Starting phenix.real_space_refine on Wed Feb 14 10:11:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m1h_30047/02_2024/6m1h_30047.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m1h_30047/02_2024/6m1h_30047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m1h_30047/02_2024/6m1h_30047.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m1h_30047/02_2024/6m1h_30047.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m1h_30047/02_2024/6m1h_30047.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m1h_30047/02_2024/6m1h_30047.pdb" } resolution = 3.6 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: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 5745 2.51 5 N 1563 2.21 5 O 1665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 71": "OE1" <-> "OE2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A GLU 262": "OE1" <-> "OE2" Residue "A ARG 350": "NH1" <-> "NH2" Residue "A ARG 379": "NH1" <-> "NH2" Residue "A TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A GLU 410": "OE1" <-> "OE2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "C PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 3": "OE1" <-> "OE2" Residue "F GLU 21": "OE1" <-> "OE2" Residue "F PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 370": "OE1" <-> "OE2" Residue "F ARG 374": "NH1" <-> "NH2" Residue "F GLU 392": "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: 9036 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2765 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 328} Chain breaks: 3 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 476 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "C" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "D" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 2595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2595 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1803 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 209} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.38, per 1000 atoms: 0.60 Number of scatterers: 9036 At special positions: 0 Unit cell: (102.554, 106.918, 153.831, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1665 8.00 N 1563 7.00 C 5745 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 118 " distance=2.03 Simple disulfide: pdb=" SG CYS A 77 " - pdb=" SG CYS A 134 " distance=2.03 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 296 " distance=2.03 Simple disulfide: pdb=" SG CYS B 1 " - pdb=" SG CYS B 5 " distance=2.03 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 51 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 107 " distance=2.02 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: 3.63 Conformation dependent library (CDL) restraints added in 1.9 seconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2142 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 13 sheets defined 37.9% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 28 through 36 Processing helix chain 'A' and resid 78 through 82 Processing helix chain 'A' and resid 129 through 134 removed outlier: 3.722A pdb=" N ALA A 133 " --> pdb=" O HIS A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 178 removed outlier: 3.630A pdb=" N LEU A 151 " --> pdb=" O ASP A 147 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER A 152 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER A 162 " --> pdb=" O THR A 158 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 170 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A 171 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A 175 " --> pdb=" O ALA A 171 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG A 177 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 205 removed outlier: 3.648A pdb=" N HIS A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN A 191 " --> pdb=" O PHE A 187 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N SER A 195 " --> pdb=" O ASN A 191 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 203 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 218 removed outlier: 3.910A pdb=" N HIS A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 253 removed outlier: 4.168A pdb=" N ALA A 228 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL A 238 " --> pdb=" O HIS A 234 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE A 242 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE A 245 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 261 through 268 removed outlier: 3.642A pdb=" N PHE A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TRP A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 290 removed outlier: 3.576A pdb=" N LEU A 278 " --> pdb=" O TRP A 274 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TRP A 284 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR A 290 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 336 removed outlier: 3.716A pdb=" N ILE A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Proline residue: A 312 - end of helix removed outlier: 3.510A pdb=" N PHE A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL A 322 " --> pdb=" O MET A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 363 Proline residue: A 360 - end of helix Processing helix chain 'A' and resid 366 through 372 Processing helix chain 'A' and resid 381 through 391 removed outlier: 4.187A pdb=" N LEU A 388 " --> pdb=" O PHE A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 397 removed outlier: 3.527A pdb=" N ALA A 397 " --> pdb=" O GLY A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 416 removed outlier: 4.363A pdb=" N ARG A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 31 removed outlier: 3.521A pdb=" N ASP B 13 " --> pdb=" O LYS B 9 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N HIS B 20 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 28 " --> pdb=" O LEU B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 42 Processing helix chain 'B' and resid 44 through 56 removed outlier: 3.608A pdb=" N LYS B 49 " --> pdb=" O ASN B 45 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET B 52 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLN B 54 " --> pdb=" O GLU B 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 61 through 65 Processing helix chain 'D' and resid 7 through 13 removed outlier: 4.094A pdb=" N GLN D 11 " --> pdb=" O ALA D 7 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA D 12 " --> pdb=" O SER D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 24 removed outlier: 4.081A pdb=" N LEU D 19 " --> pdb=" O LEU D 15 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU D 22 " --> pdb=" O GLN D 18 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 4.024A pdb=" N LEU D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU D 42 " --> pdb=" O MET D 38 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 23 removed outlier: 4.096A pdb=" N ALA E 21 " --> pdb=" O GLN E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 26 No H-bonds generated for 'chain 'E' and resid 24 through 26' Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.741A pdb=" N ILE E 33 " --> pdb=" O THR E 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 14 Processing helix chain 'F' and resid 15 through 37 removed outlier: 3.959A pdb=" N ARG F 20 " --> pdb=" O GLU F 16 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU F 21 " --> pdb=" O LYS F 17 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS F 25 " --> pdb=" O GLU F 21 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LYS F 32 " --> pdb=" O LYS F 28 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP F 33 " --> pdb=" O GLN F 29 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN F 35 " --> pdb=" O GLN F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 278 removed outlier: 3.886A pdb=" N LYS F 271 " --> pdb=" O GLN F 267 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU F 272 " --> pdb=" O ALA F 268 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE F 276 " --> pdb=" O LEU F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 312 Processing helix chain 'F' and resid 313 through 318 removed outlier: 3.554A pdb=" N ALA F 316 " --> pdb=" O PRO F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 350 removed outlier: 3.613A pdb=" N LYS F 338 " --> pdb=" O VAL F 334 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE F 341 " --> pdb=" O ALA F 337 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG F 342 " --> pdb=" O LYS F 338 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP F 343 " --> pdb=" O TYR F 339 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU F 346 " --> pdb=" O ARG F 342 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE F 348 " --> pdb=" O GLU F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 391 removed outlier: 4.520A pdb=" N ASP F 378 " --> pdb=" O ARG F 374 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG F 380 " --> pdb=" O PHE F 376 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE F 382 " --> pdb=" O ASP F 378 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N HIS F 387 " --> pdb=" O ILE F 383 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 58 Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 76 removed outlier: 3.723A pdb=" N GLU A 71 " --> pdb=" O CYS A 118 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N CYS A 118 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 73 " --> pdb=" O ARG A 116 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 3 through 4 removed outlier: 3.650A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.606A pdb=" N GLY C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 37 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N MET C 34 " --> pdb=" O ASP C 50 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ASP C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 17 through 21 removed outlier: 3.696A pdb=" N ASP C 73 " --> pdb=" O THR C 78 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 46 through 51 removed outlier: 6.966A pdb=" N ILE E 338 " --> pdb=" O ARG E 48 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR E 50 " --> pdb=" O LEU E 336 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU E 336 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N CYS E 317 " --> pdb=" O GLY E 330 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 58 through 63 removed outlier: 3.562A pdb=" N ALA E 60 " --> pdb=" O ALA E 73 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER E 74 " --> pdb=" O LYS E 78 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS E 78 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU E 79 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA E 92 " --> pdb=" O LEU E 79 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE E 81 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 100 through 105 removed outlier: 6.370A pdb=" N CYS E 121 " --> pdb=" O GLU E 138 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLU E 138 " --> pdb=" O CYS E 121 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE E 123 " --> pdb=" O SER E 136 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG E 134 " --> pdb=" O ASN E 125 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 149 through 151 removed outlier: 3.935A pdb=" N ILE E 157 " --> pdb=" O TRP E 169 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA E 167 " --> pdb=" O THR E 159 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN E 175 " --> pdb=" O ASP E 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 187 through 192 removed outlier: 3.528A pdb=" N SER E 189 " --> pdb=" O GLY E 202 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL E 200 " --> pdb=" O SER E 191 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER E 201 " --> pdb=" O LYS E 209 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS E 209 " --> pdb=" O SER E 201 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER E 207 " --> pdb=" O ALA E 203 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 229 through 234 removed outlier: 6.845A pdb=" N GLY E 244 " --> pdb=" O ASN E 230 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ILE E 232 " --> pdb=" O ALA E 242 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ALA E 242 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N PHE E 234 " --> pdb=" O ALA E 240 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ALA E 240 " --> pdb=" O PHE E 234 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE E 241 " --> pdb=" O PHE E 253 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET E 262 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ASP E 254 " --> pdb=" O GLU E 260 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLU E 260 " --> pdb=" O ASP E 254 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 273 through 278 removed outlier: 4.194A pdb=" N SER E 275 " --> pdb=" O GLY E 288 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ASP E 298 " --> pdb=" O ARG E 304 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ARG E 304 " --> pdb=" O ASP E 298 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 210 through 214 removed outlier: 3.628A pdb=" N PHE F 212 " --> pdb=" O PHE F 219 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU F 45 " --> pdb=" O PHE F 222 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ARG F 42 " --> pdb=" O ALA F 243 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ILE F 245 " --> pdb=" O ARG F 42 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU F 44 " --> pdb=" O ILE F 245 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL F 247 " --> pdb=" O LEU F 44 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU F 46 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ILE F 244 " --> pdb=" O ILE F 288 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N PHE F 290 " --> pdb=" O ILE F 244 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N PHE F 246 " --> pdb=" O PHE F 290 " (cutoff:3.500A) 317 hydrogen bonds defined for protein. 882 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: 2.58 Time building geometry restraints manager: 3.93 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: 2920 1.34 - 1.46: 2132 1.46 - 1.58: 4097 1.58 - 1.70: 0 1.70 - 1.82: 86 Bond restraints: 9235 Sorted by residual: bond pdb=" N VAL A 368 " pdb=" CA VAL A 368 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 8.04e+00 bond pdb=" N THR A 367 " pdb=" CA THR A 367 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.21e-02 6.83e+03 6.87e+00 bond pdb=" N THR A 355 " pdb=" CA THR A 355 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.21e-02 6.83e+03 6.85e+00 bond pdb=" N PHE A 371 " pdb=" CA PHE A 371 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.32e-02 5.74e+03 5.97e+00 bond pdb=" N LEU A 35 " pdb=" CA LEU A 35 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.86e+00 ... (remaining 9230 not shown) Histogram of bond angle deviations from ideal: 99.43 - 106.39: 197 106.39 - 113.36: 4960 113.36 - 120.33: 3673 120.33 - 127.29: 3573 127.29 - 134.26: 100 Bond angle restraints: 12503 Sorted by residual: angle pdb=" N ILE F 372 " pdb=" CA ILE F 372 " pdb=" C ILE F 372 " ideal model delta sigma weight residual 111.62 105.62 6.00 7.90e-01 1.60e+00 5.76e+01 angle pdb=" N ILE F 56 " pdb=" CA ILE F 56 " pdb=" C ILE F 56 " ideal model delta sigma weight residual 111.77 105.90 5.87 1.04e+00 9.25e-01 3.18e+01 angle pdb=" N VAL F 57 " pdb=" CA VAL F 57 " pdb=" C VAL F 57 " ideal model delta sigma weight residual 111.91 107.45 4.46 8.90e-01 1.26e+00 2.51e+01 angle pdb=" C ASP E 195 " pdb=" N THR E 196 " pdb=" CA THR E 196 " ideal model delta sigma weight residual 121.54 129.78 -8.24 1.91e+00 2.74e-01 1.86e+01 angle pdb=" N LYS B 56 " pdb=" CA LYS B 56 " pdb=" C LYS B 56 " ideal model delta sigma weight residual 113.28 108.06 5.22 1.22e+00 6.72e-01 1.83e+01 ... (remaining 12498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 4789 17.33 - 34.67: 551 34.67 - 52.00: 108 52.00 - 69.34: 17 69.34 - 86.67: 10 Dihedral angle restraints: 5475 sinusoidal: 2166 harmonic: 3309 Sorted by residual: dihedral pdb=" CA ARG A 177 " pdb=" C ARG A 177 " pdb=" N PHE A 178 " pdb=" CA PHE A 178 " ideal model delta harmonic sigma weight residual -180.00 -137.40 -42.60 0 5.00e+00 4.00e-02 7.26e+01 dihedral pdb=" CB CYS A 226 " pdb=" SG CYS A 226 " pdb=" SG CYS A 296 " pdb=" CB CYS A 296 " ideal model delta sinusoidal sigma weight residual 93.00 19.71 73.29 1 1.00e+01 1.00e-02 6.84e+01 dihedral pdb=" CA ASP E 312 " pdb=" C ASP E 312 " pdb=" N ASN E 313 " pdb=" CA ASN E 313 " ideal model delta harmonic sigma weight residual 180.00 151.88 28.12 0 5.00e+00 4.00e-02 3.16e+01 ... (remaining 5472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 995 0.059 - 0.118: 307 0.118 - 0.177: 67 0.177 - 0.236: 10 0.236 - 0.295: 1 Chirality restraints: 1380 Sorted by residual: chirality pdb=" CB ILE C 70 " pdb=" CA ILE C 70 " pdb=" CG1 ILE C 70 " pdb=" CG2 ILE C 70 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CB THR C 91 " pdb=" CA THR C 91 " pdb=" OG1 THR C 91 " pdb=" CG2 THR C 91 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB ILE E 232 " pdb=" CA ILE E 232 " pdb=" CG1 ILE E 232 " pdb=" CG2 ILE E 232 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 1377 not shown) Planarity restraints: 1597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 276 " 0.050 5.00e-02 4.00e+02 7.47e-02 8.93e+00 pdb=" N PRO A 277 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 277 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 277 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 235 " 0.047 5.00e-02 4.00e+02 7.06e-02 7.98e+00 pdb=" N PRO E 236 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO E 236 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 236 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 101 " -0.042 5.00e-02 4.00e+02 6.35e-02 6.46e+00 pdb=" N PRO C 102 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO C 102 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 102 " -0.035 5.00e-02 4.00e+02 ... (remaining 1594 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 43 2.41 - 3.03: 4970 3.03 - 3.65: 13930 3.65 - 4.28: 20265 4.28 - 4.90: 32966 Nonbonded interactions: 72174 Sorted by model distance: nonbonded pdb=" CD2 PHE A 369 " pdb=" CG GLU A 385 " model vdw 1.782 3.740 nonbonded pdb=" CE2 PHE A 369 " pdb=" CG GLU A 385 " model vdw 1.855 3.740 nonbonded pdb=" CE2 PHE A 369 " pdb=" CB GLU A 385 " model vdw 2.060 3.740 nonbonded pdb=" CA GLN A 31 " pdb=" SG CYS A 34 " model vdw 2.171 3.830 nonbonded pdb=" OG SER E 331 " pdb=" OD1 ASP E 333 " model vdw 2.227 2.440 ... (remaining 72169 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.810 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 28.040 Find NCS groups from input model: 0.270 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 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 : 0.007 0.063 9235 Z= 0.471 Angle : 0.957 13.242 12503 Z= 0.556 Chirality : 0.059 0.295 1380 Planarity : 0.007 0.075 1597 Dihedral : 15.336 86.669 3312 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.21 % Allowed : 12.45 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.70 (0.21), residues: 1115 helix: -3.94 (0.16), residues: 387 sheet: -2.34 (0.32), residues: 223 loop : -2.66 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 306 HIS 0.012 0.002 HIS A 218 PHE 0.025 0.003 PHE F 363 TYR 0.034 0.002 TYR E 59 ARG 0.007 0.001 ARG E 22 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 234 time to evaluate : 1.100 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: A 123 TRP cc_start: 0.5849 (m100) cc_final: 0.5121 (m100) REVERT: A 232 PHE cc_start: 0.8849 (t80) cc_final: 0.8546 (t80) REVERT: B 16 LYS cc_start: 0.9072 (mttm) cc_final: 0.8800 (mtpp) REVERT: B 37 MET cc_start: 0.6953 (tpp) cc_final: 0.6285 (tpt) REVERT: B 55 LYS cc_start: 0.9301 (mmmt) cc_final: 0.9098 (mmmt) REVERT: C 73 ASP cc_start: 0.6762 (t0) cc_final: 0.5173 (t0) REVERT: C 90 ASP cc_start: 0.8441 (m-30) cc_final: 0.8083 (m-30) REVERT: E 58 ILE cc_start: 0.9319 (mt) cc_final: 0.8672 (tt) REVERT: E 118 ASP cc_start: 0.8535 (p0) cc_final: 0.8001 (p0) REVERT: E 120 ILE cc_start: 0.8987 (mt) cc_final: 0.8697 (mm) REVERT: E 297 TRP cc_start: 0.8316 (m100) cc_final: 0.7172 (m100) REVERT: F 35 GLN cc_start: 0.7602 (pp30) cc_final: 0.7373 (pp30) REVERT: F 222 PHE cc_start: 0.7446 (m-80) cc_final: 0.7119 (m-10) outliers start: 2 outliers final: 1 residues processed: 236 average time/residue: 0.2615 time to fit residues: 81.0019 Evaluate side-chains 179 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 178 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 33 optimal weight: 0.3980 chunk 52 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 404 ASN C 123 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 GLN E 266 HIS E 340 ASN ** F 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 HIS F 220 HIS F 279 ASN F 377 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9235 Z= 0.217 Angle : 0.606 6.860 12503 Z= 0.330 Chirality : 0.043 0.157 1380 Planarity : 0.005 0.053 1597 Dihedral : 5.905 35.056 1237 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.09 % Allowed : 16.67 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.22), residues: 1115 helix: -2.58 (0.21), residues: 398 sheet: -1.91 (0.31), residues: 233 loop : -2.38 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 306 HIS 0.009 0.001 HIS A 218 PHE 0.014 0.001 PHE F 376 TYR 0.023 0.001 TYR A 157 ARG 0.008 0.000 ARG F 347 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 209 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 TRP cc_start: 0.5505 (m100) cc_final: 0.4702 (m100) REVERT: A 230 MET cc_start: 0.7944 (tpt) cc_final: 0.7734 (mmm) REVERT: A 310 LYS cc_start: 0.8462 (ptpt) cc_final: 0.8194 (ptpt) REVERT: B 15 GLN cc_start: 0.8672 (mt0) cc_final: 0.8458 (mt0) REVERT: B 16 LYS cc_start: 0.9162 (mttm) cc_final: 0.8934 (mtpp) REVERT: B 47 VAL cc_start: 0.9077 (t) cc_final: 0.8673 (p) REVERT: B 48 PHE cc_start: 0.8886 (t80) cc_final: 0.8686 (t80) REVERT: C 18 LEU cc_start: 0.8285 (tp) cc_final: 0.7706 (tp) REVERT: C 39 GLN cc_start: 0.7679 (tt0) cc_final: 0.7261 (tp40) REVERT: C 53 GLN cc_start: 0.7111 (OUTLIER) cc_final: 0.5936 (mp10) REVERT: C 73 ASP cc_start: 0.7221 (t0) cc_final: 0.6689 (t0) REVERT: C 80 TYR cc_start: 0.7511 (m-80) cc_final: 0.6843 (m-80) REVERT: C 83 MET cc_start: 0.7450 (mpp) cc_final: 0.6967 (mpp) REVERT: C 95 TYR cc_start: 0.7833 (m-80) cc_final: 0.7608 (m-10) REVERT: D 18 GLN cc_start: 0.7236 (mp10) cc_final: 0.6816 (mp10) REVERT: D 32 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.9033 (ptpp) REVERT: E 118 ASP cc_start: 0.8474 (p0) cc_final: 0.8113 (p0) REVERT: E 169 TRP cc_start: 0.8416 (m100) cc_final: 0.8199 (m-10) REVERT: F 360 TYR cc_start: 0.8161 (m-80) cc_final: 0.7949 (m-80) outliers start: 30 outliers final: 17 residues processed: 223 average time/residue: 0.2197 time to fit residues: 67.2329 Evaluate side-chains 189 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 170 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 312 ASP Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 236 GLN Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 341 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 109 optimal weight: 0.1980 chunk 89 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 HIS C 31 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 HIS E 340 ASN ** F 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9235 Z= 0.209 Angle : 0.598 11.281 12503 Z= 0.319 Chirality : 0.043 0.141 1380 Planarity : 0.004 0.043 1597 Dihedral : 5.396 32.370 1237 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.01 % Allowed : 19.65 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.23), residues: 1115 helix: -1.73 (0.23), residues: 392 sheet: -1.68 (0.31), residues: 232 loop : -2.04 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 243 HIS 0.008 0.001 HIS B 20 PHE 0.012 0.001 PHE A 260 TYR 0.021 0.001 TYR A 157 ARG 0.005 0.000 ARG F 347 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 194 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 TRP cc_start: 0.5514 (m100) cc_final: 0.4708 (m100) REVERT: A 230 MET cc_start: 0.8014 (tpt) cc_final: 0.7813 (mmm) REVERT: A 306 TRP cc_start: 0.7792 (OUTLIER) cc_final: 0.6846 (t60) REVERT: C 18 LEU cc_start: 0.8293 (tp) cc_final: 0.7587 (tp) REVERT: C 34 MET cc_start: 0.7896 (mmm) cc_final: 0.7625 (mmm) REVERT: C 39 GLN cc_start: 0.7499 (tt0) cc_final: 0.7274 (tp40) REVERT: C 80 TYR cc_start: 0.7345 (m-80) cc_final: 0.7139 (m-80) REVERT: C 83 MET cc_start: 0.7485 (mpp) cc_final: 0.6969 (mpp) REVERT: E 118 ASP cc_start: 0.8444 (p0) cc_final: 0.8131 (p0) REVERT: F 208 PHE cc_start: 0.7046 (m-80) cc_final: 0.6832 (m-80) REVERT: F 235 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8734 (tt) outliers start: 39 outliers final: 24 residues processed: 218 average time/residue: 0.2017 time to fit residues: 61.0340 Evaluate side-chains 198 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 172 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 312 ASP Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 236 GLN Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 341 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 chunk 89 optimal weight: 0.0870 chunk 60 optimal weight: 10.0000 overall best weight: 1.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN B 20 HIS E 142 HIS ** E 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 ASN F 12 GLN ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9235 Z= 0.222 Angle : 0.600 10.564 12503 Z= 0.318 Chirality : 0.043 0.172 1380 Planarity : 0.004 0.038 1597 Dihedral : 5.225 31.741 1237 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.42 % Allowed : 20.68 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.24), residues: 1115 helix: -1.37 (0.24), residues: 398 sheet: -1.45 (0.32), residues: 232 loop : -1.91 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 243 HIS 0.008 0.001 HIS B 20 PHE 0.017 0.001 PHE F 363 TYR 0.019 0.001 TYR C 115 ARG 0.004 0.000 ARG F 342 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 196 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 TRP cc_start: 0.5594 (m100) cc_final: 0.4808 (m100) REVERT: A 230 MET cc_start: 0.7915 (tpt) cc_final: 0.7713 (mmm) REVERT: A 232 PHE cc_start: 0.8854 (t80) cc_final: 0.8653 (t80) REVERT: A 306 TRP cc_start: 0.7677 (OUTLIER) cc_final: 0.6632 (t60) REVERT: B 15 GLN cc_start: 0.8679 (mm110) cc_final: 0.8175 (mp10) REVERT: C 53 GLN cc_start: 0.6938 (OUTLIER) cc_final: 0.5916 (mp10) REVERT: C 83 MET cc_start: 0.7495 (mpp) cc_final: 0.7099 (mpp) REVERT: E 118 ASP cc_start: 0.8492 (p0) cc_final: 0.8243 (p0) REVERT: F 235 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8770 (tt) REVERT: F 272 LEU cc_start: 0.9353 (tp) cc_final: 0.9116 (tt) REVERT: F 360 TYR cc_start: 0.8082 (m-80) cc_final: 0.7705 (m-80) outliers start: 43 outliers final: 29 residues processed: 223 average time/residue: 0.2115 time to fit residues: 64.9946 Evaluate side-chains 208 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 176 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 312 ASP Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 236 GLN Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 341 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 27 optimal weight: 0.0870 chunk 36 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN B 20 HIS E 225 HIS ** E 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 236 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9235 Z= 0.150 Angle : 0.563 11.153 12503 Z= 0.294 Chirality : 0.041 0.169 1380 Planarity : 0.003 0.040 1597 Dihedral : 4.729 27.961 1237 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.60 % Allowed : 22.33 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.25), residues: 1115 helix: -1.08 (0.25), residues: 405 sheet: -1.41 (0.33), residues: 226 loop : -1.66 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 243 HIS 0.009 0.001 HIS B 20 PHE 0.014 0.001 PHE C 103 TYR 0.021 0.001 TYR C 115 ARG 0.005 0.000 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 214 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 TRP cc_start: 0.5540 (m100) cc_final: 0.4756 (m100) REVERT: A 232 PHE cc_start: 0.8669 (t80) cc_final: 0.8139 (t80) REVERT: A 267 TYR cc_start: 0.7236 (t80) cc_final: 0.6981 (t80) REVERT: A 297 TRP cc_start: 0.5494 (m-90) cc_final: 0.3053 (m-90) REVERT: A 306 TRP cc_start: 0.7620 (OUTLIER) cc_final: 0.6784 (t60) REVERT: B 15 GLN cc_start: 0.8652 (mm110) cc_final: 0.8014 (mp10) REVERT: C 18 LEU cc_start: 0.8548 (tp) cc_final: 0.7895 (tp) REVERT: C 83 MET cc_start: 0.7555 (mpp) cc_final: 0.7234 (mpp) REVERT: E 138 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7133 (pm20) REVERT: F 208 PHE cc_start: 0.6940 (m-80) cc_final: 0.6676 (m-10) REVERT: F 360 TYR cc_start: 0.7941 (m-80) cc_final: 0.7617 (m-80) outliers start: 35 outliers final: 19 residues processed: 233 average time/residue: 0.2312 time to fit residues: 74.0851 Evaluate side-chains 215 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 194 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain E residue 225 HIS Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 312 ASP Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 341 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 107 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 103 optimal weight: 0.2980 chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 HIS E 225 HIS ** E 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9235 Z= 0.178 Angle : 0.595 11.120 12503 Z= 0.305 Chirality : 0.042 0.165 1380 Planarity : 0.004 0.043 1597 Dihedral : 4.701 27.285 1235 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.01 % Allowed : 22.84 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.00 (0.25), residues: 1115 helix: -0.89 (0.25), residues: 401 sheet: -1.17 (0.33), residues: 232 loop : -1.65 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 243 HIS 0.011 0.001 HIS B 20 PHE 0.021 0.001 PHE E 241 TYR 0.023 0.001 TYR C 115 ARG 0.004 0.000 ARG F 342 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 193 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 TRP cc_start: 0.5666 (m100) cc_final: 0.4898 (m100) REVERT: A 267 TYR cc_start: 0.7318 (t80) cc_final: 0.7087 (t80) REVERT: A 306 TRP cc_start: 0.7669 (OUTLIER) cc_final: 0.6932 (t60) REVERT: B 15 GLN cc_start: 0.8711 (mm110) cc_final: 0.8116 (mp10) REVERT: C 53 GLN cc_start: 0.7037 (OUTLIER) cc_final: 0.6102 (mp10) REVERT: C 83 MET cc_start: 0.7611 (mpp) cc_final: 0.7274 (mpp) REVERT: E 138 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.7008 (pm20) REVERT: F 208 PHE cc_start: 0.6804 (m-80) cc_final: 0.6528 (m-10) REVERT: F 360 TYR cc_start: 0.7851 (m-80) cc_final: 0.7614 (m-80) outliers start: 39 outliers final: 28 residues processed: 210 average time/residue: 0.2203 time to fit residues: 62.8538 Evaluate side-chains 210 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 179 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain B residue 20 HIS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain E residue 225 HIS Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 312 ASP Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 341 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 90 optimal weight: 0.0870 chunk 59 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 63 optimal weight: 0.6980 chunk 32 optimal weight: 0.0570 overall best weight: 1.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 HIS E 225 HIS ** E 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9235 Z= 0.208 Angle : 0.607 12.024 12503 Z= 0.314 Chirality : 0.043 0.181 1380 Planarity : 0.004 0.041 1597 Dihedral : 4.795 27.704 1235 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.22 % Allowed : 24.07 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.92 (0.25), residues: 1115 helix: -0.77 (0.25), residues: 399 sheet: -1.12 (0.34), residues: 230 loop : -1.67 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 243 HIS 0.018 0.001 HIS B 20 PHE 0.016 0.001 PHE E 253 TYR 0.025 0.001 TYR C 80 ARG 0.007 0.000 ARG E 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 186 time to evaluate : 1.133 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: A 123 TRP cc_start: 0.5706 (m100) cc_final: 0.4945 (m100) REVERT: A 267 TYR cc_start: 0.7362 (t80) cc_final: 0.7105 (t80) REVERT: A 306 TRP cc_start: 0.7713 (OUTLIER) cc_final: 0.7061 (t60) REVERT: C 53 GLN cc_start: 0.7107 (OUTLIER) cc_final: 0.6141 (mp10) REVERT: C 83 MET cc_start: 0.7697 (mpp) cc_final: 0.7309 (mpp) REVERT: E 138 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7143 (pm20) REVERT: F 208 PHE cc_start: 0.6867 (m-80) cc_final: 0.6560 (m-10) outliers start: 41 outliers final: 30 residues processed: 210 average time/residue: 0.2206 time to fit residues: 63.2179 Evaluate side-chains 209 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 176 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 225 HIS Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 312 ASP Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 325 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 HIS E 225 HIS ** E 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9235 Z= 0.196 Angle : 0.596 12.445 12503 Z= 0.311 Chirality : 0.043 0.199 1380 Planarity : 0.004 0.041 1597 Dihedral : 4.763 26.782 1235 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.22 % Allowed : 23.97 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.81 (0.25), residues: 1115 helix: -0.62 (0.25), residues: 393 sheet: -1.06 (0.34), residues: 235 loop : -1.65 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 243 HIS 0.012 0.001 HIS B 20 PHE 0.017 0.001 PHE F 222 TYR 0.025 0.001 TYR C 115 ARG 0.006 0.000 ARG C 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 189 time to evaluate : 1.182 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: A 123 TRP cc_start: 0.5688 (m100) cc_final: 0.4958 (m100) REVERT: A 267 TYR cc_start: 0.7370 (t80) cc_final: 0.7115 (t80) REVERT: A 306 TRP cc_start: 0.7620 (OUTLIER) cc_final: 0.7028 (t60) REVERT: B 46 SER cc_start: 0.8987 (m) cc_final: 0.8586 (p) REVERT: C 34 MET cc_start: 0.7745 (mmm) cc_final: 0.7466 (mmm) REVERT: C 53 GLN cc_start: 0.7124 (OUTLIER) cc_final: 0.6163 (mp10) REVERT: C 83 MET cc_start: 0.7626 (mpp) cc_final: 0.7271 (mpp) REVERT: E 138 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7122 (pm20) REVERT: F 208 PHE cc_start: 0.6944 (m-80) cc_final: 0.6588 (m-10) outliers start: 41 outliers final: 34 residues processed: 212 average time/residue: 0.2147 time to fit residues: 62.3159 Evaluate side-chains 214 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 177 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain B residue 20 HIS Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 225 HIS Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 312 ASP Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 325 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 94 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 HIS ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 HIS ** E 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 HIS ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 9235 Z= 0.392 Angle : 0.723 12.877 12503 Z= 0.381 Chirality : 0.047 0.163 1380 Planarity : 0.005 0.072 1597 Dihedral : 5.540 32.660 1235 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 4.22 % Allowed : 24.79 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.24), residues: 1115 helix: -0.89 (0.24), residues: 389 sheet: -1.17 (0.33), residues: 232 loop : -1.89 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 243 HIS 0.006 0.002 HIS A 218 PHE 0.024 0.002 PHE F 222 TYR 0.019 0.002 TYR A 157 ARG 0.008 0.001 ARG E 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 177 time to evaluate : 1.115 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: A 123 TRP cc_start: 0.5685 (m100) cc_final: 0.5054 (m100) REVERT: A 306 TRP cc_start: 0.7870 (OUTLIER) cc_final: 0.6966 (t60) REVERT: B 29 GLN cc_start: 0.9330 (tp-100) cc_final: 0.9119 (tp-100) REVERT: B 49 LYS cc_start: 0.8669 (tttp) cc_final: 0.8457 (ttpp) REVERT: C 53 GLN cc_start: 0.7252 (OUTLIER) cc_final: 0.6198 (mp10) REVERT: C 83 MET cc_start: 0.7601 (mpp) cc_final: 0.7165 (mpp) REVERT: E 226 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7916 (mm-30) REVERT: F 208 PHE cc_start: 0.7190 (m-80) cc_final: 0.6873 (m-10) outliers start: 41 outliers final: 35 residues processed: 206 average time/residue: 0.2378 time to fit residues: 67.0684 Evaluate side-chains 206 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 169 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain B residue 20 HIS Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 225 HIS Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 312 ASP Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 325 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 26 optimal weight: 0.3980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 HIS E 225 HIS ** E 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9235 Z= 0.199 Angle : 0.628 12.463 12503 Z= 0.326 Chirality : 0.044 0.218 1380 Planarity : 0.004 0.041 1597 Dihedral : 5.084 28.159 1235 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.29 % Allowed : 25.51 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.90 (0.24), residues: 1115 helix: -0.65 (0.25), residues: 392 sheet: -1.11 (0.33), residues: 235 loop : -1.75 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 243 HIS 0.022 0.001 HIS B 20 PHE 0.018 0.001 PHE C 103 TYR 0.020 0.001 TYR A 157 ARG 0.006 0.000 ARG C 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 186 time to evaluate : 1.269 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: A 123 TRP cc_start: 0.5536 (m100) cc_final: 0.4952 (m100) REVERT: A 306 TRP cc_start: 0.7798 (OUTLIER) cc_final: 0.7011 (t60) REVERT: B 9 LYS cc_start: 0.8699 (pptt) cc_final: 0.8224 (mmtm) REVERT: B 29 GLN cc_start: 0.9326 (tp-100) cc_final: 0.9110 (tp-100) REVERT: B 49 LYS cc_start: 0.8656 (tttp) cc_final: 0.8455 (ttpp) REVERT: C 32 TYR cc_start: 0.8128 (m-80) cc_final: 0.7885 (m-80) REVERT: C 53 GLN cc_start: 0.7139 (OUTLIER) cc_final: 0.6158 (mp10) REVERT: C 83 MET cc_start: 0.7646 (mpp) cc_final: 0.7269 (mpp) REVERT: E 105 TYR cc_start: 0.7776 (t80) cc_final: 0.7373 (t80) REVERT: F 208 PHE cc_start: 0.6978 (m-80) cc_final: 0.6651 (m-10) outliers start: 32 outliers final: 28 residues processed: 204 average time/residue: 0.2282 time to fit residues: 63.4920 Evaluate side-chains 210 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 180 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain B residue 20 HIS Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 225 HIS Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 312 ASP Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 325 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 36 optimal weight: 0.6980 chunk 90 optimal weight: 0.0270 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 5 optimal weight: 30.0000 chunk 63 optimal weight: 0.1980 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 HIS E 225 HIS ** E 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 HIS ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.116355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.092700 restraints weight = 25049.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.095156 restraints weight = 12988.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.096716 restraints weight = 8813.015| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9235 Z= 0.164 Angle : 0.611 13.421 12503 Z= 0.314 Chirality : 0.042 0.201 1380 Planarity : 0.004 0.040 1597 Dihedral : 4.803 31.784 1235 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.88 % Allowed : 26.65 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.25), residues: 1115 helix: -0.46 (0.26), residues: 399 sheet: -1.03 (0.34), residues: 234 loop : -1.68 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 243 HIS 0.008 0.001 HIS B 20 PHE 0.027 0.001 PHE C 103 TYR 0.025 0.001 TYR C 115 ARG 0.006 0.000 ARG A 350 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2147.70 seconds wall clock time: 39 minutes 52.57 seconds (2392.57 seconds total)