pdb=" O GLY F 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 56 No H-bonds generated for 'chain 'D' and resid 53 through 56' Processing helix chain 'D' and resid 78 through 84 removed outlier: 3.836A pdb=" N ALA D 82 " --> pdb=" O SER D 78 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLU D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 78 through 84' Processing helix chain 'D' and resid 104 through 108 removed outlier: 3.993A pdb=" N VAL D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 104 through 108' Processing helix chain 'D' and resid 110 through 114 removed outlier: 3.505A pdb=" N ILE D 114 " --> pdb=" O MET D 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 110 through 114' Processing helix chain 'D' and resid 119 through 133 removed outlier: 4.259A pdb=" N ASN D 123 " --> pdb=" O PRO D 119 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N SER D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET D 129 " --> pdb=" O ARG D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 159 removed outlier: 3.857A pdb=" N VAL D 154 " --> pdb=" O GLU D 150 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA D 155 " --> pdb=" O ARG D 151 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA D 159 " --> pdb=" O ALA D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 190 Processing sheet with id= A, first strand: chain 'C' and resid 67 through 69 removed outlier: 3.533A pdb=" N SER C 69 " --> pdb=" O LYS C 245 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 93 through 96 removed outlier: 3.578A pdb=" N ILE C 96 " --> pdb=" O GLY C 221 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY C 221 " --> pdb=" O ILE C 96 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 102 through 104 removed outlier: 3.743A pdb=" N VAL C 164 " --> pdb=" O ARG C 182 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER C 180 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N LEU C 146 " --> pdb=" O ILE C 187 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N THR C 189 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 113 through 117 removed outlier: 3.687A pdb=" N MET C 201 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 67 through 69 removed outlier: 3.718A pdb=" N GLU E 67 " --> pdb=" O LYS E 252 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 94 through 96 Processing sheet with id= G, first strand: chain 'E' and resid 165 through 170 removed outlier: 3.788A pdb=" N VAL E 185 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS E 183 " --> pdb=" O ILE E 170 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 89 through 93 removed outlier: 7.249A pdb=" N LEU F 166 " --> pdb=" O GLY F 90 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N ILE F 92 " --> pdb=" O LEU F 166 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU F 168 " --> pdb=" O ILE F 92 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 13 through 17 removed outlier: 4.290A pdb=" N LEU F 25 " --> pdb=" O LYS F 13 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TYR F 15 " --> pdb=" O ASP F 23 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ASP F 23 " --> pdb=" O TYR F 15 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLU F 17 " --> pdb=" O GLN F 21 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLN F 21 " --> pdb=" O GLU F 17 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 6 through 9 removed outlier: 3.597A pdb=" N CYS D 8 " --> pdb=" O PHE D 30 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 89 through 92 removed outlier: 6.915A pdb=" N LEU D 166 " --> pdb=" O GLY D 90 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ILE D 92 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU D 168 " --> pdb=" O ILE D 92 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ALA D 198 " --> pdb=" O VAL D 167 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ALA D 169 " --> pdb=" O ALA D 198 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU D 200 " --> pdb=" O ALA D 169 " (cutoff:3.500A) No H-bonds generated for sheet with id= K 198 hydrogen bonds defined for protein. 576 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.09 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3066 1.34 - 1.46: 1148 1.46 - 1.57: 5315 1.57 - 1.69: 6 1.69 - 1.81: 89 Bond restraints: 9624 Sorted by residual: bond pdb=" C19 Z41 C 401 " pdb=" O3 Z41 C 401 " ideal model delta sigma weight residual 1.333 1.457 -0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" C16 Z41 C 401 " pdb=" O2 Z41 C 401 " ideal model delta sigma weight residual 1.332 1.454 -0.122 2.00e-02 2.50e+03 3.71e+01 bond pdb=" C LEU E 129 " pdb=" N PRO E 130 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.91e+00 bond pdb=" C1 PLM V 201 " pdb=" C2 PLM V 201 " ideal model delta sigma weight residual 1.542 1.511 0.031 2.00e-02 2.50e+03 2.45e+00 bond pdb=" N GLN E 146 " pdb=" CA GLN E 146 " ideal model delta sigma weight residual 1.460 1.482 -0.022 1.42e-02 4.96e+03 2.44e+00 ... (remaining 9619 not shown) Histogram of bond angle deviations from ideal: 100.58 - 107.70: 382 107.70 - 114.81: 5805 114.81 - 121.93: 4709 121.93 - 129.04: 2095 129.04 - 136.16: 68 Bond angle restraints: 13059 Sorted by residual: angle pdb=" CA LEU D 51 " pdb=" CB LEU D 51 " pdb=" CG LEU D 51 " ideal model delta sigma weight residual 116.30 131.59 -15.29 3.50e+00 8.16e-02 1.91e+01 angle pdb=" C PHE D 68 " pdb=" N ASN D 69 " pdb=" CA ASN D 69 " ideal model delta sigma weight residual 121.54 128.86 -7.32 1.91e+00 2.74e-01 1.47e+01 angle pdb=" C GLU E 145 " pdb=" N GLN E 146 " pdb=" CA GLN E 146 " ideal model delta sigma weight residual 122.82 127.89 -5.07 1.42e+00 4.96e-01 1.27e+01 angle pdb=" C ASP F 170 " pdb=" N GLU F 171 " pdb=" CA GLU F 171 " ideal model delta sigma weight residual 121.80 130.32 -8.52 2.44e+00 1.68e-01 1.22e+01 angle pdb=" N ARG D 211 " pdb=" CA ARG D 211 " pdb=" C ARG D 211 " ideal model delta sigma weight residual 114.31 109.90 4.41 1.29e+00 6.01e-01 1.17e+01 ... (remaining 13054 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.89: 5461 21.89 - 43.77: 294 43.77 - 65.66: 30 65.66 - 87.54: 8 87.54 - 109.43: 1 Dihedral angle restraints: 5794 sinusoidal: 2224 harmonic: 3570 Sorted by residual: dihedral pdb=" O1B ADP D 301 " pdb=" O3A ADP D 301 " pdb=" PB ADP D 301 " pdb=" PA ADP D 301 " ideal model delta sinusoidal sigma weight residual -60.00 -169.43 109.43 1 2.00e+01 2.50e-03 3.20e+01 dihedral pdb=" CA ASP C 160 " pdb=" CB ASP C 160 " pdb=" CG ASP C 160 " pdb=" OD1 ASP C 160 " ideal model delta sinusoidal sigma weight residual -30.00 -82.10 52.10 1 2.00e+01 2.50e-03 9.26e+00 dihedral pdb=" CB MET D 129 " pdb=" CG MET D 129 " pdb=" SD MET D 129 " pdb=" CE MET D 129 " ideal model delta sinusoidal sigma weight residual 60.00 113.02 -53.02 3 1.50e+01 4.44e-03 9.17e+00 ... (remaining 5791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 970 0.035 - 0.071: 386 0.071 - 0.106: 136 0.106 - 0.141: 40 0.141 - 0.176: 10 Chirality restraints: 1542 Sorted by residual: chirality pdb=" CB VAL C 130 " pdb=" CA VAL C 130 " pdb=" CG1 VAL C 130 " pdb=" CG2 VAL C 130 " both_signs ideal model delta sigma weight residual False -2.63 -2.81 0.18 2.00e-01 2.50e+01 7.78e-01 chirality pdb=" CB ILE D 67 " pdb=" CA ILE D 67 " pdb=" CG1 ILE D 67 " pdb=" CG2 ILE D 67 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.67e-01 chirality pdb=" CB ILE E 148 " pdb=" CA ILE E 148 " pdb=" CG1 ILE E 148 " pdb=" CG2 ILE E 148 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.51e-01 ... (remaining 1539 not shown) Planarity restraints: 1664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 346 " 0.037 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO E 347 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO E 347 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 347 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 110 " 0.034 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO D 111 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 111 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 111 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET F 110 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.51e+00 pdb=" N PRO F 111 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO F 111 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 111 " -0.027 5.00e-02 4.00e+02 ... (remaining 1661 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 3300 2.88 - 3.39: 8052 3.39 - 3.89: 14490 3.89 - 4.40: 16357 4.40 - 4.90: 28336 Nonbonded interactions: 70535 Sorted by model distance: nonbonded pdb=" OG SER C 170 " pdb=" O ILE C 178 " model vdw 2.378 2.440 nonbonded pdb=" O GLU E 105 " pdb=" OG SER E 167 " model vdw 2.383 2.440 nonbonded pdb=" OH TYR E 248 " pdb=" O LEU V 10 " model vdw 2.397 2.440 nonbonded pdb=" OG SER C 74 " pdb=" O ILE C 219 " model vdw 2.413 2.440 nonbonded pdb=" O SER E 342 " pdb=" OG SER E 373 " model vdw 2.424 2.440 ... (remaining 70530 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'D' and (resid 4 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 16 or (resid 17 and (name N or name CA \ or name C or name O or name CB )) or (resid 18 through 21 and (name N or name C \ A or name C or name O or name CB )) or resid 22 through 26 or (resid 27 and (nam \ e N or name CA or name C or name O or name CB )) or resid 28 through 35 or (resi \ d 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throug \ h 64 or (resid 65 and (name N or name CA or name C or name O or name CB )) or re \ sid 66 through 105 or (resid 106 and (name N or name CA or name C or name O or n \ ame CB )) or resid 107 through 116 or (resid 117 through 118 and (name N or name \ CA or name C or name O or name CB )) or resid 119 through 120 or (resid 121 and \ (name N or name CA or name C or name O or name CB )) or resid 122 through 127 o \ r (resid 128 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 29 through 141 or (resid 142 and (name N or name CA or name C or name O or name \ CB )) or resid 143 through 152 or (resid 153 and (name N or name CA or name C or \ name O or name CB )) or resid 154 through 185 or (resid 186 through 187 and (na \ me N or name CA or name C or name O or name CB )) or resid 188 through 191 or (r \ esid 192 through 195 and (name N or name CA or name C or name O or name CB )) or \ resid 196 or (resid 197 through 198 and (name N or name CA or name C or name O \ or name CB )) or resid 199 through 206 or (resid 207 through 212 and (name N or \ name CA or name C or name O or name CB )) or resid 213 through 214 or (resid 215 \ and (name N or name CA or name C or name O or name CB )) or resid 216 through 2 \ 18 or (resid 219 through 220 and (name N or name CA or name C or name O or name \ CB )) or (resid 221 through 225 and (name N or name CA or name C or name O or na \ me CB )) or resid 301 through 302)) selection = (chain 'F' and (resid 4 through 8 or (resid 9 through 10 and (name N or name CA \ or name C or name O or name CB )) or resid 11 through 33 or (resid 34 and (name \ N or name CA or name C or name O or name CB )) or resid 35 through 37 or (resid \ 38 through 39 and (name N or name CA or name C or name O or name CB )) or resid \ 40 through 45 or (resid 46 and (name N or name CA or name C or name O or name CB \ )) or resid 47 or (resid 48 and (name N or name CA or name C or name O or name \ CB )) or resid 49 through 73 or (resid 74 and (name N or name CA or name C or na \ me O or name CB )) or resid 75 through 179 or (resid 180 through 182 and (name N \ or name CA or name C or name O or name CB )) or resid 183 through 210 or (resid \ 211 through 212 and (name N or name CA or name C or name O or name CB )) or res \ id 213 through 225 or resid 301 through 302)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 3.490 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.030 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 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 : 0.003 0.124 9624 Z= 0.224 Angle : 0.730 15.294 13059 Z= 0.356 Chirality : 0.046 0.176 1542 Planarity : 0.005 0.055 1664 Dihedral : 13.091 109.426 3496 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.83 (0.15), residues: 1244 helix: -5.07 (0.05), residues: 413 sheet: -2.45 (0.43), residues: 132 loop : -3.47 (0.16), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 321 HIS 0.001 0.000 HIS E 188 PHE 0.011 0.001 PHE F 30 TYR 0.007 0.001 TYR C 199 ARG 0.002 0.000 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 142 TYR cc_start: 0.8049 (m-10) cc_final: 0.7803 (m-10) REVERT: C 175 MET cc_start: 0.2773 (ppp) cc_final: 0.2452 (ppp) REVERT: C 193 ASN cc_start: 0.8372 (t0) cc_final: 0.8128 (t0) REVERT: C 201 MET cc_start: 0.8586 (ptt) cc_final: 0.8373 (ptm) REVERT: E 77 ASN cc_start: 0.8200 (p0) cc_final: 0.7921 (p0) REVERT: E 98 ILE cc_start: 0.8313 (mt) cc_final: 0.7943 (pt) REVERT: E 145 GLU cc_start: 0.6768 (pm20) cc_final: 0.5617 (pm20) REVERT: E 147 GLN cc_start: 0.8322 (mt0) cc_final: 0.8028 (mt0) REVERT: E 321 TRP cc_start: 0.5316 (m-90) cc_final: 0.4800 (t-100) REVERT: D 8 CYS cc_start: 0.7322 (m) cc_final: 0.7015 (m) REVERT: D 71 GLN cc_start: 0.7815 (tm-30) cc_final: 0.7563 (tm-30) REVERT: D 107 ASN cc_start: 0.8223 (m-40) cc_final: 0.8012 (m110) REVERT: D 110 MET cc_start: 0.8454 (tpp) cc_final: 0.8225 (tpt) REVERT: D 171 GLU cc_start: 0.8187 (mp0) cc_final: 0.7523 (mp0) REVERT: D 192 ASN cc_start: 0.7165 (p0) cc_final: 0.5776 (t0) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.2468 time to fit residues: 97.2836 Evaluate side-chains 229 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.5980 chunk 93 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 37 optimal weight: 0.5980 chunk 59 optimal weight: 0.0020 chunk 72 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 GLN C 79 GLN C 104 GLN C 309 GLN E 56 ASN E 134 GLN E 172 ASN E 213 GLN F 71 GLN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 HIS F 162 ASN D 96 HIS D 140 ASN V 4 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9624 Z= 0.169 Angle : 0.573 9.644 13059 Z= 0.266 Chirality : 0.041 0.136 1542 Planarity : 0.004 0.036 1664 Dihedral : 5.936 72.958 1401 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.28 % Allowed : 15.15 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.60 (0.18), residues: 1244 helix: -3.47 (0.15), residues: 453 sheet: -1.89 (0.44), residues: 144 loop : -3.03 (0.18), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 246 HIS 0.007 0.001 HIS F 96 PHE 0.013 0.001 PHE E 319 TYR 0.016 0.001 TYR E 322 ARG 0.003 0.000 ARG C 261 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 237 time to evaluate : 1.088 Fit side-chains revert: symmetry clash REVERT: C 96 ILE cc_start: 0.8629 (tp) cc_final: 0.8380 (tp) REVERT: C 107 ARG cc_start: 0.7260 (mpt-90) cc_final: 0.7013 (mpt-90) REVERT: C 142 TYR cc_start: 0.8100 (m-10) cc_final: 0.7673 (m-10) REVERT: C 175 MET cc_start: 0.2924 (ppp) cc_final: 0.2445 (ppp) REVERT: C 193 ASN cc_start: 0.8632 (t0) cc_final: 0.8351 (t0) REVERT: C 255 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7356 (mp0) REVERT: C 262 MET cc_start: 0.7583 (tmm) cc_final: 0.7277 (ttp) REVERT: C 296 GLU cc_start: 0.8103 (mp0) cc_final: 0.7802 (mp0) REVERT: E 145 GLU cc_start: 0.6717 (pm20) cc_final: 0.5522 (pm20) REVERT: E 147 GLN cc_start: 0.8398 (mt0) cc_final: 0.7945 (mt0) REVERT: E 321 TRP cc_start: 0.5388 (m-90) cc_final: 0.4692 (t-100) REVERT: E 374 GLU cc_start: 0.8238 (tt0) cc_final: 0.8034 (tt0) REVERT: F 48 LYS cc_start: 0.7035 (mtmt) cc_final: 0.6834 (mtmm) REVERT: F 73 MET cc_start: 0.7960 (mmm) cc_final: 0.7364 (tpp) REVERT: F 125 ARG cc_start: 0.8189 (tpp80) cc_final: 0.7507 (mtp180) REVERT: F 158 ARG cc_start: 0.8657 (tmm-80) cc_final: 0.8380 (ttp-170) REVERT: D 8 CYS cc_start: 0.7593 (m) cc_final: 0.7151 (m) REVERT: D 71 GLN cc_start: 0.7824 (tm-30) cc_final: 0.7605 (tm-30) REVERT: D 110 MET cc_start: 0.8599 (tpp) cc_final: 0.8260 (tpt) REVERT: D 121 GLU cc_start: 0.7812 (pm20) cc_final: 0.7368 (pm20) REVERT: D 151 ARG cc_start: 0.7732 (mtm-85) cc_final: 0.6088 (ttp80) REVERT: D 165 ARG cc_start: 0.7426 (mmm-85) cc_final: 0.7069 (mmm160) REVERT: D 171 GLU cc_start: 0.8247 (mp0) cc_final: 0.7518 (mp0) REVERT: D 192 ASN cc_start: 0.7419 (p0) cc_final: 0.6127 (t0) REVERT: D 212 MET cc_start: 0.6122 (pmm) cc_final: 0.4905 (ppp) outliers start: 22 outliers final: 12 residues processed: 243 average time/residue: 0.2388 time to fit residues: 77.3269 Evaluate side-chains 234 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 221 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 204 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 0.7980 chunk 34 optimal weight: 0.0170 chunk 93 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 chunk 121 optimal weight: 0.0670 chunk 100 optimal weight: 20.0000 chunk 111 optimal weight: 4.9990 chunk 38 optimal weight: 0.0670 chunk 90 optimal weight: 7.9990 overall best weight: 0.3094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 121 GLN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 HIS F 152 GLN F 162 ASN D 107 ASN D 140 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9624 Z= 0.122 Angle : 0.521 10.665 13059 Z= 0.237 Chirality : 0.040 0.144 1542 Planarity : 0.003 0.026 1664 Dihedral : 5.490 55.096 1401 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.59 % Allowed : 15.98 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.20), residues: 1244 helix: -2.22 (0.20), residues: 464 sheet: -1.61 (0.44), residues: 144 loop : -2.75 (0.20), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 246 HIS 0.006 0.000 HIS F 96 PHE 0.010 0.001 PHE F 68 TYR 0.011 0.001 TYR E 322 ARG 0.004 0.000 ARG C 15 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 223 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 58 ASN cc_start: 0.8065 (t0) cc_final: 0.7593 (t0) REVERT: C 107 ARG cc_start: 0.7231 (mpt-90) cc_final: 0.6998 (mpt-90) REVERT: C 142 TYR cc_start: 0.8054 (m-10) cc_final: 0.7725 (m-10) REVERT: C 175 MET cc_start: 0.3138 (ppp) cc_final: 0.2637 (ppp) REVERT: C 212 MET cc_start: 0.4381 (mtp) cc_final: 0.4015 (mtp) REVERT: C 255 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7398 (mp0) REVERT: C 262 MET cc_start: 0.7417 (tmm) cc_final: 0.7189 (ttp) REVERT: C 296 GLU cc_start: 0.8098 (mp0) cc_final: 0.7832 (mp0) REVERT: E 145 GLU cc_start: 0.6766 (pm20) cc_final: 0.5704 (pm20) REVERT: E 147 GLN cc_start: 0.8368 (mt0) cc_final: 0.7957 (mt0) REVERT: E 321 TRP cc_start: 0.5301 (m-90) cc_final: 0.4731 (t-100) REVERT: E 374 GLU cc_start: 0.8234 (tt0) cc_final: 0.8006 (tt0) REVERT: F 48 LYS cc_start: 0.7053 (mtmt) cc_final: 0.6841 (mtmm) REVERT: F 125 ARG cc_start: 0.8176 (tpp80) cc_final: 0.7444 (mtp180) REVERT: F 150 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7309 (tp30) REVERT: D 8 CYS cc_start: 0.7477 (m) cc_final: 0.7254 (m) REVERT: D 71 GLN cc_start: 0.7872 (tm-30) cc_final: 0.7587 (tm-30) REVERT: D 121 GLU cc_start: 0.7832 (pm20) cc_final: 0.7305 (pm20) REVERT: D 165 ARG cc_start: 0.7593 (mmm-85) cc_final: 0.7182 (mmm160) REVERT: D 171 GLU cc_start: 0.8302 (mp0) cc_final: 0.7603 (mp0) REVERT: D 192 ASN cc_start: 0.7430 (p0) cc_final: 0.6106 (t0) outliers start: 25 outliers final: 15 residues processed: 231 average time/residue: 0.2713 time to fit residues: 84.6841 Evaluate side-chains 228 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 212 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 204 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 75 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 59 optimal weight: 0.3980 chunk 107 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN C 281 ASN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 HIS F 152 GLN F 162 ASN D 140 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9624 Z= 0.220 Angle : 0.603 8.600 13059 Z= 0.285 Chirality : 0.042 0.176 1542 Planarity : 0.003 0.026 1664 Dihedral : 6.033 59.761 1401 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.32 % Allowed : 16.60 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.22), residues: 1244 helix: -1.41 (0.22), residues: 471 sheet: -1.46 (0.44), residues: 145 loop : -2.40 (0.21), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 321 HIS 0.010 0.001 HIS F 96 PHE 0.020 0.002 PHE E 319 TYR 0.015 0.001 TYR E 366 ARG 0.004 0.001 ARG E 12 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 214 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 142 TYR cc_start: 0.8069 (m-10) cc_final: 0.7698 (m-10) REVERT: C 175 MET cc_start: 0.3205 (ppp) cc_final: 0.2662 (ppp) REVERT: C 231 LYS cc_start: 0.8956 (ptpt) cc_final: 0.8717 (ptpp) REVERT: C 255 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: C 296 GLU cc_start: 0.8227 (mp0) cc_final: 0.7952 (mp0) REVERT: E 45 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8162 (mp) REVERT: E 374 GLU cc_start: 0.8319 (tt0) cc_final: 0.8004 (tt0) REVERT: F 125 ARG cc_start: 0.8062 (tpp80) cc_final: 0.7346 (mtp180) REVERT: D 71 GLN cc_start: 0.7927 (tm-30) cc_final: 0.7194 (tm-30) REVERT: D 73 MET cc_start: 0.7404 (tpp) cc_final: 0.6790 (mmm) REVERT: D 121 GLU cc_start: 0.7805 (pm20) cc_final: 0.7393 (pm20) REVERT: D 162 ASN cc_start: 0.7807 (OUTLIER) cc_final: 0.7535 (m-40) REVERT: D 165 ARG cc_start: 0.7614 (mmm-85) cc_final: 0.7201 (mmm160) REVERT: D 171 GLU cc_start: 0.8252 (mp0) cc_final: 0.7589 (mp0) REVERT: D 212 MET cc_start: 0.6111 (pmm) cc_final: 0.5361 (ppp) outliers start: 32 outliers final: 19 residues processed: 227 average time/residue: 0.2276 time to fit residues: 70.1633 Evaluate side-chains 216 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 194 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 368 ILE Chi-restraints excluded: chain F residue 48 LYS Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 204 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.0270 chunk 68 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 49 optimal weight: 0.1980 chunk 102 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 0 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 30 optimal weight: 0.0970 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN C 131 ASN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 GLN E 172 ASN F 152 GLN F 162 ASN D 140 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9624 Z= 0.136 Angle : 0.529 8.825 13059 Z= 0.245 Chirality : 0.040 0.149 1542 Planarity : 0.003 0.025 1664 Dihedral : 5.691 58.951 1401 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.11 % Allowed : 18.36 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.22), residues: 1244 helix: -0.74 (0.24), residues: 468 sheet: -1.28 (0.45), residues: 144 loop : -2.30 (0.22), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 138 HIS 0.003 0.000 HIS F 96 PHE 0.007 0.001 PHE E 319 TYR 0.009 0.001 TYR E 322 ARG 0.004 0.000 ARG C 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 207 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.7348 (ttp80) cc_final: 0.6968 (ttp80) REVERT: C 58 ASN cc_start: 0.8164 (t0) cc_final: 0.7832 (t0) REVERT: C 142 TYR cc_start: 0.8050 (m-10) cc_final: 0.7712 (m-10) REVERT: C 175 MET cc_start: 0.3132 (ppp) cc_final: 0.2626 (ppp) REVERT: C 212 MET cc_start: 0.4366 (mtp) cc_final: 0.4042 (mtp) REVERT: C 231 LYS cc_start: 0.8938 (ptpt) cc_final: 0.8707 (ptpp) REVERT: C 255 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7328 (mp0) REVERT: E 374 GLU cc_start: 0.8246 (tt0) cc_final: 0.7935 (tt0) REVERT: F 125 ARG cc_start: 0.8018 (tpp80) cc_final: 0.7276 (mtp180) REVERT: D 54 LEU cc_start: 0.7220 (mt) cc_final: 0.7002 (mt) REVERT: D 71 GLN cc_start: 0.7937 (tm-30) cc_final: 0.7176 (tm-30) REVERT: D 73 MET cc_start: 0.7425 (tpp) cc_final: 0.6794 (mmm) REVERT: D 165 ARG cc_start: 0.7684 (mmm-85) cc_final: 0.7242 (mmm160) REVERT: D 171 GLU cc_start: 0.8226 (mp0) cc_final: 0.7595 (mp0) outliers start: 30 outliers final: 20 residues processed: 223 average time/residue: 0.2434 time to fit residues: 72.9472 Evaluate side-chains 222 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 201 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 204 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 99 optimal weight: 20.0000 chunk 55 optimal weight: 7.9990 chunk 9 optimal weight: 0.0770 chunk 39 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 162 ASN D 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9624 Z= 0.179 Angle : 0.546 7.774 13059 Z= 0.254 Chirality : 0.041 0.138 1542 Planarity : 0.003 0.025 1664 Dihedral : 5.757 49.684 1401 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.63 % Allowed : 18.26 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.23), residues: 1244 helix: -0.38 (0.24), residues: 467 sheet: -1.10 (0.43), residues: 153 loop : -2.14 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 246 HIS 0.002 0.000 HIS E 177 PHE 0.013 0.001 PHE E 319 TYR 0.009 0.001 TYR E 366 ARG 0.004 0.000 ARG C 107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 211 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.7363 (ttp80) cc_final: 0.6953 (ttp80) REVERT: C 118 ASP cc_start: 0.8116 (t0) cc_final: 0.7865 (t0) REVERT: C 142 TYR cc_start: 0.8072 (m-10) cc_final: 0.7362 (m-10) REVERT: C 175 MET cc_start: 0.3306 (ppp) cc_final: 0.2738 (ppp) REVERT: C 212 MET cc_start: 0.4426 (mtp) cc_final: 0.4098 (mtp) REVERT: C 255 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7322 (mp0) REVERT: E 351 TRP cc_start: 0.7909 (t60) cc_final: 0.7419 (t60) REVERT: E 374 GLU cc_start: 0.8230 (tt0) cc_final: 0.7938 (tt0) REVERT: F 83 GLU cc_start: 0.8456 (tp30) cc_final: 0.8165 (tp30) REVERT: F 125 ARG cc_start: 0.7976 (tpp80) cc_final: 0.7280 (mtp180) REVERT: D 71 GLN cc_start: 0.7966 (tm-30) cc_final: 0.7610 (tm-30) REVERT: D 73 MET cc_start: 0.7433 (tpp) cc_final: 0.6759 (mmm) REVERT: D 121 GLU cc_start: 0.7891 (pm20) cc_final: 0.7511 (pm20) REVERT: D 165 ARG cc_start: 0.7795 (mmm-85) cc_final: 0.7305 (mmm160) REVERT: D 171 GLU cc_start: 0.8251 (mp0) cc_final: 0.7647 (mp0) REVERT: D 212 MET cc_start: 0.6346 (pmm) cc_final: 0.4961 (ppp) outliers start: 35 outliers final: 24 residues processed: 228 average time/residue: 0.2393 time to fit residues: 73.3558 Evaluate side-chains 219 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 194 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 336 ILE Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 204 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 100 optimal weight: 8.9990 chunk 66 optimal weight: 0.5980 chunk 119 optimal weight: 9.9990 chunk 74 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 ASN C 281 ASN F 152 GLN F 162 ASN D 140 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.5068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9624 Z= 0.178 Angle : 0.555 9.579 13059 Z= 0.258 Chirality : 0.041 0.135 1542 Planarity : 0.003 0.030 1664 Dihedral : 5.846 57.077 1401 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.63 % Allowed : 19.50 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.23), residues: 1244 helix: -0.08 (0.25), residues: 469 sheet: -0.98 (0.43), residues: 152 loop : -2.06 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 246 HIS 0.002 0.000 HIS F 137 PHE 0.012 0.001 PHE E 319 TYR 0.013 0.001 TYR E 258 ARG 0.009 0.000 ARG C 182 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 203 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.7400 (ttp80) cc_final: 0.6971 (ttp80) REVERT: C 175 MET cc_start: 0.3349 (ppp) cc_final: 0.2758 (ppp) REVERT: C 212 MET cc_start: 0.4438 (mtp) cc_final: 0.4157 (mtp) REVERT: C 230 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8055 (mm) REVERT: C 255 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7327 (mp0) REVERT: E 145 GLU cc_start: 0.6926 (pm20) cc_final: 0.6710 (pm20) REVERT: E 351 TRP cc_start: 0.7938 (t60) cc_final: 0.7461 (t60) REVERT: E 374 GLU cc_start: 0.8195 (tt0) cc_final: 0.7904 (tt0) REVERT: F 83 GLU cc_start: 0.8489 (tp30) cc_final: 0.8175 (tp30) REVERT: F 125 ARG cc_start: 0.7955 (tpp80) cc_final: 0.7254 (mtp180) REVERT: D 71 GLN cc_start: 0.7989 (tm-30) cc_final: 0.7611 (tm-30) REVERT: D 73 MET cc_start: 0.7462 (tpp) cc_final: 0.6784 (mmm) REVERT: D 121 GLU cc_start: 0.7851 (pm20) cc_final: 0.7523 (pm20) REVERT: D 165 ARG cc_start: 0.7846 (mmm-85) cc_final: 0.7340 (mmm160) REVERT: D 171 GLU cc_start: 0.8191 (mp0) cc_final: 0.7477 (mp0) REVERT: D 212 MET cc_start: 0.6366 (pmm) cc_final: 0.5200 (ppp) REVERT: D 214 ARG cc_start: 0.4968 (OUTLIER) cc_final: 0.4754 (ttp-170) outliers start: 35 outliers final: 29 residues processed: 222 average time/residue: 0.2583 time to fit residues: 76.1969 Evaluate side-chains 230 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 198 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain E residue 336 ILE Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 204 HIS Chi-restraints excluded: chain D residue 214 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.9990 chunk 47 optimal weight: 0.1980 chunk 71 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 152 GLN F 162 ASN D 140 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.5334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9624 Z= 0.177 Angle : 0.561 10.074 13059 Z= 0.261 Chirality : 0.041 0.151 1542 Planarity : 0.003 0.029 1664 Dihedral : 5.710 49.832 1401 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.63 % Allowed : 20.23 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.23), residues: 1244 helix: 0.03 (0.25), residues: 478 sheet: -1.10 (0.44), residues: 149 loop : -1.97 (0.23), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 246 HIS 0.003 0.000 HIS F 137 PHE 0.012 0.001 PHE E 319 TYR 0.013 0.001 TYR C 142 ARG 0.006 0.000 ARG F 211 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 208 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.7391 (ttp80) cc_final: 0.6949 (ttp80) REVERT: C 175 MET cc_start: 0.3141 (ppp) cc_final: 0.2570 (ppp) REVERT: C 212 MET cc_start: 0.4407 (mtp) cc_final: 0.4067 (mtp) REVERT: C 230 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8026 (mm) REVERT: C 255 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: E 301 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7504 (m-30) REVERT: E 336 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8683 (mm) REVERT: E 351 TRP cc_start: 0.8031 (t60) cc_final: 0.7499 (t60) REVERT: F 125 ARG cc_start: 0.7965 (tpp80) cc_final: 0.7268 (mtp180) REVERT: D 36 GLU cc_start: 0.5002 (mt-10) cc_final: 0.4497 (mt-10) REVERT: D 71 GLN cc_start: 0.8100 (tm-30) cc_final: 0.7716 (tm-30) REVERT: D 73 MET cc_start: 0.7525 (tpp) cc_final: 0.6840 (mmm) REVERT: D 121 GLU cc_start: 0.7860 (pm20) cc_final: 0.7588 (pm20) REVERT: D 165 ARG cc_start: 0.7884 (mmm-85) cc_final: 0.7337 (mmm160) REVERT: D 171 GLU cc_start: 0.8130 (mp0) cc_final: 0.7420 (mp0) REVERT: D 212 MET cc_start: 0.6297 (pmm) cc_final: 0.5125 (ppp) REVERT: D 214 ARG cc_start: 0.5103 (OUTLIER) cc_final: 0.4858 (ttp-170) outliers start: 35 outliers final: 28 residues processed: 227 average time/residue: 0.2449 time to fit residues: 74.2788 Evaluate side-chains 235 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 202 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain E residue 336 ILE Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 204 HIS Chi-restraints excluded: chain D residue 214 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.9980 chunk 104 optimal weight: 7.9990 chunk 111 optimal weight: 0.3980 chunk 67 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 100 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 110 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 134 GLN E 201 HIS F 152 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.5559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9624 Z= 0.178 Angle : 0.564 11.195 13059 Z= 0.263 Chirality : 0.041 0.147 1542 Planarity : 0.003 0.031 1664 Dihedral : 5.571 42.233 1401 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.73 % Allowed : 19.61 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.24), residues: 1244 helix: 0.17 (0.25), residues: 481 sheet: -1.09 (0.43), residues: 149 loop : -1.91 (0.23), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 246 HIS 0.003 0.000 HIS E 201 PHE 0.013 0.001 PHE E 319 TYR 0.017 0.001 TYR C 142 ARG 0.008 0.000 ARG F 211 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 201 time to evaluate : 1.105 Fit side-chains revert: symmetry clash REVERT: C 24 ARG cc_start: 0.7387 (ttp80) cc_final: 0.6971 (ttp80) REVERT: C 175 MET cc_start: 0.3076 (ppp) cc_final: 0.2508 (ppp) REVERT: C 212 MET cc_start: 0.4452 (mtp) cc_final: 0.4172 (mtp) REVERT: C 230 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8061 (mm) REVERT: C 255 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7376 (mp0) REVERT: C 281 ASN cc_start: 0.8316 (t0) cc_final: 0.8030 (t0) REVERT: E 77 ASN cc_start: 0.8148 (p0) cc_final: 0.7928 (p0) REVERT: E 145 GLU cc_start: 0.7101 (pm20) cc_final: 0.6680 (pm20) REVERT: E 293 MET cc_start: 0.7791 (tpp) cc_final: 0.7557 (mmm) REVERT: E 301 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7514 (m-30) REVERT: E 351 TRP cc_start: 0.8100 (t60) cc_final: 0.7546 (t60) REVERT: E 374 GLU cc_start: 0.8125 (tt0) cc_final: 0.7825 (tt0) REVERT: F 125 ARG cc_start: 0.7972 (tpp80) cc_final: 0.7269 (mtp180) REVERT: D 71 GLN cc_start: 0.8133 (tm-30) cc_final: 0.7733 (tm-30) REVERT: D 73 MET cc_start: 0.7536 (tpp) cc_final: 0.6831 (mmm) REVERT: D 121 GLU cc_start: 0.7879 (pm20) cc_final: 0.7666 (pm20) REVERT: D 165 ARG cc_start: 0.7882 (mmm-85) cc_final: 0.7337 (mmm160) REVERT: D 171 GLU cc_start: 0.8137 (mp0) cc_final: 0.7394 (mp0) REVERT: D 186 GLN cc_start: 0.8603 (tp40) cc_final: 0.8339 (tp-100) outliers start: 36 outliers final: 25 residues processed: 223 average time/residue: 0.2530 time to fit residues: 75.0374 Evaluate side-chains 222 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 194 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 201 HIS Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 204 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 78 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 201 HIS F 152 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.5900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9624 Z= 0.266 Angle : 0.643 11.551 13059 Z= 0.303 Chirality : 0.044 0.147 1542 Planarity : 0.003 0.039 1664 Dihedral : 5.895 44.102 1401 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.32 % Allowed : 20.12 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.24), residues: 1244 helix: 0.05 (0.25), residues: 483 sheet: -0.99 (0.42), residues: 161 loop : -1.88 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP E 321 HIS 0.013 0.001 HIS E 201 PHE 0.014 0.002 PHE E 13 TYR 0.016 0.002 TYR E 258 ARG 0.008 0.000 ARG F 211 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 196 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.7387 (ttp80) cc_final: 0.6969 (ttp80) REVERT: C 91 ASN cc_start: 0.7650 (p0) cc_final: 0.7350 (p0) REVERT: C 175 MET cc_start: 0.3276 (ppp) cc_final: 0.2718 (ppp) REVERT: C 230 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8105 (mm) REVERT: C 255 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7420 (mp0) REVERT: E 145 GLU cc_start: 0.6955 (pm20) cc_final: 0.6538 (pm20) REVERT: E 301 ASP cc_start: 0.8188 (OUTLIER) cc_final: 0.7574 (m-30) REVERT: E 351 TRP cc_start: 0.8130 (t60) cc_final: 0.7556 (t60) REVERT: F 125 ARG cc_start: 0.8001 (tpp80) cc_final: 0.7295 (mtp180) REVERT: D 71 GLN cc_start: 0.8157 (tm-30) cc_final: 0.7752 (tm-30) REVERT: D 73 MET cc_start: 0.7701 (tpp) cc_final: 0.7015 (mmm) REVERT: D 145 GLU cc_start: 0.7624 (pm20) cc_final: 0.7164 (pm20) REVERT: D 165 ARG cc_start: 0.7924 (mmm-85) cc_final: 0.7364 (mmm160) REVERT: D 171 GLU cc_start: 0.8179 (mp0) cc_final: 0.7418 (mp0) REVERT: D 186 GLN cc_start: 0.8589 (tp40) cc_final: 0.8323 (tp-100) REVERT: D 212 MET cc_start: 0.6111 (pmm) cc_final: 0.4900 (ppp) outliers start: 32 outliers final: 24 residues processed: 214 average time/residue: 0.2529 time to fit residues: 72.0441 Evaluate side-chains 221 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 194 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 201 HIS Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 204 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 201 HIS ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.188271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.127983 restraints weight = 10893.446| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.94 r_work: 0.3250 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.5961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9624 Z= 0.190 Angle : 0.607 11.363 13059 Z= 0.284 Chirality : 0.042 0.148 1542 Planarity : 0.003 0.052 1664 Dihedral : 5.757 41.008 1401 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.90 % Allowed : 21.37 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.24), residues: 1244 helix: 0.18 (0.25), residues: 489 sheet: -0.90 (0.44), residues: 150 loop : -1.90 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 321 HIS 0.004 0.001 HIS E 201 PHE 0.014 0.001 PHE E 13 TYR 0.012 0.001 TYR E 258 ARG 0.009 0.000 ARG D 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2443.12 seconds wall clock time: 44 minutes 34.78 seconds (2674.78 seconds total)