Starting phenix.real_space_refine on Sun Apr 7 09:37:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyw_26196/04_2024/7tyw_26196.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyw_26196/04_2024/7tyw_26196.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyw_26196/04_2024/7tyw_26196.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyw_26196/04_2024/7tyw_26196.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyw_26196/04_2024/7tyw_26196.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyw_26196/04_2024/7tyw_26196.pdb" } resolution = 3.0 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 427 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 6238 2.51 5 N 1683 2.21 5 O 1788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 140": "OE1" <-> "OE2" Residue "R GLU 255": "OE1" <-> "OE2" Residue "R GLU 397": "OE1" <-> "OE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "N GLU 6": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9779 Number of models: 1 Model: "" Number of chains: 10 Chain: "E" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 650 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 103} Chain breaks: 1 Unresolved non-hydrogen bonds: 247 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 3, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 168 Chain: "P" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 239 Unusual residues: {'NH2': 1} Classifications: {'peptide': 32, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 2, 'TRANS': 29} Chain: "R" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2898 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 16, 'TRANS': 353} Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 154 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 118 Chain: "A" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1879 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 2 Chain: "B" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2598 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 413 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "E" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 116 Unusual residues: {'NAG': 2, 'PLM': 1, 'Y01': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.12, per 1000 atoms: 0.63 Number of scatterers: 9779 At special positions: 0 Unit cell: (92.448, 101.864, 160.928, 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 70 16.00 O 1788 8.00 N 1683 7.00 C 6238 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS E 27 " - pdb=" SG CYS E 82 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 104 " distance=2.03 Simple disulfide: pdb=" SG CYS P 1 " - pdb=" SG CYS P 7 " distance=2.04 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.04 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.02 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 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 Links applied NAG-ASN " NAG R 501 " - " ASN R 130 " " NAG R 502 " - " ASN R 73 " Time building additional restraints: 3.96 Conformation dependent library (CDL) restraints added in 1.8 seconds 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2364 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 11 sheets defined 42.8% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'E' and resid 29 through 35 removed outlier: 3.985A pdb=" N GLY E 33 " --> pdb=" O GLU E 29 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU E 35 " --> pdb=" O ASN E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 38 No H-bonds generated for 'chain 'E' and resid 36 through 38' Processing helix chain 'E' and resid 40 through 52 removed outlier: 3.720A pdb=" N GLU E 49 " --> pdb=" O GLN E 45 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY E 52 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 68 removed outlier: 3.904A pdb=" N GLU E 68 " --> pdb=" O ARG E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 80 removed outlier: 4.282A pdb=" N THR E 73 " --> pdb=" O LEU E 69 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS E 79 " --> pdb=" O HIS E 75 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU E 80 " --> pdb=" O MET E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 98 removed outlier: 3.677A pdb=" N ASP E 90 " --> pdb=" O ASN E 86 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS E 97 " --> pdb=" O PHE E 93 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY E 98 " --> pdb=" O LEU E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 143 removed outlier: 3.615A pdb=" N ILE E 127 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG E 143 " --> pdb=" O TRP E 139 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 6 No H-bonds generated for 'chain 'P' and resid 4 through 6' Processing helix chain 'P' and resid 7 through 22 Processing helix chain 'R' and resid 39 through 62 removed outlier: 4.048A pdb=" N ARG R 45 " --> pdb=" O TYR R 41 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR R 56 " --> pdb=" O GLN R 52 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASP R 57 " --> pdb=" O TYR R 53 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN R 60 " --> pdb=" O TYR R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 173 removed outlier: 3.528A pdb=" N ALA R 145 " --> pdb=" O LYS R 141 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR R 146 " --> pdb=" O LEU R 142 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL R 147 " --> pdb=" O LYS R 143 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE R 153 " --> pdb=" O TYR R 149 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE R 160 " --> pdb=" O HIS R 156 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE R 165 " --> pdb=" O PHE R 161 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE R 169 " --> pdb=" O ILE R 165 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 177 Processing helix chain 'R' and resid 178 through 205 removed outlier: 3.680A pdb=" N TYR R 191 " --> pdb=" O MET R 187 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL R 203 " --> pdb=" O ILE R 199 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 215 removed outlier: 3.539A pdb=" N VAL R 212 " --> pdb=" O ASN R 208 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG R 214 " --> pdb=" O GLU R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 249 removed outlier: 3.739A pdb=" N MET R 237 " --> pdb=" O ASN R 233 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU R 238 " --> pdb=" O TYR R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 267 Processing helix chain 'R' and resid 270 through 284 Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 298 through 328 Proline residue: R 304 - end of helix removed outlier: 3.761A pdb=" N VAL R 311 " --> pdb=" O ALA R 307 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN R 312 " --> pdb=" O ALA R 308 " (cutoff:3.500A) Processing helix chain 'R' and resid 333 through 347 removed outlier: 3.731A pdb=" N TYR R 338 " --> pdb=" O GLU R 334 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU R 339 " --> pdb=" O SER R 335 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA R 341 " --> pdb=" O MET R 337 " (cutoff:3.500A) Processing helix chain 'R' and resid 348 through 353 Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 365 through 382 Processing helix chain 'R' and resid 382 through 392 removed outlier: 3.619A pdb=" N ALA R 388 " --> pdb=" O GLY R 384 " (cutoff:3.500A) Processing helix chain 'R' and resid 395 through 404 removed outlier: 4.048A pdb=" N THR R 401 " --> pdb=" O GLU R 397 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS R 403 " --> pdb=" O GLN R 399 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG R 404 " --> pdb=" O THR R 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 40 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.748A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.966A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.990A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.510A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.617A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.593A pdb=" N LEU B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.509A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 22 removed outlier: 3.597A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 43 removed outlier: 3.536A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.778A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.953A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 92 through 94 Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.250A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 48 through 51 removed outlier: 4.659A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE B 338 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.614A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.254A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.720A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.775A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.691A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.765A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 11 removed outlier: 3.718A pdb=" N GLY N 10 " --> pdb=" O GLN N 123 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 418 hydrogen bonds defined for protein. 1203 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: 2.71 Time building geometry restraints manager: 4.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1642 1.32 - 1.45: 2734 1.45 - 1.57: 5526 1.57 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 9998 Sorted by residual: bond pdb=" CA ARG N 98 " pdb=" C ARG N 98 " ideal model delta sigma weight residual 1.522 1.453 0.070 1.20e-02 6.94e+03 3.37e+01 bond pdb=" N ARG N 98 " pdb=" CA ARG N 98 " ideal model delta sigma weight residual 1.454 1.399 0.055 1.23e-02 6.61e+03 1.99e+01 bond pdb=" CA CYS N 96 " pdb=" C CYS N 96 " ideal model delta sigma weight residual 1.522 1.475 0.047 1.20e-02 6.94e+03 1.52e+01 bond pdb=" CA ALA N 97 " pdb=" C ALA N 97 " ideal model delta sigma weight residual 1.523 1.477 0.046 1.21e-02 6.83e+03 1.43e+01 bond pdb=" CA ASN N 31 " pdb=" C ASN N 31 " ideal model delta sigma weight residual 1.522 1.476 0.046 1.31e-02 5.83e+03 1.23e+01 ... (remaining 9993 not shown) Histogram of bond angle deviations from ideal: 90.32 - 101.93: 33 101.93 - 113.55: 5668 113.55 - 125.16: 7699 125.16 - 136.78: 182 136.78 - 148.40: 1 Bond angle restraints: 13583 Sorted by residual: angle pdb=" CA PRO P 32 " pdb=" N PRO P 32 " pdb=" CD PRO P 32 " ideal model delta sigma weight residual 112.00 90.32 21.68 1.40e+00 5.10e-01 2.40e+02 angle pdb=" N ARG N 98 " pdb=" CA ARG N 98 " pdb=" C ARG N 98 " ideal model delta sigma weight residual 109.72 99.59 10.13 1.60e+00 3.91e-01 4.01e+01 angle pdb=" N PRO N 102 " pdb=" CA PRO N 102 " pdb=" C PRO N 102 " ideal model delta sigma weight residual 112.01 122.57 -10.56 1.84e+00 2.95e-01 3.29e+01 angle pdb=" C THR P 31 " pdb=" N PRO P 32 " pdb=" CD PRO P 32 " ideal model delta sigma weight residual 125.00 148.40 -23.40 4.10e+00 5.95e-02 3.26e+01 angle pdb=" N ASP N 109 " pdb=" CA ASP N 109 " pdb=" C ASP N 109 " ideal model delta sigma weight residual 113.23 119.81 -6.58 1.22e+00 6.72e-01 2.91e+01 ... (remaining 13578 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.90: 5715 22.90 - 45.79: 281 45.79 - 68.69: 47 68.69 - 91.58: 14 91.58 - 114.48: 2 Dihedral angle restraints: 6059 sinusoidal: 2403 harmonic: 3656 Sorted by residual: dihedral pdb=" CB CYS E 40 " pdb=" SG CYS E 40 " pdb=" SG CYS E 72 " pdb=" CB CYS E 72 " ideal model delta sinusoidal sigma weight residual 93.00 169.62 -76.62 1 1.00e+01 1.00e-02 7.38e+01 dihedral pdb=" CB CYS E 57 " pdb=" SG CYS E 57 " pdb=" SG CYS E 104 " pdb=" CB CYS E 104 " ideal model delta sinusoidal sigma weight residual 93.00 22.37 70.63 1 1.00e+01 1.00e-02 6.42e+01 dihedral pdb=" CB CYS R 55 " pdb=" SG CYS R 55 " pdb=" SG CYS R 81 " pdb=" CB CYS R 81 " ideal model delta sinusoidal sigma weight residual -86.00 -145.94 59.94 1 1.00e+01 1.00e-02 4.79e+01 ... (remaining 6056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1428 0.078 - 0.157: 94 0.157 - 0.235: 11 0.235 - 0.313: 1 0.313 - 0.392: 2 Chirality restraints: 1536 Sorted by residual: chirality pdb=" CA ASP N 109 " pdb=" N ASP N 109 " pdb=" C ASP N 109 " pdb=" CB ASP N 109 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" C1 NAG R 502 " pdb=" ND2 ASN R 73 " pdb=" C2 NAG R 502 " pdb=" O5 NAG R 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA PRO N 102 " pdb=" N PRO N 102 " pdb=" C PRO N 102 " pdb=" CB PRO N 102 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1533 not shown) Planarity restraints: 1723 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR N 113 " -0.016 2.00e-02 2.50e+03 3.16e-02 1.00e+01 pdb=" C THR N 113 " 0.055 2.00e-02 2.50e+03 pdb=" O THR N 113 " -0.020 2.00e-02 2.50e+03 pdb=" N THR N 114 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR P 31 " 0.037 5.00e-02 4.00e+02 4.79e-02 3.66e+00 pdb=" N PRO P 32 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO P 32 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO P 32 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS R 302 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.18e+00 pdb=" C HIS R 302 " 0.031 2.00e-02 2.50e+03 pdb=" O HIS R 302 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY R 303 " -0.011 2.00e-02 2.50e+03 ... (remaining 1720 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 661 2.74 - 3.28: 9603 3.28 - 3.82: 15631 3.82 - 4.36: 19571 4.36 - 4.90: 33176 Nonbonded interactions: 78642 Sorted by model distance: nonbonded pdb=" O TYR R 374 " pdb=" OG SER R 378 " model vdw 2.199 2.440 nonbonded pdb=" O THR R 162 " pdb=" OG SER R 166 " model vdw 2.213 2.440 nonbonded pdb=" O SER R 105 " pdb=" OG SER R 105 " model vdw 2.249 2.440 nonbonded pdb=" NH2 ARG N 38 " pdb=" O GLU N 89 " model vdw 2.260 2.520 nonbonded pdb=" O LEU R 271 " pdb=" OG1 THR R 275 " model vdw 2.265 2.440 ... (remaining 78637 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 6.330 Check model and map are aligned: 0.160 Set scattering table: 0.080 Process input model: 29.400 Find NCS groups from input model: 0.240 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:12.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 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 0.070 9998 Z= 0.256 Angle : 0.677 23.397 13583 Z= 0.410 Chirality : 0.045 0.392 1536 Planarity : 0.003 0.048 1721 Dihedral : 13.381 114.481 3665 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.41 % Allowed : 14.62 % Favored : 83.97 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.38 % 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: -4.19 (0.18), residues: 1236 helix: -3.38 (0.14), residues: 479 sheet: -2.07 (0.30), residues: 231 loop : -2.31 (0.22), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 36 HIS 0.003 0.000 HIS R 302 PHE 0.023 0.001 PHE N 108 TYR 0.022 0.001 TYR N 32 ARG 0.002 0.000 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 186 time to evaluate : 1.132 Fit side-chains REVERT: R 99 PHE cc_start: 0.5445 (m-80) cc_final: 0.5146 (m-80) REVERT: R 337 MET cc_start: 0.5881 (ttm) cc_final: 0.5608 (ttp) REVERT: R 405 GLN cc_start: 0.5504 (OUTLIER) cc_final: 0.5089 (tm-30) REVERT: A 15 GLU cc_start: 0.6585 (mm-30) cc_final: 0.6139 (mm-30) REVERT: A 372 ILE cc_start: 0.7950 (pt) cc_final: 0.7632 (pp) REVERT: A 389 ARG cc_start: 0.7450 (tpp80) cc_final: 0.7078 (ttp-110) REVERT: B 22 ARG cc_start: 0.6628 (mtt180) cc_final: 0.6309 (mtt90) REVERT: B 45 MET cc_start: 0.6743 (mtt) cc_final: 0.5611 (mmp) REVERT: G 22 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7068 (mt-10) REVERT: N 43 LYS cc_start: 0.5702 (ptpt) cc_final: 0.5405 (pptt) REVERT: N 46 GLU cc_start: 0.6655 (mm-30) cc_final: 0.5646 (mm-30) REVERT: N 89 GLU cc_start: 0.5176 (OUTLIER) cc_final: 0.4814 (mm-30) outliers start: 14 outliers final: 5 residues processed: 197 average time/residue: 1.1970 time to fit residues: 252.9927 Evaluate side-chains 147 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 140 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 32 PRO Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain R residue 405 GLN Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 135 ASN R 179 GLN R 227 GLN R 257 GLN A 14 ASN A 357 HIS A 384 GLN B 75 GLN B 155 ASN N 5 GLN N 77 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9998 Z= 0.247 Angle : 0.574 8.354 13583 Z= 0.302 Chirality : 0.043 0.357 1536 Planarity : 0.005 0.054 1721 Dihedral : 8.219 84.837 1582 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.64 % Allowed : 17.94 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -2.39 (0.21), residues: 1236 helix: -1.08 (0.21), residues: 493 sheet: -1.63 (0.33), residues: 216 loop : -1.94 (0.23), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.006 0.001 HIS B 225 PHE 0.018 0.002 PHE B 199 TYR 0.017 0.001 TYR N 60 ARG 0.005 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 150 time to evaluate : 0.984 Fit side-chains REVERT: P 3 ASN cc_start: 0.8325 (m-40) cc_final: 0.8062 (m110) REVERT: R 133 MET cc_start: 0.6441 (mpp) cc_final: 0.6216 (ttm) REVERT: R 140 GLU cc_start: 0.6373 (OUTLIER) cc_final: 0.5332 (pt0) REVERT: R 187 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.7630 (tpt) REVERT: A 15 GLU cc_start: 0.6378 (mm-30) cc_final: 0.6117 (mm-30) REVERT: A 280 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7764 (pttm) REVERT: A 290 PHE cc_start: 0.7485 (m-10) cc_final: 0.7280 (m-10) REVERT: A 389 ARG cc_start: 0.7519 (tpp80) cc_final: 0.6875 (ttm110) REVERT: B 44 GLN cc_start: 0.7271 (OUTLIER) cc_final: 0.6786 (mt0) REVERT: B 45 MET cc_start: 0.6799 (mtt) cc_final: 0.5654 (mmp) REVERT: B 234 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.8149 (m-80) REVERT: N 5 GLN cc_start: 0.6155 (OUTLIER) cc_final: 0.5867 (mp-120) REVERT: N 43 LYS cc_start: 0.6374 (ptpt) cc_final: 0.5797 (pptt) REVERT: N 89 GLU cc_start: 0.4942 (OUTLIER) cc_final: 0.4735 (mm-30) outliers start: 46 outliers final: 15 residues processed: 180 average time/residue: 1.2034 time to fit residues: 232.6746 Evaluate side-chains 161 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 139 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 187 MET Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 397 GLU Chi-restraints excluded: chain R residue 402 VAL Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 110 optimal weight: 0.0370 chunk 119 optimal weight: 2.9990 chunk 98 optimal weight: 0.0770 chunk 37 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 257 GLN ** R 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN A 357 HIS B 155 ASN B 156 GLN N 5 GLN N 123 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9998 Z= 0.139 Angle : 0.485 7.451 13583 Z= 0.253 Chirality : 0.040 0.339 1536 Planarity : 0.003 0.037 1721 Dihedral : 7.109 77.375 1573 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 4.13 % Allowed : 19.86 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.27 (0.22), residues: 1236 helix: 0.25 (0.23), residues: 494 sheet: -1.15 (0.33), residues: 218 loop : -1.72 (0.24), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS A 362 PHE 0.012 0.001 PHE B 199 TYR 0.014 0.001 TYR N 95 ARG 0.005 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 144 time to evaluate : 1.108 Fit side-chains REVERT: P 3 ASN cc_start: 0.8288 (m-40) cc_final: 0.8019 (m110) REVERT: R 141 LYS cc_start: 0.7210 (mtmm) cc_final: 0.6996 (mtmm) REVERT: R 187 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.7583 (tpt) REVERT: A 15 GLU cc_start: 0.6337 (mm-30) cc_final: 0.6066 (mm-30) REVERT: A 35 GLN cc_start: 0.7470 (mm-40) cc_final: 0.7248 (mm110) REVERT: A 389 ARG cc_start: 0.7480 (tpp80) cc_final: 0.6930 (ttm110) REVERT: B 44 GLN cc_start: 0.7155 (OUTLIER) cc_final: 0.6721 (mt0) REVERT: B 45 MET cc_start: 0.6716 (mtt) cc_final: 0.5640 (mmp) REVERT: B 234 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.7990 (m-80) REVERT: N 43 LYS cc_start: 0.6385 (ptpt) cc_final: 0.5830 (pptt) REVERT: N 89 GLU cc_start: 0.5009 (OUTLIER) cc_final: 0.4786 (mm-30) outliers start: 41 outliers final: 14 residues processed: 169 average time/residue: 1.1536 time to fit residues: 210.5626 Evaluate side-chains 148 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 130 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain R residue 187 MET Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 392 CYS Chi-restraints excluded: chain R residue 397 GLU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 5.9990 chunk 57 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 98 optimal weight: 0.0870 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 227 GLN R 257 GLN R 383 GLN R 399 GLN A 292 ASN A 357 HIS B 155 ASN B 293 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9998 Z= 0.198 Angle : 0.520 7.999 13583 Z= 0.271 Chirality : 0.041 0.351 1536 Planarity : 0.004 0.040 1721 Dihedral : 7.146 68.121 1573 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.94 % Allowed : 19.96 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.23), residues: 1236 helix: 0.69 (0.24), residues: 494 sheet: -1.15 (0.33), residues: 224 loop : -1.67 (0.24), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 362 PHE 0.012 0.001 PHE B 199 TYR 0.017 0.001 TYR N 95 ARG 0.008 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 144 time to evaluate : 1.024 Fit side-chains REVERT: P 3 ASN cc_start: 0.8243 (m-40) cc_final: 0.7991 (m110) REVERT: R 48 MET cc_start: 0.4700 (ttm) cc_final: 0.4455 (ttm) REVERT: R 99 PHE cc_start: 0.5992 (m-80) cc_final: 0.5776 (m-80) REVERT: R 140 GLU cc_start: 0.6370 (OUTLIER) cc_final: 0.5266 (pt0) REVERT: R 187 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7625 (tpt) REVERT: R 397 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7008 (mt-10) REVERT: R 405 GLN cc_start: 0.6287 (OUTLIER) cc_final: 0.5684 (mp-120) REVERT: A 15 GLU cc_start: 0.6370 (mm-30) cc_final: 0.6051 (mm-30) REVERT: A 21 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6405 (tt0) REVERT: A 27 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6666 (mp0) REVERT: A 34 LYS cc_start: 0.8613 (tttt) cc_final: 0.8374 (tttp) REVERT: A 35 GLN cc_start: 0.7415 (mm-40) cc_final: 0.7158 (mm110) REVERT: A 58 LYS cc_start: 0.4605 (OUTLIER) cc_final: 0.3536 (mppt) REVERT: A 389 ARG cc_start: 0.7570 (tpp80) cc_final: 0.6928 (ttm110) REVERT: B 44 GLN cc_start: 0.7177 (OUTLIER) cc_final: 0.6723 (mt0) REVERT: B 45 MET cc_start: 0.6741 (mtt) cc_final: 0.5687 (mmp) REVERT: B 234 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.8059 (m-80) REVERT: N 89 GLU cc_start: 0.4843 (OUTLIER) cc_final: 0.3179 (tp30) outliers start: 49 outliers final: 21 residues processed: 180 average time/residue: 1.1694 time to fit residues: 226.7212 Evaluate side-chains 171 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 140 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 187 MET Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 335 SER Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 397 GLU Chi-restraints excluded: chain R residue 405 GLN Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 0.9990 chunk 1 optimal weight: 30.0000 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 chunk 60 optimal weight: 0.6980 chunk 105 optimal weight: 0.0670 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS B 155 ASN B 293 ASN N 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9998 Z= 0.222 Angle : 0.543 8.533 13583 Z= 0.283 Chirality : 0.042 0.356 1536 Planarity : 0.004 0.039 1721 Dihedral : 7.088 66.309 1573 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 5.04 % Allowed : 20.77 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.23), residues: 1236 helix: 0.89 (0.24), residues: 488 sheet: -1.07 (0.33), residues: 226 loop : -1.49 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.013 0.002 PHE B 199 TYR 0.020 0.001 TYR N 95 ARG 0.011 0.001 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 134 time to evaluate : 1.006 Fit side-chains REVERT: P 3 ASN cc_start: 0.8273 (m-40) cc_final: 0.8042 (m110) REVERT: R 99 PHE cc_start: 0.5990 (m-80) cc_final: 0.5651 (m-80) REVERT: R 140 GLU cc_start: 0.6350 (OUTLIER) cc_final: 0.5266 (pt0) REVERT: R 141 LYS cc_start: 0.7216 (mtmm) cc_final: 0.6931 (mtmm) REVERT: R 187 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7631 (tpt) REVERT: R 255 GLU cc_start: 0.6118 (mm-30) cc_final: 0.5878 (pm20) REVERT: R 397 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7055 (mt-10) REVERT: R 405 GLN cc_start: 0.6394 (OUTLIER) cc_final: 0.5697 (mp-120) REVERT: A 15 GLU cc_start: 0.6341 (mm-30) cc_final: 0.6015 (mm-30) REVERT: A 21 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.6485 (tt0) REVERT: A 27 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6740 (mp0) REVERT: A 34 LYS cc_start: 0.8634 (tttt) cc_final: 0.8372 (tttp) REVERT: A 35 GLN cc_start: 0.7410 (mm-40) cc_final: 0.7129 (mm110) REVERT: A 58 LYS cc_start: 0.4456 (OUTLIER) cc_final: 0.3384 (mppt) REVERT: A 389 ARG cc_start: 0.7585 (tpp80) cc_final: 0.6989 (ttm110) REVERT: B 44 GLN cc_start: 0.7197 (OUTLIER) cc_final: 0.6766 (mt0) REVERT: B 45 MET cc_start: 0.6852 (mtt) cc_final: 0.5803 (mmp) REVERT: B 234 PHE cc_start: 0.8481 (OUTLIER) cc_final: 0.8088 (m-80) REVERT: N 5 GLN cc_start: 0.5750 (OUTLIER) cc_final: 0.5307 (mp10) REVERT: N 43 LYS cc_start: 0.6142 (pttt) cc_final: 0.5826 (pptt) outliers start: 50 outliers final: 26 residues processed: 173 average time/residue: 1.0750 time to fit residues: 201.2471 Evaluate side-chains 170 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 134 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 187 MET Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 335 SER Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 397 GLU Chi-restraints excluded: chain R residue 405 GLN Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 118 optimal weight: 0.4980 chunk 97 optimal weight: 0.7980 chunk 54 optimal weight: 0.0010 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 383 GLN A 357 HIS B 155 ASN B 293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9998 Z= 0.142 Angle : 0.479 7.127 13583 Z= 0.249 Chirality : 0.040 0.345 1536 Planarity : 0.003 0.036 1721 Dihedral : 6.279 62.015 1573 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.33 % Allowed : 21.27 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.24), residues: 1236 helix: 1.16 (0.24), residues: 495 sheet: -0.85 (0.34), residues: 224 loop : -1.42 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.003 0.001 HIS A 362 PHE 0.012 0.001 PHE B 199 TYR 0.014 0.001 TYR N 95 ARG 0.008 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 136 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: P 3 ASN cc_start: 0.8174 (m-40) cc_final: 0.7937 (m110) REVERT: R 99 PHE cc_start: 0.5989 (m-80) cc_final: 0.5662 (m-80) REVERT: R 140 GLU cc_start: 0.6205 (OUTLIER) cc_final: 0.5165 (pt0) REVERT: R 141 LYS cc_start: 0.7145 (mtmm) cc_final: 0.6932 (mtmm) REVERT: R 187 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.7533 (tpt) REVERT: R 397 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7104 (mt-10) REVERT: R 405 GLN cc_start: 0.6368 (OUTLIER) cc_final: 0.5701 (mp-120) REVERT: A 15 GLU cc_start: 0.6327 (mm-30) cc_final: 0.6024 (mm-30) REVERT: A 34 LYS cc_start: 0.8589 (tttt) cc_final: 0.8328 (tttp) REVERT: A 35 GLN cc_start: 0.7429 (mm-40) cc_final: 0.7189 (mm110) REVERT: A 58 LYS cc_start: 0.4284 (OUTLIER) cc_final: 0.3322 (mppt) REVERT: A 389 ARG cc_start: 0.7552 (tpp80) cc_final: 0.6979 (ttm110) REVERT: B 44 GLN cc_start: 0.7172 (OUTLIER) cc_final: 0.6756 (mt0) REVERT: B 45 MET cc_start: 0.6664 (mtt) cc_final: 0.5655 (mmp) REVERT: B 234 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.7957 (m-80) REVERT: N 5 GLN cc_start: 0.5746 (OUTLIER) cc_final: 0.5238 (mp10) REVERT: N 43 LYS cc_start: 0.6025 (pttt) cc_final: 0.5713 (pptt) REVERT: N 108 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.8401 (m-80) outliers start: 43 outliers final: 20 residues processed: 167 average time/residue: 1.1474 time to fit residues: 206.8612 Evaluate side-chains 161 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 132 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 187 MET Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 397 GLU Chi-restraints excluded: chain R residue 405 GLN Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 54 optimal weight: 0.0000 chunk 72 optimal weight: 0.9980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS B 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9998 Z= 0.152 Angle : 0.485 7.088 13583 Z= 0.253 Chirality : 0.041 0.345 1536 Planarity : 0.003 0.036 1721 Dihedral : 6.173 61.825 1573 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.33 % Allowed : 21.37 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.24), residues: 1236 helix: 1.28 (0.24), residues: 495 sheet: -0.75 (0.34), residues: 231 loop : -1.35 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 362 PHE 0.015 0.001 PHE R 285 TYR 0.015 0.001 TYR N 95 ARG 0.013 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 134 time to evaluate : 1.090 Fit side-chains revert: symmetry clash REVERT: P 3 ASN cc_start: 0.8177 (m-40) cc_final: 0.7941 (m110) REVERT: R 99 PHE cc_start: 0.5966 (m-80) cc_final: 0.5675 (m-80) REVERT: R 140 GLU cc_start: 0.6175 (OUTLIER) cc_final: 0.5118 (pt0) REVERT: R 187 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7516 (tpt) REVERT: R 328 ARG cc_start: 0.5705 (mtt-85) cc_final: 0.5290 (mtm110) REVERT: R 370 LYS cc_start: 0.6658 (mtpt) cc_final: 0.6290 (mttt) REVERT: R 397 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7042 (mt-10) REVERT: A 15 GLU cc_start: 0.6321 (mm-30) cc_final: 0.6043 (mm-30) REVERT: A 34 LYS cc_start: 0.8581 (tttt) cc_final: 0.8358 (tttp) REVERT: A 58 LYS cc_start: 0.4392 (OUTLIER) cc_final: 0.3337 (mppt) REVERT: A 389 ARG cc_start: 0.7587 (tpp80) cc_final: 0.7001 (ttm110) REVERT: B 44 GLN cc_start: 0.7170 (OUTLIER) cc_final: 0.6741 (mt0) REVERT: B 45 MET cc_start: 0.6706 (mtt) cc_final: 0.5709 (mmp) REVERT: B 234 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.7955 (m-80) REVERT: N 5 GLN cc_start: 0.5744 (OUTLIER) cc_final: 0.5247 (mp10) REVERT: N 43 LYS cc_start: 0.5965 (pttt) cc_final: 0.5661 (pptt) REVERT: N 108 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.8420 (m-80) outliers start: 43 outliers final: 24 residues processed: 166 average time/residue: 1.1964 time to fit residues: 213.9807 Evaluate side-chains 165 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 133 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 187 MET Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 397 GLU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 357 HIS B 155 ASN N 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9998 Z= 0.219 Angle : 0.537 7.142 13583 Z= 0.282 Chirality : 0.042 0.348 1536 Planarity : 0.004 0.037 1721 Dihedral : 6.401 63.216 1573 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.44 % Allowed : 21.17 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.24), residues: 1236 helix: 1.23 (0.24), residues: 490 sheet: -0.83 (0.34), residues: 226 loop : -1.35 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS A 220 PHE 0.012 0.002 PHE A 212 TYR 0.019 0.001 TYR N 95 ARG 0.014 0.001 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 132 time to evaluate : 1.055 Fit side-chains REVERT: P 3 ASN cc_start: 0.8210 (m-40) cc_final: 0.7991 (m110) REVERT: R 99 PHE cc_start: 0.5995 (m-80) cc_final: 0.5714 (m-80) REVERT: R 187 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.7638 (tpt) REVERT: R 192 ILE cc_start: 0.7760 (OUTLIER) cc_final: 0.6851 (tp) REVERT: R 196 MET cc_start: 0.7185 (mtt) cc_final: 0.6981 (mtp) REVERT: R 255 GLU cc_start: 0.6169 (mm-30) cc_final: 0.5918 (pm20) REVERT: R 328 ARG cc_start: 0.5865 (mtt-85) cc_final: 0.5264 (mtm110) REVERT: R 397 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7070 (mt-10) REVERT: A 15 GLU cc_start: 0.6325 (mm-30) cc_final: 0.6042 (mm-30) REVERT: A 21 GLU cc_start: 0.6719 (OUTLIER) cc_final: 0.6443 (tt0) REVERT: A 27 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6681 (mp0) REVERT: A 34 LYS cc_start: 0.8624 (tttt) cc_final: 0.8357 (tttp) REVERT: A 35 GLN cc_start: 0.7350 (mm-40) cc_final: 0.7138 (mm110) REVERT: A 58 LYS cc_start: 0.4397 (OUTLIER) cc_final: 0.3270 (mppt) REVERT: A 389 ARG cc_start: 0.7625 (tpp80) cc_final: 0.7042 (ttm110) REVERT: B 44 GLN cc_start: 0.7153 (OUTLIER) cc_final: 0.6701 (mt0) REVERT: B 45 MET cc_start: 0.6882 (mtt) cc_final: 0.5843 (mmp) REVERT: B 234 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.8075 (m-80) REVERT: N 5 GLN cc_start: 0.5816 (OUTLIER) cc_final: 0.5468 (mp10) REVERT: N 43 LYS cc_start: 0.6215 (pttt) cc_final: 0.5765 (pptt) outliers start: 44 outliers final: 27 residues processed: 164 average time/residue: 1.1792 time to fit residues: 207.7844 Evaluate side-chains 166 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 130 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 187 MET Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 335 SER Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 397 GLU Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 103 optimal weight: 0.1980 chunk 71 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS B 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9998 Z= 0.157 Angle : 0.498 7.100 13583 Z= 0.260 Chirality : 0.041 0.342 1536 Planarity : 0.003 0.037 1721 Dihedral : 6.022 60.726 1573 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 4.13 % Allowed : 21.67 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.24), residues: 1236 helix: 1.41 (0.24), residues: 490 sheet: -0.71 (0.34), residues: 231 loop : -1.29 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 362 PHE 0.020 0.001 PHE R 285 TYR 0.016 0.001 TYR N 95 ARG 0.015 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 132 time to evaluate : 1.173 Fit side-chains REVERT: P 3 ASN cc_start: 0.8155 (m-40) cc_final: 0.7936 (m110) REVERT: R 99 PHE cc_start: 0.6010 (m-80) cc_final: 0.5706 (m-80) REVERT: R 133 MET cc_start: 0.6509 (mpp) cc_final: 0.6065 (ttp) REVERT: R 187 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7532 (tpt) REVERT: R 192 ILE cc_start: 0.7765 (OUTLIER) cc_final: 0.6871 (tp) REVERT: R 255 GLU cc_start: 0.6107 (mm-30) cc_final: 0.5877 (pm20) REVERT: R 328 ARG cc_start: 0.5872 (mtt-85) cc_final: 0.5299 (mtm110) REVERT: R 370 LYS cc_start: 0.6721 (mtpt) cc_final: 0.6415 (mmpt) REVERT: R 397 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7106 (mt-10) REVERT: A 15 GLU cc_start: 0.6300 (mm-30) cc_final: 0.6036 (mm-30) REVERT: A 21 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.6420 (tt0) REVERT: A 27 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6667 (mp0) REVERT: A 34 LYS cc_start: 0.8612 (tttt) cc_final: 0.8343 (tttp) REVERT: A 35 GLN cc_start: 0.7372 (mm-40) cc_final: 0.7110 (mm110) REVERT: A 58 LYS cc_start: 0.4391 (OUTLIER) cc_final: 0.3249 (mppt) REVERT: A 389 ARG cc_start: 0.7631 (tpp80) cc_final: 0.7121 (ttm110) REVERT: B 44 GLN cc_start: 0.7152 (OUTLIER) cc_final: 0.6729 (mt0) REVERT: B 45 MET cc_start: 0.6765 (mtt) cc_final: 0.5818 (mmp) REVERT: B 234 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.7985 (m-80) REVERT: N 5 GLN cc_start: 0.5786 (OUTLIER) cc_final: 0.5370 (mp10) REVERT: N 43 LYS cc_start: 0.6091 (pttt) cc_final: 0.5693 (pptt) outliers start: 41 outliers final: 26 residues processed: 162 average time/residue: 1.1883 time to fit residues: 207.4828 Evaluate side-chains 164 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 129 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 187 MET Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 292 SER Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 397 GLU Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 80 optimal weight: 0.0270 chunk 121 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 96 optimal weight: 0.3980 chunk 10 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 59 optimal weight: 0.1980 chunk 76 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS B 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9998 Z= 0.196 Angle : 0.526 7.147 13583 Z= 0.275 Chirality : 0.041 0.342 1536 Planarity : 0.004 0.038 1721 Dihedral : 6.142 61.520 1573 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.23 % Allowed : 21.98 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.24), residues: 1236 helix: 1.35 (0.24), residues: 492 sheet: -0.76 (0.34), residues: 226 loop : -1.37 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS A 220 PHE 0.012 0.001 PHE B 199 TYR 0.018 0.001 TYR N 95 ARG 0.017 0.001 ARG A 347 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 134 time to evaluate : 1.129 Fit side-chains REVERT: P 3 ASN cc_start: 0.8180 (m-40) cc_final: 0.7967 (m110) REVERT: R 133 MET cc_start: 0.6517 (mpp) cc_final: 0.6070 (ttp) REVERT: R 187 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.7568 (tpt) REVERT: R 255 GLU cc_start: 0.6180 (mm-30) cc_final: 0.5964 (pm20) REVERT: R 328 ARG cc_start: 0.5938 (mtt-85) cc_final: 0.5330 (mtm110) REVERT: R 370 LYS cc_start: 0.6814 (mtpt) cc_final: 0.6528 (mmpt) REVERT: R 397 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7134 (mt-10) REVERT: A 15 GLU cc_start: 0.6305 (mm-30) cc_final: 0.6037 (mm-30) REVERT: A 21 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6499 (tt0) REVERT: A 27 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6691 (mp0) REVERT: A 34 LYS cc_start: 0.8615 (tttt) cc_final: 0.8356 (tttp) REVERT: A 35 GLN cc_start: 0.7353 (mm-40) cc_final: 0.7128 (mm110) REVERT: A 58 LYS cc_start: 0.4449 (OUTLIER) cc_final: 0.3352 (mppt) REVERT: A 389 ARG cc_start: 0.7652 (tpp80) cc_final: 0.7138 (ttm110) REVERT: B 44 GLN cc_start: 0.7172 (OUTLIER) cc_final: 0.6731 (mt0) REVERT: B 45 MET cc_start: 0.6876 (mtt) cc_final: 0.5839 (mmp) REVERT: B 234 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.8026 (m-80) REVERT: N 5 GLN cc_start: 0.5809 (OUTLIER) cc_final: 0.5499 (mp10) REVERT: N 43 LYS cc_start: 0.6150 (pttt) cc_final: 0.5707 (pptt) outliers start: 42 outliers final: 29 residues processed: 163 average time/residue: 1.2284 time to fit residues: 214.9615 Evaluate side-chains 169 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 132 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 187 MET Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 292 SER Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 397 GLU Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 0.0980 chunk 40 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS B 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.200906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.161562 restraints weight = 11022.544| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 1.71 r_work: 0.3543 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9998 Z= 0.256 Angle : 0.567 7.542 13583 Z= 0.298 Chirality : 0.043 0.346 1536 Planarity : 0.004 0.038 1721 Dihedral : 6.442 62.017 1573 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.13 % Allowed : 22.18 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.24), residues: 1236 helix: 1.16 (0.24), residues: 495 sheet: -0.82 (0.34), residues: 226 loop : -1.40 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.005 0.001 HIS A 220 PHE 0.028 0.002 PHE R 285 TYR 0.020 0.002 TYR N 95 ARG 0.022 0.001 ARG A 347 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4087.29 seconds wall clock time: 73 minutes 41.49 seconds (4421.49 seconds total)