Starting phenix.real_space_refine on Thu Mar 14 19:31:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ark_11885/03_2024/7ark_11885_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ark_11885/03_2024/7ark_11885.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ark_11885/03_2024/7ark_11885.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ark_11885/03_2024/7ark_11885.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ark_11885/03_2024/7ark_11885_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ark_11885/03_2024/7ark_11885_updated.pdb" } resolution = 4.1 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 51 5.16 5 C 6070 2.51 5 N 1686 2.21 5 O 1755 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 8": "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 GLU 148": "OE1" <-> "OE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C ARG 397": "NH1" <-> "NH2" Residue "E ARG 58": "NH1" <-> "NH2" Residue "E ARG 111": "NH1" <-> "NH2" Residue "E ARG 125": "NH1" <-> "NH2" Residue "E ARG 139": "NH1" <-> "NH2" Residue "E ARG 184": "NH1" <-> "NH2" Residue "E ARG 239": "NH1" <-> "NH2" Residue "E ASP 240": "OD1" <-> "OD2" Residue "E TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 312": "OD1" <-> "OD2" Residue "E PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D ASP 65": "OD1" <-> "OD2" Residue "D TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 136": "OD1" <-> "OD2" Residue "D ARG 151": "NH1" <-> "NH2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D GLU 190": "OE1" <-> "OE2" Residue "D PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 220": "OD1" <-> "OD2" Residue "D GLU 226": "OE1" <-> "OE2" Residue "F ASP 9": "OD1" <-> "OD2" Residue "F TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 17": "OE1" <-> "OE2" Residue "F PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 101": "OD1" <-> "OD2" Residue "F PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 106": "OE1" <-> "OE2" Residue "F ARG 151": "NH1" <-> "NH2" Residue "F PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 226": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9570 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 2922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 2922 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 365} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 3125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3125 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 14, 'TRANS': 390} Chain breaks: 1 Chain: "D" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1730 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 8, 'TRANS': 217} Chain: "F" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1729 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 8, 'TRANS': 217} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.56, per 1000 atoms: 0.58 Number of scatterers: 9570 At special positions: 0 Unit cell: (126.75, 90.246, 138.918, 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 51 16.00 P 6 15.00 Mg 2 11.99 O 1755 8.00 N 1686 7.00 C 6070 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=0, symmetry=0 Time building additional restraints: 3.08 Conformation dependent library (CDL) restraints added in 1.6 seconds 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2272 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 10 sheets defined 28.1% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'C' and resid 29 through 39 Processing helix chain 'C' and resid 44 through 58 removed outlier: 3.695A pdb=" N GLU C 54 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU C 55 " --> pdb=" O PHE C 51 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN C 56 " --> pdb=" O GLU C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 199 removed outlier: 4.484A pdb=" N TYR C 199 " --> pdb=" O VAL C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 237 No H-bonds generated for 'chain 'C' and resid 235 through 237' Processing helix chain 'C' and resid 256 through 271 removed outlier: 4.295A pdb=" N GLU C 263 " --> pdb=" O ALA C 259 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LYS C 264 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU C 269 " --> pdb=" O ASN C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 286 removed outlier: 3.553A pdb=" N ALA C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA C 279 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE C 280 " --> pdb=" O ALA C 276 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 292 No H-bonds generated for 'chain 'C' and resid 289 through 292' Processing helix chain 'C' and resid 311 through 317 removed outlier: 4.044A pdb=" N PHE C 314 " --> pdb=" O MET C 311 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N MET C 315 " --> pdb=" O MET C 312 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL C 316 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN C 317 " --> pdb=" O PHE C 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 311 through 317' Processing helix chain 'C' and resid 320 through 337 removed outlier: 3.858A pdb=" N ILE C 324 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA C 326 " --> pdb=" O GLY C 322 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C 327 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA C 331 " --> pdb=" O ILE C 327 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU C 336 " --> pdb=" O LEU C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 378 removed outlier: 4.025A pdb=" N ILE C 366 " --> pdb=" O PRO C 362 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL C 367 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU C 370 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA C 372 " --> pdb=" O ILE C 368 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET C 373 " --> pdb=" O ALA C 369 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ALA C 376 " --> pdb=" O ALA C 372 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU C 377 " --> pdb=" O MET C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 386 removed outlier: 3.973A pdb=" N ARG C 386 " --> pdb=" O TYR C 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 33 removed outlier: 3.676A pdb=" N VAL E 28 " --> pdb=" O SER E 24 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ILE E 29 " --> pdb=" O LEU E 25 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER E 30 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N THR E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ILE E 32 " --> pdb=" O VAL E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 39 No H-bonds generated for 'chain 'E' and resid 36 through 39' Processing helix chain 'E' and resid 41 through 58 removed outlier: 3.593A pdb=" N SER E 46 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN E 49 " --> pdb=" O LEU E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 84 removed outlier: 3.823A pdb=" N ASP E 83 " --> pdb=" O GLN E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 158 removed outlier: 3.941A pdb=" N ALA E 157 " --> pdb=" O GLY E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 214 removed outlier: 3.677A pdb=" N GLN E 213 " --> pdb=" O ALA E 209 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR E 214 " --> pdb=" O ASP E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 266 removed outlier: 3.938A pdb=" N ASP E 264 " --> pdb=" O TYR E 260 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ILE E 265 " --> pdb=" O MET E 261 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN E 266 " --> pdb=" O TYR E 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 260 through 266' Processing helix chain 'E' and resid 271 through 273 No H-bonds generated for 'chain 'E' and resid 271 through 273' Processing helix chain 'E' and resid 278 through 293 removed outlier: 4.428A pdb=" N PHE E 285 " --> pdb=" O GLY E 281 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASN E 286 " --> pdb=" O VAL E 282 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ILE E 287 " --> pdb=" O ALA E 283 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL E 288 " --> pdb=" O CYS E 284 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR E 290 " --> pdb=" O ASN E 286 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 316 No H-bonds generated for 'chain 'E' and resid 313 through 316' Processing helix chain 'E' and resid 319 through 342 removed outlier: 3.795A pdb=" N GLY E 323 " --> pdb=" O PHE E 319 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU E 324 " --> pdb=" O VAL E 320 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA E 326 " --> pdb=" O TYR E 322 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N PHE E 329 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL E 335 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE E 336 " --> pdb=" O LEU E 332 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE E 337 " --> pdb=" O CYS E 333 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL E 339 " --> pdb=" O VAL E 335 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL E 340 " --> pdb=" O ILE E 336 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL E 341 " --> pdb=" O ILE E 337 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER E 342 " --> pdb=" O GLY E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 385 No H-bonds generated for 'chain 'E' and resid 382 through 385' Processing helix chain 'E' and resid 390 through 394 Processing helix chain 'E' and resid 396 through 400 Processing helix chain 'D' and resid 50 through 54 Processing helix chain 'D' and resid 104 through 108 removed outlier: 3.959A 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 112 No H-bonds generated for 'chain 'D' and resid 110 through 112' Processing helix chain 'D' and resid 119 through 133 removed outlier: 3.721A pdb=" N ILE D 122 " --> pdb=" O PRO D 119 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASN D 123 " --> pdb=" O ALA D 120 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER D 124 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG D 125 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ALA D 126 " --> pdb=" O ASN D 123 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU D 127 " --> pdb=" O SER D 124 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU D 128 " --> pdb=" O ARG D 125 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N MET D 129 " --> pdb=" O ALA D 126 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS D 131 " --> pdb=" O GLU D 128 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA D 132 " --> pdb=" O MET D 129 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL D 133 " --> pdb=" O LEU D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 156 removed outlier: 3.668A pdb=" N ILE D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 185 removed outlier: 3.852A pdb=" N SER D 183 " --> pdb=" O ARG D 179 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE D 184 " --> pdb=" O ASN D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 194 removed outlier: 3.721A pdb=" N LEU D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN D 192 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 211 No H-bonds generated for 'chain 'D' and resid 209 through 211' Processing helix chain 'F' and resid 48 through 52 Processing helix chain 'F' and resid 78 through 84 removed outlier: 3.776A pdb=" N LYS F 81 " --> pdb=" O SER F 78 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ALA F 82 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU F 83 " --> pdb=" O ALA F 80 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU F 84 " --> pdb=" O LYS F 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 78 through 84' Processing helix chain 'F' and resid 104 through 108 Processing helix chain 'F' and resid 110 through 114 removed outlier: 3.747A 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 122 through 133 removed outlier: 4.031A pdb=" N ALA F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU F 127 " --> pdb=" O ASN F 123 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU F 128 " --> pdb=" O SER F 124 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET F 129 " --> pdb=" O ARG F 125 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU F 130 " --> pdb=" O ALA F 126 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS F 131 " --> pdb=" O LEU F 127 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA F 132 " --> pdb=" O GLU F 128 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL F 133 " --> pdb=" O MET F 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 122 through 133' Processing helix chain 'F' and resid 148 through 159 removed outlier: 4.046A pdb=" N GLN F 152 " --> pdb=" O GLY F 148 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ARG F 153 " --> pdb=" O GLY F 149 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA F 155 " --> pdb=" O ARG F 151 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE F 156 " --> pdb=" O GLN F 152 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA F 157 " --> pdb=" O ARG F 153 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA F 159 " --> pdb=" O ALA F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 188 removed outlier: 3.726A pdb=" N ASP F 182 " --> pdb=" O ALA F 178 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N SER F 183 " --> pdb=" O ARG F 179 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN F 186 " --> pdb=" O ASP F 182 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU F 187 " --> pdb=" O SER F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 211 removed outlier: 4.227A pdb=" N ARG F 211 " --> pdb=" O LEU F 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 208 through 211' Processing sheet with id= A, first strand: chain 'C' and resid 94 through 96 removed outlier: 3.502A pdb=" N ALA C 94 " --> pdb=" O ARG C 223 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE C 96 " --> pdb=" O GLY C 221 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY C 221 " --> pdb=" O ILE C 96 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 109 through 113 removed outlier: 3.718A pdb=" N ALA C 110 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG C 163 " --> pdb=" O GLN C 104 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL C 164 " --> pdb=" O ARG C 182 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG C 182 " --> pdb=" O VAL C 164 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 143 through 146 removed outlier: 6.244A pdb=" N ASN C 185 " --> pdb=" O VAL C 144 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU C 146 " --> pdb=" O ASN C 185 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ILE C 187 " --> pdb=" O LEU C 146 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'E' and resid 66 through 68 removed outlier: 3.532A pdb=" N GLY E 66 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU E 226 " --> pdb=" O GLY E 66 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS E 227 " --> pdb=" O ALA E 93 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ALA E 93 " --> pdb=" O LYS E 227 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 114 through 117 removed outlier: 4.075A pdb=" N ALA E 204 " --> pdb=" O GLN E 114 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE E 206 " --> pdb=" O LYS E 116 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 165 through 170 removed outlier: 3.628A pdb=" N ILE E 170 " --> pdb=" O LYS E 183 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS E 183 " --> pdb=" O ILE E 170 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 30 through 32 removed outlier: 3.819A pdb=" N PHE D 30 " --> pdb=" O CYS D 8 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS D 8 " --> pdb=" O PHE D 30 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN D 7 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE D 67 " --> pdb=" O GLN D 7 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASP D 9 " --> pdb=" O ASP D 65 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP D 65 " --> pdb=" O ASP D 9 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 214 through 218 removed outlier: 3.513A pdb=" N LEU D 216 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET D 38 " --> pdb=" O PHE D 199 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL D 167 " --> pdb=" O ALA D 198 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU D 200 " --> pdb=" O VAL D 167 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA D 169 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 6 through 9 removed outlier: 3.914A pdb=" N ASP F 9 " --> pdb=" O ASP F 65 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASP F 65 " --> pdb=" O ASP F 9 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 38 through 41 removed outlier: 3.645A pdb=" N MET F 38 " --> pdb=" O PHE F 199 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE F 40 " --> pdb=" O VAL F 201 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL F 167 " --> pdb=" O ALA F 198 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU F 200 " --> pdb=" O VAL F 167 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL F 202 " --> pdb=" O ALA F 169 " (cutoff:3.500A) 127 hydrogen bonds defined for protein. 369 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: 2.42 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3192 1.35 - 1.46: 1978 1.46 - 1.58: 4456 1.58 - 1.70: 6 1.70 - 1.82: 96 Bond restraints: 9728 Sorted by residual: bond pdb=" O3A ANP F 401 " pdb=" PB ANP F 401 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.23e+01 bond pdb=" O3A ANP D 401 " pdb=" PB ANP D 401 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.03e+01 bond pdb=" C LEU E 129 " pdb=" N PRO E 130 " ideal model delta sigma weight residual 1.334 1.382 -0.049 8.40e-03 1.42e+04 3.38e+01 bond pdb=" N3B ANP D 401 " pdb=" PG ANP D 401 " ideal model delta sigma weight residual 1.795 1.691 0.104 2.00e-02 2.50e+03 2.70e+01 bond pdb=" N3B ANP F 401 " pdb=" PG ANP F 401 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.58e+01 ... (remaining 9723 not shown) Histogram of bond angle deviations from ideal: 100.41 - 107.13: 307 107.13 - 113.85: 5502 113.85 - 120.57: 3734 120.57 - 127.29: 3538 127.29 - 134.01: 101 Bond angle restraints: 13182 Sorted by residual: angle pdb=" PB ANP F 401 " pdb=" N3B ANP F 401 " pdb=" PG ANP F 401 " ideal model delta sigma weight residual 126.95 109.96 16.99 3.00e+00 1.11e-01 3.21e+01 angle pdb=" PB ANP D 401 " pdb=" N3B ANP D 401 " pdb=" PG ANP D 401 " ideal model delta sigma weight residual 126.95 111.05 15.90 3.00e+00 1.11e-01 2.81e+01 angle pdb=" C PRO F 61 " pdb=" N THR F 62 " pdb=" CA THR F 62 " ideal model delta sigma weight residual 121.54 130.43 -8.89 1.91e+00 2.74e-01 2.17e+01 angle pdb=" C LEU E 158 " pdb=" N LYS E 159 " pdb=" CA LYS E 159 " ideal model delta sigma weight residual 121.54 129.23 -7.69 1.91e+00 2.74e-01 1.62e+01 angle pdb=" C ILE E 302 " pdb=" N ALA E 303 " pdb=" CA ALA E 303 " ideal model delta sigma weight residual 120.38 125.74 -5.36 1.37e+00 5.33e-01 1.53e+01 ... (remaining 13177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.75: 5515 21.75 - 43.49: 347 43.49 - 65.24: 32 65.24 - 86.98: 22 86.98 - 108.73: 3 Dihedral angle restraints: 5919 sinusoidal: 2389 harmonic: 3530 Sorted by residual: dihedral pdb=" O1B ANP F 401 " pdb=" N3B ANP F 401 " pdb=" PB ANP F 401 " pdb=" PG ANP F 401 " ideal model delta sinusoidal sigma weight residual 35.15 -73.58 108.73 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" O1A ANP D 401 " pdb=" O3A ANP D 401 " pdb=" PA ANP D 401 " pdb=" PB ANP D 401 " ideal model delta sinusoidal sigma weight residual 83.11 -168.48 -108.41 1 3.00e+01 1.11e-03 1.40e+01 dihedral pdb=" CA GLY D 47 " pdb=" C GLY D 47 " pdb=" N LYS D 48 " pdb=" CA LYS D 48 " ideal model delta harmonic sigma weight residual 180.00 -162.75 -17.25 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 5916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1216 0.055 - 0.110: 268 0.110 - 0.165: 45 0.165 - 0.220: 5 0.220 - 0.275: 2 Chirality restraints: 1536 Sorted by residual: chirality pdb=" C3' ANP F 401 " pdb=" C2' ANP F 401 " pdb=" C4' ANP F 401 " pdb=" O3' ANP F 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C3' ANP D 401 " pdb=" C2' ANP D 401 " pdb=" C4' ANP D 401 " pdb=" O3' ANP D 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA THR F 62 " pdb=" N THR F 62 " pdb=" C THR F 62 " pdb=" CB THR F 62 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.40e-01 ... (remaining 1533 not shown) Planarity restraints: 1682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 382 " 0.032 5.00e-02 4.00e+02 4.79e-02 3.68e+00 pdb=" N PRO C 383 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 383 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 383 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 397 " -0.031 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO E 398 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO E 398 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 398 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 206 " -0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO E 207 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO E 207 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 207 " -0.025 5.00e-02 4.00e+02 ... (remaining 1679 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 479 2.73 - 3.27: 8393 3.27 - 3.82: 14732 3.82 - 4.36: 17194 4.36 - 4.90: 28352 Nonbonded interactions: 69150 Sorted by model distance: nonbonded pdb=" O1G ANP D 401 " pdb="MG MG D 402 " model vdw 2.191 2.170 nonbonded pdb=" OD1 ASP F 170 " pdb="MG MG F 402 " model vdw 2.205 2.170 nonbonded pdb=" NE2 GLN D 94 " pdb="MG MG D 402 " model vdw 2.258 2.250 nonbonded pdb=" O ILE C 96 " pdb=" OG1 THR C 220 " model vdw 2.326 2.440 nonbonded pdb=" OE2 GLU D 36 " pdb=" OG SER D 213 " model vdw 2.327 2.440 ... (remaining 69145 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 3 and (name CA or name C or name O or name CB or name CG \ or name CD or name CE or name NZ )) or resid 4 through 228 or resid 401 through \ 402)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.010 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.580 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5542 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 : 0.004 0.145 9728 Z= 0.299 Angle : 0.850 16.989 13182 Z= 0.404 Chirality : 0.049 0.275 1536 Planarity : 0.005 0.048 1682 Dihedral : 14.620 108.725 3647 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.10 % Allowed : 9.70 % Favored : 90.21 % 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: -5.58 (0.16), residues: 1229 helix: -5.05 (0.08), residues: 333 sheet: -2.38 (0.44), residues: 119 loop : -3.49 (0.16), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 249 HIS 0.002 0.001 HIS E 376 PHE 0.011 0.001 PHE F 199 TYR 0.015 0.001 TYR E 248 ARG 0.002 0.000 ARG D 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 303 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 LEU cc_start: 0.8346 (tp) cc_final: 0.7529 (tp) REVERT: C 184 PHE cc_start: 0.7113 (m-80) cc_final: 0.6834 (m-80) REVERT: C 315 MET cc_start: 0.7886 (ppp) cc_final: 0.7584 (tmm) REVERT: E 237 LEU cc_start: 0.5024 (tt) cc_final: 0.3412 (mm) REVERT: E 285 PHE cc_start: 0.3833 (m-80) cc_final: 0.2992 (m-80) REVERT: D 37 MET cc_start: 0.6105 (mpp) cc_final: 0.5823 (mpp) REVERT: F 24 VAL cc_start: 0.7397 (m) cc_final: 0.7066 (p) REVERT: F 25 LEU cc_start: 0.6648 (tp) cc_final: 0.6359 (tt) REVERT: F 99 LEU cc_start: 0.6611 (mp) cc_final: 0.5718 (mt) outliers start: 1 outliers final: 0 residues processed: 303 average time/residue: 0.2351 time to fit residues: 94.6380 Evaluate side-chains 212 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 10.0000 chunk 92 optimal weight: 20.0000 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 0.0370 chunk 62 optimal weight: 0.0030 chunk 49 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 37 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.9472 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN E 86 GLN E 109 ASN E 146 GLN ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 GLN ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 ASN F 204 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5889 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9728 Z= 0.184 Angle : 0.574 8.412 13182 Z= 0.279 Chirality : 0.042 0.132 1536 Planarity : 0.004 0.051 1682 Dihedral : 8.377 93.452 1391 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.20 % Allowed : 5.48 % Favored : 94.32 % 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: -4.75 (0.18), residues: 1229 helix: -3.93 (0.16), residues: 372 sheet: -1.45 (0.48), residues: 118 loop : -3.16 (0.17), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 165 HIS 0.005 0.001 HIS F 96 PHE 0.012 0.001 PHE E 329 TYR 0.014 0.001 TYR C 128 ARG 0.006 0.001 ARG D 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 252 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 TRP cc_start: 0.5286 (m-90) cc_final: 0.5026 (m-90) REVERT: C 88 ASP cc_start: 0.4064 (p0) cc_final: 0.3728 (p0) REVERT: C 164 VAL cc_start: 0.8831 (t) cc_final: 0.8536 (t) REVERT: C 184 PHE cc_start: 0.7211 (m-80) cc_final: 0.6700 (m-80) REVERT: C 253 LYS cc_start: 0.6598 (mmmt) cc_final: 0.6200 (tppt) REVERT: C 291 MET cc_start: 0.6389 (ptp) cc_final: 0.6062 (ptp) REVERT: D 23 ASP cc_start: 0.5663 (m-30) cc_final: 0.5342 (m-30) REVERT: D 103 THR cc_start: 0.7182 (m) cc_final: 0.6673 (m) REVERT: D 195 GLN cc_start: 0.6088 (pm20) cc_final: 0.5757 (pm20) REVERT: F 38 MET cc_start: 0.7331 (ptp) cc_final: 0.7025 (ptp) REVERT: F 81 LYS cc_start: 0.8594 (pttt) cc_final: 0.8344 (pttt) REVERT: F 186 GLN cc_start: 0.8045 (mm110) cc_final: 0.7843 (mm110) outliers start: 2 outliers final: 1 residues processed: 254 average time/residue: 0.2317 time to fit residues: 79.4551 Evaluate side-chains 205 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 204 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 chunk 92 optimal weight: 0.0020 chunk 75 optimal weight: 0.0870 chunk 30 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 119 optimal weight: 0.2980 chunk 98 optimal weight: 9.9990 chunk 37 optimal weight: 0.1980 chunk 89 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 overall best weight: 0.3166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 ASN E 198 GLN ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 ASN F 97 HIS F 107 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5881 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9728 Z= 0.150 Angle : 0.538 6.731 13182 Z= 0.259 Chirality : 0.040 0.145 1536 Planarity : 0.003 0.032 1682 Dihedral : 7.944 90.928 1391 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % 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: -4.09 (0.20), residues: 1229 helix: -3.05 (0.22), residues: 366 sheet: -1.29 (0.47), residues: 118 loop : -2.90 (0.18), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 377 HIS 0.005 0.001 HIS F 204 PHE 0.024 0.001 PHE C 257 TYR 0.009 0.001 TYR C 199 ARG 0.008 0.000 ARG C 261 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 TRP cc_start: 0.5477 (m-90) cc_final: 0.5083 (m-90) REVERT: C 29 LEU cc_start: 0.8351 (tp) cc_final: 0.7066 (tp) REVERT: C 88 ASP cc_start: 0.4110 (p0) cc_final: 0.3839 (p0) REVERT: C 184 PHE cc_start: 0.7310 (m-80) cc_final: 0.6844 (m-80) REVERT: C 201 MET cc_start: 0.5825 (tpt) cc_final: 0.3733 (ptp) REVERT: C 253 LYS cc_start: 0.6506 (mmmt) cc_final: 0.5939 (pttm) REVERT: E 285 PHE cc_start: 0.4190 (m-80) cc_final: 0.2867 (m-80) REVERT: D 23 ASP cc_start: 0.5709 (m-30) cc_final: 0.5461 (m-30) REVERT: D 171 GLU cc_start: 0.7939 (tp30) cc_final: 0.7154 (tp30) REVERT: D 190 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6984 (mt-10) REVERT: D 195 GLN cc_start: 0.5940 (pm20) cc_final: 0.5586 (pm20) REVERT: F 81 LYS cc_start: 0.8461 (pttt) cc_final: 0.8218 (pttt) REVERT: F 99 LEU cc_start: 0.7820 (mp) cc_final: 0.6785 (mt) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.2153 time to fit residues: 70.9295 Evaluate side-chains 202 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 52 optimal weight: 20.0000 chunk 74 optimal weight: 7.9990 chunk 111 optimal weight: 0.8980 chunk 117 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 chunk 105 optimal weight: 0.9990 chunk 31 optimal weight: 0.0570 chunk 98 optimal weight: 1.9990 overall best weight: 0.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 ASN E 212 GLN ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 286 ASN D 53 HIS ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 HIS F 107 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6054 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 9728 Z= 0.151 Angle : 0.543 7.691 13182 Z= 0.259 Chirality : 0.040 0.127 1536 Planarity : 0.003 0.030 1682 Dihedral : 7.879 90.113 1391 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % 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: -3.65 (0.21), residues: 1229 helix: -2.53 (0.24), residues: 372 sheet: -1.16 (0.50), residues: 113 loop : -2.69 (0.19), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 377 HIS 0.005 0.001 HIS F 96 PHE 0.009 0.001 PHE D 30 TYR 0.010 0.001 TYR D 15 ARG 0.004 0.000 ARG D 142 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 TRP cc_start: 0.5521 (m-90) cc_final: 0.5199 (m-90) REVERT: C 29 LEU cc_start: 0.8511 (tp) cc_final: 0.7012 (tp) REVERT: C 88 ASP cc_start: 0.4327 (p0) cc_final: 0.4098 (p0) REVERT: C 164 VAL cc_start: 0.8802 (t) cc_final: 0.8517 (t) REVERT: C 184 PHE cc_start: 0.7330 (m-80) cc_final: 0.6869 (m-80) REVERT: C 201 MET cc_start: 0.6035 (tpt) cc_final: 0.3520 (ptp) REVERT: C 202 LEU cc_start: 0.6201 (pt) cc_final: 0.5385 (pp) REVERT: C 253 LYS cc_start: 0.6863 (mmmt) cc_final: 0.6347 (tppt) REVERT: E 272 MET cc_start: 0.5309 (mmp) cc_final: 0.5080 (mmp) REVERT: E 276 MET cc_start: 0.6063 (mmp) cc_final: 0.5537 (mmp) REVERT: E 285 PHE cc_start: 0.4399 (m-80) cc_final: 0.3031 (m-80) REVERT: D 23 ASP cc_start: 0.5749 (m-30) cc_final: 0.5459 (m-30) REVERT: D 144 SER cc_start: 0.8893 (m) cc_final: 0.8639 (p) REVERT: D 171 GLU cc_start: 0.7892 (tp30) cc_final: 0.7148 (tp30) REVERT: D 190 GLU cc_start: 0.7332 (mt-10) cc_final: 0.7056 (mt-10) REVERT: D 195 GLN cc_start: 0.6133 (pm20) cc_final: 0.5753 (pm20) REVERT: F 81 LYS cc_start: 0.8635 (pttt) cc_final: 0.8369 (pttt) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.2265 time to fit residues: 73.2969 Evaluate side-chains 193 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 87 optimal weight: 0.1980 chunk 48 optimal weight: 20.0000 chunk 100 optimal weight: 0.2980 chunk 81 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 105 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 GLN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 ASN F 215 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6096 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9728 Z= 0.138 Angle : 0.530 6.839 13182 Z= 0.251 Chirality : 0.041 0.153 1536 Planarity : 0.003 0.038 1682 Dihedral : 7.818 90.479 1391 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % 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: -3.35 (0.21), residues: 1229 helix: -2.25 (0.24), residues: 382 sheet: -0.73 (0.53), residues: 108 loop : -2.55 (0.20), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 377 HIS 0.003 0.001 HIS E 376 PHE 0.009 0.001 PHE F 199 TYR 0.009 0.001 TYR C 199 ARG 0.010 0.000 ARG C 261 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 TRP cc_start: 0.5664 (m-90) cc_final: 0.5274 (m-90) REVERT: C 29 LEU cc_start: 0.8487 (tp) cc_final: 0.6863 (tp) REVERT: C 88 ASP cc_start: 0.4365 (p0) cc_final: 0.4136 (p0) REVERT: C 164 VAL cc_start: 0.8829 (t) cc_final: 0.8544 (t) REVERT: C 184 PHE cc_start: 0.7363 (m-80) cc_final: 0.6951 (m-80) REVERT: C 201 MET cc_start: 0.6047 (tpt) cc_final: 0.3820 (ptp) REVERT: C 202 LEU cc_start: 0.6230 (pt) cc_final: 0.5186 (pp) REVERT: C 253 LYS cc_start: 0.6885 (mmmt) cc_final: 0.6425 (tppt) REVERT: E 228 MET cc_start: 0.1900 (ptt) cc_final: 0.1691 (ptp) REVERT: E 285 PHE cc_start: 0.4388 (m-80) cc_final: 0.3056 (m-80) REVERT: E 337 ILE cc_start: 0.8721 (pt) cc_final: 0.8094 (mp) REVERT: D 23 ASP cc_start: 0.5919 (m-30) cc_final: 0.5696 (m-30) REVERT: D 103 THR cc_start: 0.7677 (m) cc_final: 0.6839 (m) REVERT: D 171 GLU cc_start: 0.7833 (tp30) cc_final: 0.7174 (tp30) REVERT: D 190 GLU cc_start: 0.7403 (mt-10) cc_final: 0.7194 (mt-10) REVERT: D 195 GLN cc_start: 0.5860 (pm20) cc_final: 0.5523 (pm20) REVERT: D 220 ASP cc_start: 0.7846 (m-30) cc_final: 0.7616 (m-30) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.2215 time to fit residues: 71.1337 Evaluate side-chains 196 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 118 optimal weight: 0.1980 chunk 97 optimal weight: 6.9990 chunk 54 optimal weight: 0.0970 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 0.0010 chunk 61 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 ASN F 94 GLN F 96 HIS F 107 ASN F 215 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6195 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9728 Z= 0.151 Angle : 0.550 7.168 13182 Z= 0.264 Chirality : 0.041 0.169 1536 Planarity : 0.004 0.072 1682 Dihedral : 7.884 92.046 1391 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % 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: -3.10 (0.22), residues: 1229 helix: -2.03 (0.25), residues: 381 sheet: -0.70 (0.52), residues: 109 loop : -2.39 (0.20), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 321 HIS 0.004 0.001 HIS D 96 PHE 0.026 0.001 PHE F 185 TYR 0.012 0.001 TYR C 199 ARG 0.011 0.000 ARG C 261 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 TRP cc_start: 0.5719 (m-90) cc_final: 0.5419 (m-90) REVERT: C 29 LEU cc_start: 0.8534 (tp) cc_final: 0.6904 (tp) REVERT: C 114 MET cc_start: 0.4834 (ppp) cc_final: 0.4623 (ppp) REVERT: C 164 VAL cc_start: 0.8784 (t) cc_final: 0.8456 (p) REVERT: C 184 PHE cc_start: 0.7604 (m-80) cc_final: 0.6699 (m-80) REVERT: C 253 LYS cc_start: 0.6972 (mmmt) cc_final: 0.6141 (pttm) REVERT: E 228 MET cc_start: 0.1934 (ptt) cc_final: 0.1721 (ptp) REVERT: E 285 PHE cc_start: 0.4514 (m-80) cc_final: 0.3218 (m-80) REVERT: E 337 ILE cc_start: 0.8740 (pt) cc_final: 0.8112 (mp) REVERT: D 23 ASP cc_start: 0.6190 (m-30) cc_final: 0.5927 (m-30) REVERT: D 38 MET cc_start: 0.7265 (ptp) cc_final: 0.6899 (ptm) REVERT: D 103 THR cc_start: 0.7742 (m) cc_final: 0.6438 (m) REVERT: D 171 GLU cc_start: 0.7812 (tp30) cc_final: 0.7292 (tp30) REVERT: D 190 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7210 (mt-10) REVERT: D 195 GLN cc_start: 0.5856 (pm20) cc_final: 0.5615 (pm20) REVERT: F 69 ASN cc_start: 0.6167 (t0) cc_final: 0.5958 (t0) REVERT: F 81 LYS cc_start: 0.8545 (pttt) cc_final: 0.8280 (pttt) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.2248 time to fit residues: 71.3056 Evaluate side-chains 191 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 72 optimal weight: 0.0030 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 265 ASN E 266 GLN ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 ASN ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 180 ASN ** F 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6459 moved from start: 0.5639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9728 Z= 0.211 Angle : 0.641 8.221 13182 Z= 0.308 Chirality : 0.043 0.139 1536 Planarity : 0.004 0.040 1682 Dihedral : 8.292 94.605 1391 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.20 % Allowed : 3.04 % Favored : 96.77 % 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: -3.09 (0.22), residues: 1229 helix: -2.02 (0.24), residues: 399 sheet: -0.61 (0.50), residues: 109 loop : -2.38 (0.21), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 351 HIS 0.005 0.001 HIS F 97 PHE 0.017 0.002 PHE D 102 TYR 0.020 0.001 TYR F 93 ARG 0.009 0.001 ARG D 14 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 236 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 TRP cc_start: 0.5688 (m-90) cc_final: 0.5268 (m-90) REVERT: C 88 ASP cc_start: 0.4052 (p0) cc_final: 0.3556 (p0) REVERT: C 114 MET cc_start: 0.5034 (ppp) cc_final: 0.4675 (ppp) REVERT: C 164 VAL cc_start: 0.8836 (t) cc_final: 0.8612 (p) REVERT: C 184 PHE cc_start: 0.7776 (m-80) cc_final: 0.6925 (m-80) REVERT: C 201 MET cc_start: 0.5462 (tpt) cc_final: 0.3691 (ptp) REVERT: C 253 LYS cc_start: 0.7224 (mmmt) cc_final: 0.6290 (pttm) REVERT: C 289 MET cc_start: 0.8613 (mmp) cc_final: 0.8320 (mmp) REVERT: C 366 ILE cc_start: 0.7850 (tt) cc_final: 0.7301 (mt) REVERT: E 228 MET cc_start: 0.2135 (ptt) cc_final: 0.1483 (ptt) REVERT: E 337 ILE cc_start: 0.8794 (pt) cc_final: 0.8312 (mp) REVERT: D 38 MET cc_start: 0.7513 (ptp) cc_final: 0.7046 (ptp) REVERT: D 103 THR cc_start: 0.7948 (m) cc_final: 0.7557 (m) outliers start: 2 outliers final: 1 residues processed: 238 average time/residue: 0.2076 time to fit residues: 68.8147 Evaluate side-chains 202 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 201 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 23 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 58 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 ASN C 265 ASN ** C 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 ASN E 65 HIS ** E 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 ASN ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 ASN ** F 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.7322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 9728 Z= 0.308 Angle : 0.824 11.253 13182 Z= 0.399 Chirality : 0.048 0.188 1536 Planarity : 0.005 0.080 1682 Dihedral : 9.026 104.961 1391 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % 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: -3.14 (0.22), residues: 1229 helix: -2.30 (0.23), residues: 374 sheet: -0.48 (0.51), residues: 113 loop : -2.32 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP E 377 HIS 0.013 0.002 HIS D 96 PHE 0.037 0.003 PHE E 319 TYR 0.015 0.002 TYR D 15 ARG 0.008 0.001 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 TRP cc_start: 0.5912 (m-90) cc_final: 0.5484 (m-90) REVERT: C 88 ASP cc_start: 0.4954 (p0) cc_final: 0.4480 (p0) REVERT: C 114 MET cc_start: 0.5174 (ppp) cc_final: 0.4602 (ppp) REVERT: C 164 VAL cc_start: 0.8915 (t) cc_final: 0.8620 (p) REVERT: C 184 PHE cc_start: 0.7951 (m-80) cc_final: 0.6979 (m-80) REVERT: C 289 MET cc_start: 0.8717 (mmp) cc_final: 0.8026 (mmp) REVERT: C 292 GLU cc_start: 0.7604 (pt0) cc_final: 0.6840 (pt0) REVERT: C 366 ILE cc_start: 0.7992 (tt) cc_final: 0.7470 (mm) REVERT: E 99 ASN cc_start: 0.7988 (p0) cc_final: 0.7760 (p0) REVERT: E 293 MET cc_start: 0.7596 (tpt) cc_final: 0.7384 (tpt) REVERT: E 298 LYS cc_start: 0.4491 (mmtt) cc_final: 0.3827 (tptt) REVERT: E 337 ILE cc_start: 0.8793 (pt) cc_final: 0.8500 (mp) REVERT: D 38 MET cc_start: 0.7513 (ptp) cc_final: 0.7187 (ptp) REVERT: D 145 GLU cc_start: 0.7069 (pt0) cc_final: 0.5568 (pt0) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.2047 time to fit residues: 67.8715 Evaluate side-chains 205 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 115 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 238 GLN ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 HIS ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.7305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9728 Z= 0.175 Angle : 0.662 12.318 13182 Z= 0.311 Chirality : 0.044 0.150 1536 Planarity : 0.004 0.069 1682 Dihedral : 8.192 102.185 1391 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.22), residues: 1229 helix: -1.86 (0.25), residues: 384 sheet: -0.59 (0.51), residues: 116 loop : -2.24 (0.21), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 321 HIS 0.006 0.001 HIS D 96 PHE 0.018 0.001 PHE E 285 TYR 0.009 0.001 TYR D 15 ARG 0.005 0.001 ARG C 17 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 TRP cc_start: 0.5879 (m-90) cc_final: 0.5465 (m-90) REVERT: C 54 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7294 (mp0) REVERT: C 88 ASP cc_start: 0.4816 (p0) cc_final: 0.4347 (p0) REVERT: C 114 MET cc_start: 0.5446 (ppp) cc_final: 0.4966 (ppp) REVERT: C 164 VAL cc_start: 0.8778 (t) cc_final: 0.8499 (p) REVERT: C 184 PHE cc_start: 0.7819 (m-80) cc_final: 0.6834 (m-80) REVERT: C 201 MET cc_start: 0.5803 (tpt) cc_final: 0.4092 (ptp) REVERT: C 289 MET cc_start: 0.8697 (mmp) cc_final: 0.8254 (mmp) REVERT: C 292 GLU cc_start: 0.7409 (pt0) cc_final: 0.7031 (pt0) REVERT: C 311 MET cc_start: 0.4622 (pmm) cc_final: 0.4116 (mmt) REVERT: C 366 ILE cc_start: 0.7943 (tt) cc_final: 0.7387 (mm) REVERT: E 15 ARG cc_start: 0.7160 (ttm-80) cc_final: 0.6296 (ttm-80) REVERT: E 48 MET cc_start: 0.8821 (tmm) cc_final: 0.8577 (tmm) REVERT: E 298 LYS cc_start: 0.3486 (mmtt) cc_final: 0.2494 (mmtt) REVERT: E 337 ILE cc_start: 0.8726 (pt) cc_final: 0.8370 (mp) REVERT: D 53 HIS cc_start: 0.7874 (m90) cc_final: 0.7506 (m170) REVERT: D 145 GLU cc_start: 0.6839 (pt0) cc_final: 0.6214 (pt0) REVERT: D 205 ASP cc_start: 0.5656 (p0) cc_final: 0.4819 (p0) REVERT: F 166 LEU cc_start: 0.7496 (mp) cc_final: 0.7291 (mp) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.2060 time to fit residues: 71.5813 Evaluate side-chains 210 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 121 optimal weight: 20.0000 chunk 111 optimal weight: 2.9990 chunk 96 optimal weight: 0.0060 chunk 10 optimal weight: 9.9990 chunk 74 optimal weight: 0.0070 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 overall best weight: 1.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 GLN C 281 ASN C 364 GLN E 109 ASN ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 ASN F 94 GLN ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.7676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 9728 Z= 0.224 Angle : 0.692 12.880 13182 Z= 0.328 Chirality : 0.045 0.186 1536 Planarity : 0.004 0.065 1682 Dihedral : 8.223 101.845 1391 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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: -2.72 (0.23), residues: 1229 helix: -1.70 (0.26), residues: 377 sheet: -0.79 (0.49), residues: 111 loop : -2.09 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 321 HIS 0.010 0.001 HIS D 96 PHE 0.025 0.002 PHE E 285 TYR 0.038 0.002 TYR F 93 ARG 0.007 0.001 ARG C 250 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 TRP cc_start: 0.5932 (m-90) cc_final: 0.5514 (m-90) REVERT: C 88 ASP cc_start: 0.4756 (p0) cc_final: 0.4376 (p0) REVERT: C 114 MET cc_start: 0.5381 (ppp) cc_final: 0.4887 (ppp) REVERT: C 164 VAL cc_start: 0.8797 (t) cc_final: 0.8542 (p) REVERT: C 184 PHE cc_start: 0.7905 (m-80) cc_final: 0.6799 (m-80) REVERT: C 201 MET cc_start: 0.5861 (tpt) cc_final: 0.3910 (ptp) REVERT: C 253 LYS cc_start: 0.7846 (tptt) cc_final: 0.6669 (tppt) REVERT: C 289 MET cc_start: 0.8696 (mmp) cc_final: 0.8140 (mmp) REVERT: C 292 GLU cc_start: 0.7461 (pt0) cc_final: 0.7035 (pt0) REVERT: C 311 MET cc_start: 0.4559 (pmm) cc_final: 0.4349 (mmt) REVERT: C 366 ILE cc_start: 0.7982 (tt) cc_final: 0.7397 (mm) REVERT: E 48 MET cc_start: 0.8838 (tmm) cc_final: 0.8580 (tmm) REVERT: E 298 LYS cc_start: 0.3574 (mmtt) cc_final: 0.2601 (mmtt) REVERT: E 337 ILE cc_start: 0.8755 (pt) cc_final: 0.8445 (mp) REVERT: D 103 THR cc_start: 0.8366 (m) cc_final: 0.8163 (m) REVERT: D 145 GLU cc_start: 0.6960 (pt0) cc_final: 0.6579 (pt0) REVERT: D 205 ASP cc_start: 0.5758 (p0) cc_final: 0.5148 (p0) REVERT: F 14 ARG cc_start: 0.8621 (mmp-170) cc_final: 0.8333 (mmp-170) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.1997 time to fit residues: 67.4382 Evaluate side-chains 211 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.0010 chunk 89 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 12 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 chunk 85 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 109 ASN D 53 HIS ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 215 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.200740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.168030 restraints weight = 21979.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.169252 restraints weight = 16042.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.170422 restraints weight = 12667.174| |-----------------------------------------------------------------------------| r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 moved from start: 0.7714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9728 Z= 0.165 Angle : 0.669 13.658 13182 Z= 0.313 Chirality : 0.043 0.156 1536 Planarity : 0.004 0.060 1682 Dihedral : 7.928 101.965 1391 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.23), residues: 1229 helix: -1.62 (0.26), residues: 374 sheet: -0.78 (0.48), residues: 115 loop : -2.10 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 249 HIS 0.012 0.001 HIS D 53 PHE 0.018 0.002 PHE C 257 TYR 0.025 0.001 TYR F 93 ARG 0.010 0.001 ARG C 250 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2337.89 seconds wall clock time: 42 minutes 34.17 seconds (2554.17 seconds total)