Starting phenix.real_space_refine on Tue Feb 13 23:55:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cfn_30345/02_2024/7cfn_30345_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cfn_30345/02_2024/7cfn_30345.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/7cfn_30345/02_2024/7cfn_30345.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cfn_30345/02_2024/7cfn_30345.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cfn_30345/02_2024/7cfn_30345_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cfn_30345/02_2024/7cfn_30345_updated.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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 5158 2.51 5 N 1416 2.21 5 O 1492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 13": "NH1" <-> "NH2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "A ARG 342": "NH1" <-> "NH2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "B ARG 22": "NH1" <-> "NH2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "N ARG 38": "NH1" <-> "NH2" Residue "N ARG 67": "NH1" <-> "NH2" Residue "R ARG 43": "NH1" <-> "NH2" Residue "R ARG 44": "NH1" <-> "NH2" Residue "R ARG 80": "NH1" <-> "NH2" Residue "R ARG 125": "NH1" <-> "NH2" Residue "R ARG 187": "NH1" <-> "NH2" Residue "R ARG 201": "NH1" <-> "NH2" Residue "R ARG 204": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8112 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1930 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 232, 1914 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 232, 1914 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 1932 Chain: "B" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2587 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 438 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 970 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 2187 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 279, 2181 Unusual residues: {'CLR': 1, 'FX0': 2, 'PLM': 1} Classifications: {'peptide': 274, 'undetermined': 4, 'water': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 252, None: 5} Not linked: pdbres="TRP R 291 " pdbres="FX0 R 401 " Not linked: pdbres="FX0 R 401 " pdbres="CLR R 402 " Not linked: pdbres="CLR R 402 " pdbres="FX0 R 403 " Not linked: pdbres="FX0 R 403 " pdbres="PLM R 404 " Not linked: pdbres="PLM R 404 " pdbres="HOH R 501 " Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 279, 2181 Unusual residues: {'CLR': 1, 'FX0': 2, 'PLM': 1} Classifications: {'peptide': 274, 'undetermined': 4, 'water': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 252, None: 5} Not linked: pdbres="TRP R 291 " pdbres="FX0 R 401 " Not linked: pdbres="FX0 R 401 " pdbres="CLR R 402 " Not linked: pdbres="CLR R 402 " pdbres="FX0 R 403 " Not linked: pdbres="FX0 R 403 " pdbres="PLM R 404 " Not linked: pdbres="PLM R 404 " pdbres="HOH R 501 " Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 2239 Time building chain proxies: 6.74, per 1000 atoms: 0.83 Number of scatterers: 8112 At special positions: 0 Unit cell: (79.092, 115.596, 119.652, 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 46 16.00 O 1492 8.00 N 1416 7.00 C 5158 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 155 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 2.4 seconds 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1926 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 10 sheets defined 37.9% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 10 through 38 removed outlier: 3.798A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 351 removed outlier: 4.640A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 removed outlier: 3.621A pdb=" N VAL A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.292A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 22 removed outlier: 4.037A pdb=" N ALA G 10 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'R' and resid 19 through 41 removed outlier: 3.987A pdb=" N ALA R 31 " --> pdb=" O LEU R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 47 Processing helix chain 'R' and resid 49 through 66 Processing helix chain 'R' and resid 72 through 74 No H-bonds generated for 'chain 'R' and resid 72 through 74' Processing helix chain 'R' and resid 82 through 115 removed outlier: 4.151A pdb=" N LEU R 87 " --> pdb=" O TRP R 83 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL R 88 " --> pdb=" O SER R 84 " (cutoff:3.500A) Proline residue: R 92 - end of helix Processing helix chain 'R' and resid 124 through 144 Proline residue: R 135 - end of helix Proline residue: R 142 - end of helix Processing helix chain 'R' and resid 157 through 160 No H-bonds generated for 'chain 'R' and resid 157 through 160' Processing helix chain 'R' and resid 163 through 172 Processing helix chain 'R' and resid 176 through 206 removed outlier: 4.365A pdb=" N ALA R 181 " --> pdb=" O ALA R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 235 removed outlier: 3.797A pdb=" N ALA R 217 " --> pdb=" O ALA R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 237 through 252 removed outlier: 3.748A pdb=" N VAL R 241 " --> pdb=" O TRP R 237 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU R 252 " --> pdb=" O VAL R 248 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 281 removed outlier: 3.612A pdb=" N LEU R 262 " --> pdb=" O GLY R 258 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER R 264 " --> pdb=" O GLY R 260 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER R 272 " --> pdb=" O LEU R 268 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA R 273 " --> pdb=" O GLY R 269 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA R 274 " --> pdb=" O SER R 270 " (cutoff:3.500A) Proline residue: R 277 - end of helix Processing helix chain 'R' and resid 285 through 288 No H-bonds generated for 'chain 'R' and resid 285 through 288' Processing sheet with id= A, first strand: chain 'A' and resid 359 through 362 removed outlier: 7.202A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE A 290 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N VAL A 224 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.935A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.793A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.661A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.711A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.744A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.356A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 52 removed outlier: 3.540A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.733A pdb=" N LEU N 81 " --> pdb=" O LEU N 20 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 93 through 95 removed outlier: 3.537A pdb=" N ILE N 51 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP N 50 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 352 hydrogen bonds defined for protein. 1021 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: 2.22 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1954 1.33 - 1.45: 1779 1.45 - 1.58: 4492 1.58 - 1.70: 1 1.70 - 1.82: 63 Bond restraints: 8289 Sorted by residual: bond pdb=" C27 FX0 R 401 " pdb=" O04 FX0 R 401 " ideal model delta sigma weight residual 1.251 1.359 -0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" C27 FX0 R 403 " pdb=" O04 FX0 R 403 " ideal model delta sigma weight residual 1.251 1.358 -0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" C ALA R 289 " pdb=" N PRO R 290 " ideal model delta sigma weight residual 1.334 1.429 -0.095 2.34e-02 1.83e+03 1.65e+01 bond pdb=" C HIS A 387 " pdb=" O HIS A 387 " ideal model delta sigma weight residual 1.237 1.206 0.031 1.17e-02 7.31e+03 6.94e+00 bond pdb=" C LEU A 388 " pdb=" O LEU A 388 " ideal model delta sigma weight residual 1.237 1.208 0.029 1.17e-02 7.31e+03 6.09e+00 ... (remaining 8284 not shown) Histogram of bond angle deviations from ideal: 96.44 - 103.97: 103 103.97 - 111.50: 3439 111.50 - 119.03: 3273 119.03 - 126.56: 4317 126.56 - 134.10: 141 Bond angle restraints: 11273 Sorted by residual: angle pdb=" N VAL R 170 " pdb=" CA VAL R 170 " pdb=" C VAL R 170 " ideal model delta sigma weight residual 110.72 115.97 -5.25 1.01e+00 9.80e-01 2.71e+01 angle pdb=" N LEU R 90 " pdb=" CA LEU R 90 " pdb=" C LEU R 90 " ideal model delta sigma weight residual 111.69 117.96 -6.27 1.23e+00 6.61e-01 2.60e+01 angle pdb=" N GLU A 392 " pdb=" CA GLU A 392 " pdb=" C GLU A 392 " ideal model delta sigma weight residual 110.80 118.87 -8.07 2.13e+00 2.20e-01 1.43e+01 angle pdb=" C ASP B 66 " pdb=" N SER B 67 " pdb=" CA SER B 67 " ideal model delta sigma weight residual 123.47 129.26 -5.79 1.53e+00 4.27e-01 1.43e+01 angle pdb=" CA ALA R 91 " pdb=" C ALA R 91 " pdb=" N PRO R 92 " ideal model delta sigma weight residual 120.93 117.35 3.58 1.06e+00 8.90e-01 1.14e+01 ... (remaining 11268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.71: 4796 14.71 - 29.42: 238 29.42 - 44.13: 75 44.13 - 58.83: 16 58.83 - 73.54: 10 Dihedral angle restraints: 5135 sinusoidal: 2146 harmonic: 2989 Sorted by residual: dihedral pdb=" CA ASP A 331 " pdb=" C ASP A 331 " pdb=" N PRO A 332 " pdb=" CA PRO A 332 " ideal model delta harmonic sigma weight residual -180.00 -153.57 -26.43 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA ASP B 195 " pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta harmonic sigma weight residual -180.00 -156.36 -23.64 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 156.84 23.16 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 5132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1031 0.077 - 0.154: 215 0.154 - 0.231: 28 0.231 - 0.308: 6 0.308 - 0.385: 2 Chirality restraints: 1282 Sorted by residual: chirality pdb=" CA GLU A 392 " pdb=" N GLU A 392 " pdb=" C GLU A 392 " pdb=" CB GLU A 392 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA LEU R 90 " pdb=" N LEU R 90 " pdb=" C LEU R 90 " pdb=" CB LEU R 90 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CB VAL A 241 " pdb=" CA VAL A 241 " pdb=" CG1 VAL A 241 " pdb=" CG2 VAL A 241 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 1279 not shown) Planarity restraints: 1433 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS N 87 " -0.049 5.00e-02 4.00e+02 7.42e-02 8.81e+00 pdb=" N PRO N 88 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO N 88 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO N 88 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA R 289 " -0.042 5.00e-02 4.00e+02 6.48e-02 6.72e+00 pdb=" N PRO R 290 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO R 290 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO R 290 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 281 " -0.024 2.00e-02 2.50e+03 1.60e-02 6.36e+00 pdb=" CG TRP A 281 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP A 281 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 281 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 281 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 281 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 281 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 281 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 281 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 281 " -0.011 2.00e-02 2.50e+03 ... (remaining 1430 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 49 2.56 - 3.15: 6028 3.15 - 3.73: 12157 3.73 - 4.32: 16842 4.32 - 4.90: 28936 Nonbonded interactions: 64012 Sorted by model distance: nonbonded pdb=" CD2 LEU A 394 " pdb=" OXT LEU A 394 " model vdw 1.979 3.460 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.240 2.440 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.291 2.440 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.296 2.440 nonbonded pdb=" O ARG B 22 " pdb=" NE2 GLN B 259 " model vdw 2.337 2.520 ... (remaining 64007 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.930 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 27.820 Find NCS groups from input model: 0.210 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:12.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 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 : 0.008 0.108 8289 Z= 0.482 Angle : 1.039 9.772 11273 Z= 0.543 Chirality : 0.064 0.385 1282 Planarity : 0.007 0.074 1433 Dihedral : 10.747 73.543 3200 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.12 % Allowed : 3.31 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.22), residues: 1020 helix: -1.41 (0.21), residues: 398 sheet: -1.88 (0.31), residues: 236 loop : -2.04 (0.26), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP A 281 HIS 0.013 0.003 HIS A 41 PHE 0.026 0.003 PHE B 151 TYR 0.021 0.003 TYR A 339 ARG 0.013 0.001 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 172 time to evaluate : 0.820 Fit side-chains revert: symmetry clash REVERT: A 33 ASP cc_start: 0.7813 (m-30) cc_final: 0.7568 (m-30) REVERT: A 35 GLN cc_start: 0.7176 (mt0) cc_final: 0.6666 (mp10) REVERT: A 40 THR cc_start: 0.8881 (t) cc_final: 0.8556 (m) REVERT: A 60 MET cc_start: 0.4235 (ptt) cc_final: 0.3659 (pmt) REVERT: A 284 ASP cc_start: 0.8170 (m-30) cc_final: 0.7847 (m-30) REVERT: B 155 ASN cc_start: 0.7960 (t0) cc_final: 0.7641 (t0) REVERT: B 186 ASP cc_start: 0.7886 (p0) cc_final: 0.7593 (p0) REVERT: B 323 ASP cc_start: 0.7911 (m-30) cc_final: 0.7587 (m-30) REVERT: G 21 MET cc_start: 0.7013 (ttt) cc_final: 0.6603 (ttm) REVERT: R 116 ARG cc_start: 0.8070 (mtt-85) cc_final: 0.7848 (mtt-85) REVERT: R 204 ARG cc_start: 0.6992 (ttt90) cc_final: 0.6508 (ttm110) REVERT: R 254 ARG cc_start: 0.7701 (ptm-80) cc_final: 0.6945 (ptt180) REVERT: R 268 LEU cc_start: 0.8111 (tt) cc_final: 0.7754 (tp) outliers start: 1 outliers final: 0 residues processed: 173 average time/residue: 1.2116 time to fit residues: 221.6306 Evaluate side-chains 110 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 25 optimal weight: 8.9990 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 0.1980 chunk 90 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 213 GLN A 371 ASN B 44 GLN B 237 ASN B 295 ASN B 340 ASN N 31 ASN R 93 ASN ** R 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8289 Z= 0.162 Angle : 0.616 11.674 11273 Z= 0.292 Chirality : 0.042 0.289 1282 Planarity : 0.004 0.047 1433 Dihedral : 5.913 53.014 1378 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.96 % Allowed : 11.95 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.25), residues: 1020 helix: 0.78 (0.25), residues: 395 sheet: -1.27 (0.33), residues: 219 loop : -1.41 (0.27), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 149 HIS 0.003 0.001 HIS A 41 PHE 0.011 0.001 PHE A 212 TYR 0.020 0.001 TYR R 251 ARG 0.006 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 0.890 Fit side-chains REVERT: A 26 ILE cc_start: 0.7494 (mm) cc_final: 0.7246 (mt) REVERT: A 35 GLN cc_start: 0.6993 (mt0) cc_final: 0.6756 (mp10) REVERT: A 40 THR cc_start: 0.8850 (t) cc_final: 0.8587 (m) REVERT: A 209 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.6852 (tm-30) REVERT: A 220 HIS cc_start: 0.8197 (m-70) cc_final: 0.7922 (m-70) REVERT: A 284 ASP cc_start: 0.8087 (m-30) cc_final: 0.7554 (m-30) REVERT: A 356 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.5964 (ttt-90) REVERT: A 386 MET cc_start: 0.7134 (ttm) cc_final: 0.6925 (ttp) REVERT: B 150 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.6423 (mmt90) REVERT: B 155 ASN cc_start: 0.7809 (t0) cc_final: 0.7523 (t0) REVERT: B 254 ASP cc_start: 0.8332 (t0) cc_final: 0.8067 (t0) REVERT: B 268 ASN cc_start: 0.7961 (OUTLIER) cc_final: 0.7659 (m110) REVERT: B 303 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7947 (p0) REVERT: B 323 ASP cc_start: 0.7714 (m-30) cc_final: 0.7370 (m-30) REVERT: N 69 THR cc_start: 0.8526 (OUTLIER) cc_final: 0.8248 (m) REVERT: R 251 TYR cc_start: 0.8406 (t80) cc_final: 0.8182 (t80) REVERT: R 254 ARG cc_start: 0.7656 (ptm-80) cc_final: 0.6887 (ptt180) REVERT: R 268 LEU cc_start: 0.8128 (tt) cc_final: 0.7764 (tp) outliers start: 25 outliers final: 5 residues processed: 147 average time/residue: 1.0509 time to fit residues: 165.1818 Evaluate side-chains 123 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 112 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 123 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 25 optimal weight: 0.0870 chunk 90 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN B 237 ASN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8289 Z= 0.207 Angle : 0.608 10.018 11273 Z= 0.287 Chirality : 0.042 0.273 1282 Planarity : 0.004 0.040 1433 Dihedral : 5.447 55.557 1378 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.84 % Allowed : 14.44 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.26), residues: 1020 helix: 1.43 (0.26), residues: 402 sheet: -1.03 (0.33), residues: 223 loop : -1.12 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 149 HIS 0.003 0.001 HIS A 357 PHE 0.014 0.002 PHE N 108 TYR 0.017 0.001 TYR R 251 ARG 0.007 0.001 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 113 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: A 26 ILE cc_start: 0.7470 (mm) cc_final: 0.7220 (mt) REVERT: A 35 GLN cc_start: 0.7002 (mt0) cc_final: 0.6776 (mp10) REVERT: A 40 THR cc_start: 0.8915 (t) cc_final: 0.8690 (m) REVERT: A 209 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.6850 (tm-30) REVERT: A 220 HIS cc_start: 0.8163 (m-70) cc_final: 0.7883 (m-70) REVERT: A 284 ASP cc_start: 0.8110 (m-30) cc_final: 0.7225 (m-30) REVERT: A 356 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.6256 (ttt180) REVERT: A 386 MET cc_start: 0.7329 (ttm) cc_final: 0.7086 (ttp) REVERT: A 392 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7154 (mt-10) REVERT: B 150 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.6407 (mmt90) REVERT: B 155 ASN cc_start: 0.7903 (t0) cc_final: 0.7602 (t0) REVERT: B 254 ASP cc_start: 0.8304 (t0) cc_final: 0.8049 (t0) REVERT: B 303 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7927 (p0) REVERT: B 323 ASP cc_start: 0.7615 (m-30) cc_final: 0.7303 (m-30) REVERT: R 254 ARG cc_start: 0.7483 (ptm-80) cc_final: 0.6863 (ptt180) REVERT: R 268 LEU cc_start: 0.8128 (tt) cc_final: 0.7786 (tp) outliers start: 24 outliers final: 7 residues processed: 129 average time/residue: 1.1015 time to fit residues: 151.6939 Evaluate side-chains 111 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 99 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 123 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 54 optimal weight: 0.0370 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8289 Z= 0.165 Angle : 0.581 9.850 11273 Z= 0.269 Chirality : 0.041 0.286 1282 Planarity : 0.004 0.046 1433 Dihedral : 5.296 59.846 1378 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.84 % Allowed : 15.27 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.26), residues: 1020 helix: 1.92 (0.27), residues: 399 sheet: -0.86 (0.33), residues: 228 loop : -0.92 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP R 149 HIS 0.002 0.001 HIS B 183 PHE 0.012 0.001 PHE N 108 TYR 0.017 0.001 TYR R 251 ARG 0.012 0.001 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 0.951 Fit side-chains revert: symmetry clash REVERT: A 26 ILE cc_start: 0.7548 (mm) cc_final: 0.7312 (mt) REVERT: A 40 THR cc_start: 0.8905 (t) cc_final: 0.8659 (m) REVERT: A 46 LEU cc_start: 0.7941 (tt) cc_final: 0.7682 (tp) REVERT: A 209 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.6829 (tm-30) REVERT: A 284 ASP cc_start: 0.8045 (m-30) cc_final: 0.7440 (m-30) REVERT: A 356 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.6476 (ttt180) REVERT: A 386 MET cc_start: 0.7402 (ttm) cc_final: 0.7168 (ttp) REVERT: A 392 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7154 (mt-10) REVERT: B 150 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.6427 (mmt90) REVERT: B 155 ASN cc_start: 0.7831 (t0) cc_final: 0.7548 (t0) REVERT: B 254 ASP cc_start: 0.8270 (t0) cc_final: 0.8060 (t0) REVERT: B 303 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7815 (p0) REVERT: B 323 ASP cc_start: 0.7512 (m-30) cc_final: 0.7248 (m-30) REVERT: N 34 MET cc_start: 0.8361 (mmm) cc_final: 0.8147 (mmt) REVERT: R 254 ARG cc_start: 0.7435 (ptm-80) cc_final: 0.6811 (ptt180) REVERT: R 268 LEU cc_start: 0.8107 (tt) cc_final: 0.7778 (tp) outliers start: 24 outliers final: 7 residues processed: 127 average time/residue: 1.0565 time to fit residues: 144.2935 Evaluate side-chains 121 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 109 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 123 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 66 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 86 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 overall best weight: 1.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 195 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 8289 Z= 0.233 Angle : 0.607 9.747 11273 Z= 0.285 Chirality : 0.043 0.297 1282 Planarity : 0.004 0.055 1433 Dihedral : 5.362 59.766 1378 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.43 % Allowed : 16.57 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.26), residues: 1020 helix: 1.96 (0.26), residues: 405 sheet: -0.85 (0.33), residues: 233 loop : -0.78 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP R 149 HIS 0.003 0.001 HIS B 62 PHE 0.017 0.002 PHE N 108 TYR 0.017 0.001 TYR R 251 ARG 0.012 0.001 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 107 time to evaluate : 0.886 Fit side-chains revert: symmetry clash REVERT: A 26 ILE cc_start: 0.7566 (mm) cc_final: 0.7311 (mt) REVERT: A 46 LEU cc_start: 0.7928 (tt) cc_final: 0.7668 (tp) REVERT: A 284 ASP cc_start: 0.8151 (m-30) cc_final: 0.7167 (m-30) REVERT: A 356 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.6182 (ttt180) REVERT: A 386 MET cc_start: 0.7334 (ttm) cc_final: 0.7118 (ttp) REVERT: A 392 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7162 (mt-10) REVERT: B 19 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.6624 (tpp80) REVERT: B 150 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.6387 (mmt90) REVERT: B 155 ASN cc_start: 0.7977 (t0) cc_final: 0.7684 (t0) REVERT: B 186 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7481 (p0) REVERT: B 303 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7856 (p0) REVERT: B 323 ASP cc_start: 0.7518 (m-30) cc_final: 0.7278 (m-30) REVERT: G 21 MET cc_start: 0.7753 (tmt) cc_final: 0.7485 (tmm) REVERT: N 34 MET cc_start: 0.8388 (mmm) cc_final: 0.8153 (mmp) REVERT: R 33 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7083 (mp) REVERT: R 254 ARG cc_start: 0.7399 (ptm-80) cc_final: 0.6852 (ptt180) REVERT: R 268 LEU cc_start: 0.8143 (tt) cc_final: 0.7779 (tp) outliers start: 29 outliers final: 6 residues processed: 127 average time/residue: 1.0450 time to fit residues: 141.9401 Evaluate side-chains 116 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 123 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.7980 chunk 56 optimal weight: 20.0000 chunk 23 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 80 optimal weight: 0.3980 chunk 44 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 195 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8289 Z= 0.158 Angle : 0.571 9.644 11273 Z= 0.267 Chirality : 0.041 0.305 1282 Planarity : 0.004 0.051 1433 Dihedral : 5.172 58.894 1378 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.49 % Allowed : 17.99 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.27), residues: 1020 helix: 2.34 (0.26), residues: 398 sheet: -0.70 (0.34), residues: 228 loop : -0.77 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP R 149 HIS 0.002 0.001 HIS B 62 PHE 0.013 0.001 PHE N 108 TYR 0.016 0.001 TYR R 251 ARG 0.013 0.001 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 111 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: A 26 ILE cc_start: 0.7554 (mm) cc_final: 0.7317 (mt) REVERT: A 46 LEU cc_start: 0.7896 (tt) cc_final: 0.7628 (tp) REVERT: A 209 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7099 (tm-30) REVERT: A 284 ASP cc_start: 0.8067 (m-30) cc_final: 0.7523 (m-30) REVERT: A 356 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.6478 (ttt180) REVERT: A 386 MET cc_start: 0.7375 (ttm) cc_final: 0.7158 (ttp) REVERT: A 392 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7173 (mt-10) REVERT: B 19 ARG cc_start: 0.7035 (OUTLIER) cc_final: 0.6699 (tpp80) REVERT: B 150 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.6372 (mmt90) REVERT: B 155 ASN cc_start: 0.7896 (t0) cc_final: 0.7610 (t0) REVERT: B 303 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7790 (p0) REVERT: B 323 ASP cc_start: 0.7461 (m-30) cc_final: 0.7254 (m-30) REVERT: N 34 MET cc_start: 0.8397 (mmm) cc_final: 0.8154 (mmt) REVERT: R 254 ARG cc_start: 0.7334 (ptm-80) cc_final: 0.6779 (ptt180) REVERT: R 268 LEU cc_start: 0.8115 (tt) cc_final: 0.7776 (tp) outliers start: 21 outliers final: 5 residues processed: 126 average time/residue: 1.1190 time to fit residues: 150.6345 Evaluate side-chains 116 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 105 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 123 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 60 optimal weight: 0.3980 chunk 58 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 195 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8289 Z= 0.161 Angle : 0.565 9.726 11273 Z= 0.266 Chirality : 0.041 0.309 1282 Planarity : 0.003 0.034 1433 Dihedral : 5.127 59.311 1378 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.66 % Allowed : 19.53 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.27), residues: 1020 helix: 2.25 (0.26), residues: 405 sheet: -0.62 (0.34), residues: 228 loop : -0.73 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP R 149 HIS 0.002 0.001 HIS A 220 PHE 0.013 0.001 PHE N 108 TYR 0.015 0.001 TYR R 251 ARG 0.007 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 109 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: A 26 ILE cc_start: 0.7551 (mm) cc_final: 0.7311 (mt) REVERT: A 46 LEU cc_start: 0.7846 (tt) cc_final: 0.7603 (tp) REVERT: A 209 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7107 (tm-30) REVERT: A 284 ASP cc_start: 0.8068 (m-30) cc_final: 0.7522 (m-30) REVERT: A 356 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.6451 (ttt180) REVERT: A 386 MET cc_start: 0.7353 (ttm) cc_final: 0.7140 (ttp) REVERT: A 392 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7183 (mt-10) REVERT: B 150 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.6352 (mmt90) REVERT: B 155 ASN cc_start: 0.7849 (t0) cc_final: 0.7563 (t0) REVERT: B 303 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7894 (p0) REVERT: G 21 MET cc_start: 0.7813 (tmt) cc_final: 0.7469 (tmm) REVERT: N 34 MET cc_start: 0.8405 (mmm) cc_final: 0.8169 (mmt) REVERT: R 158 GLN cc_start: 0.8550 (mm-40) cc_final: 0.8299 (mp10) REVERT: R 254 ARG cc_start: 0.7307 (ptm-80) cc_final: 0.6746 (ptt180) REVERT: R 268 LEU cc_start: 0.8087 (tt) cc_final: 0.7772 (tp) outliers start: 14 outliers final: 5 residues processed: 119 average time/residue: 1.1274 time to fit residues: 143.1600 Evaluate side-chains 117 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 123 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 0.0070 chunk 65 optimal weight: 0.0570 chunk 47 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 92 optimal weight: 0.0070 chunk 84 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.2734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8289 Z= 0.121 Angle : 0.543 9.838 11273 Z= 0.254 Chirality : 0.040 0.306 1282 Planarity : 0.004 0.052 1433 Dihedral : 4.942 59.658 1378 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.01 % Allowed : 19.29 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.27), residues: 1020 helix: 2.55 (0.27), residues: 398 sheet: -0.41 (0.35), residues: 217 loop : -0.73 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP R 149 HIS 0.003 0.001 HIS A 220 PHE 0.014 0.001 PHE A 212 TYR 0.015 0.001 TYR R 251 ARG 0.012 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 116 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: A 26 ILE cc_start: 0.7566 (mm) cc_final: 0.7348 (mt) REVERT: A 209 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7119 (tm-30) REVERT: A 213 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7730 (tt0) REVERT: A 386 MET cc_start: 0.7439 (ttm) cc_final: 0.7232 (ttm) REVERT: A 392 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7158 (mt-10) REVERT: B 155 ASN cc_start: 0.7817 (t0) cc_final: 0.7530 (t0) REVERT: B 323 ASP cc_start: 0.7679 (m-30) cc_final: 0.7472 (m-30) REVERT: N 34 MET cc_start: 0.8381 (mmm) cc_final: 0.8151 (mmt) REVERT: R 254 ARG cc_start: 0.7298 (ptm-80) cc_final: 0.6732 (ptt180) REVERT: R 268 LEU cc_start: 0.8019 (tt) cc_final: 0.7766 (tp) outliers start: 17 outliers final: 7 residues processed: 127 average time/residue: 1.0608 time to fit residues: 144.2789 Evaluate side-chains 119 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 123 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 89 optimal weight: 0.4980 chunk 58 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN R 195 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8289 Z= 0.195 Angle : 0.593 10.095 11273 Z= 0.276 Chirality : 0.042 0.319 1282 Planarity : 0.004 0.061 1433 Dihedral : 4.955 57.087 1378 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.89 % Allowed : 19.76 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.27), residues: 1020 helix: 2.36 (0.27), residues: 405 sheet: -0.51 (0.34), residues: 228 loop : -0.59 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP R 149 HIS 0.003 0.001 HIS A 220 PHE 0.013 0.001 PHE A 212 TYR 0.015 0.001 TYR R 251 ARG 0.014 0.001 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 108 time to evaluate : 0.915 Fit side-chains revert: symmetry clash REVERT: A 26 ILE cc_start: 0.7563 (mm) cc_final: 0.7311 (mt) REVERT: A 209 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7094 (tm-30) REVERT: A 284 ASP cc_start: 0.8044 (m-30) cc_final: 0.7579 (m-30) REVERT: A 356 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.6057 (ttt180) REVERT: A 392 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7142 (mt-10) REVERT: B 13 GLN cc_start: 0.8153 (tp40) cc_final: 0.7728 (tp40) REVERT: B 150 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.6433 (mmt90) REVERT: B 155 ASN cc_start: 0.7850 (t0) cc_final: 0.7580 (t0) REVERT: B 323 ASP cc_start: 0.7687 (m-30) cc_final: 0.7409 (m-30) REVERT: G 21 MET cc_start: 0.7754 (tmt) cc_final: 0.7435 (tmm) REVERT: N 110 VAL cc_start: 0.8830 (t) cc_final: 0.8488 (m) REVERT: R 254 ARG cc_start: 0.7289 (ptm-80) cc_final: 0.6713 (ptt180) REVERT: R 268 LEU cc_start: 0.8051 (tt) cc_final: 0.7758 (tp) outliers start: 16 outliers final: 7 residues processed: 119 average time/residue: 1.1948 time to fit residues: 151.3419 Evaluate side-chains 115 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 149 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 7.9990 chunk 66 optimal weight: 0.5980 chunk 99 optimal weight: 0.0970 chunk 91 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 61 optimal weight: 9.9990 chunk 48 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 195 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 8289 Z= 0.151 Angle : 0.565 9.947 11273 Z= 0.265 Chirality : 0.041 0.321 1282 Planarity : 0.004 0.062 1433 Dihedral : 4.869 55.388 1378 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.42 % Allowed : 20.59 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.27), residues: 1020 helix: 2.52 (0.27), residues: 398 sheet: -0.50 (0.34), residues: 227 loop : -0.47 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP R 149 HIS 0.003 0.001 HIS A 220 PHE 0.015 0.001 PHE N 108 TYR 0.015 0.001 TYR R 251 ARG 0.015 0.001 ARG A 317 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: A 26 ILE cc_start: 0.7520 (mm) cc_final: 0.7281 (mt) REVERT: A 209 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7064 (tm-30) REVERT: A 386 MET cc_start: 0.7342 (ttm) cc_final: 0.7123 (ttp) REVERT: A 392 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7142 (mt-10) REVERT: B 13 GLN cc_start: 0.8130 (tp40) cc_final: 0.7734 (tp40) REVERT: B 150 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.6433 (mmt90) REVERT: B 155 ASN cc_start: 0.7828 (t0) cc_final: 0.7539 (t0) REVERT: B 323 ASP cc_start: 0.7633 (m-30) cc_final: 0.7361 (m-30) REVERT: G 21 MET cc_start: 0.7664 (tmt) cc_final: 0.7360 (tmm) REVERT: N 110 VAL cc_start: 0.8775 (t) cc_final: 0.8368 (m) REVERT: R 254 ARG cc_start: 0.7280 (ptm-80) cc_final: 0.6529 (ptt180) REVERT: R 268 LEU cc_start: 0.8056 (tt) cc_final: 0.7776 (tp) outliers start: 12 outliers final: 6 residues processed: 118 average time/residue: 1.3040 time to fit residues: 164.1740 Evaluate side-chains 115 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 106 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 123 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN R 195 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.150550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.109876 restraints weight = 15986.367| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 3.49 r_work: 0.3003 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8289 Z= 0.359 Angle : 0.670 10.595 11273 Z= 0.320 Chirality : 0.046 0.317 1282 Planarity : 0.004 0.070 1433 Dihedral : 5.229 48.188 1378 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.66 % Allowed : 20.47 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.27), residues: 1020 helix: 2.14 (0.26), residues: 405 sheet: -0.55 (0.34), residues: 227 loop : -0.42 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP R 149 HIS 0.005 0.002 HIS B 311 PHE 0.024 0.002 PHE N 108 TYR 0.016 0.002 TYR R 251 ARG 0.015 0.001 ARG A 317 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3207.76 seconds wall clock time: 58 minutes 4.30 seconds (3484.30 seconds total)