Starting phenix.real_space_refine on Sat Apr 6 21:54:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyl_26184/04_2024/7tyl_26184_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyl_26184/04_2024/7tyl_26184.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyl_26184/04_2024/7tyl_26184.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyl_26184/04_2024/7tyl_26184.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyl_26184/04_2024/7tyl_26184_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyl_26184/04_2024/7tyl_26184_updated.pdb" } resolution = 3.3 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= -0.001 sd= 0.076 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 5691 2.51 5 N 1579 2.21 5 O 1645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A ASP 274": "OD1" <-> "OD2" Residue "A ASP 284": "OD1" <-> "OD2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "P TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 204": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8978 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1886 Classifications: {'peptide': 228} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "P" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 274 Unusual residues: {'NH2': 1} Classifications: {'peptide': 37, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 3, 'TRANS': 33} Chain: "R" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2815 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 16, 'TRANS': 352} Unresolved non-hydrogen bonds: 267 Unresolved non-hydrogen angles: 344 Unresolved non-hydrogen dihedrals: 236 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 3, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 177 Time building chain proxies: 5.01, per 1000 atoms: 0.56 Number of scatterers: 8978 At special positions: 0 Unit cell: (80.464, 100.152, 151.512, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1645 8.00 N 1579 7.00 C 5691 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, 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=2.03 Simple disulfide: pdb=" SG CYS P 2 " - pdb=" SG CYS P 7 " distance=2.03 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=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.18 Conformation dependent library (CDL) restraints added in 1.8 seconds 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2174 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 12 sheets defined 36.2% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 13 through 37 removed outlier: 3.598A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 267 through 277 Processing helix chain 'A' and resid 294 through 303 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 352 removed outlier: 3.974A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.540A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 23 Processing helix chain 'G' and resid 30 through 47 removed outlier: 3.551A pdb=" N CYS G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N GLU G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'P' and resid 5 through 18 removed outlier: 3.685A pdb=" N ALA P 8 " --> pdb=" O ALA P 5 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR P 9 " --> pdb=" O THR P 6 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLN P 10 " --> pdb=" O CYS P 7 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG P 11 " --> pdb=" O ALA P 8 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA P 13 " --> pdb=" O GLN P 10 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASN P 14 " --> pdb=" O ARG P 11 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL P 17 " --> pdb=" O ASN P 14 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG P 18 " --> pdb=" O PHE P 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 60 removed outlier: 3.674A pdb=" N MET R 49 " --> pdb=" O ARG R 45 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP R 50 " --> pdb=" O LYS R 46 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP R 57 " --> pdb=" O TYR R 53 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 135 No H-bonds generated for 'chain 'R' and resid 133 through 135' Processing helix chain 'R' and resid 138 through 155 Processing helix chain 'R' and resid 157 through 159 No H-bonds generated for 'chain 'R' and resid 157 through 159' Processing helix chain 'R' and resid 161 through 172 removed outlier: 3.872A pdb=" N ILE R 165 " --> pdb=" O PHE R 161 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER R 166 " --> pdb=" O THR R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 203 Processing helix chain 'R' and resid 209 through 213 Processing helix chain 'R' and resid 217 through 248 removed outlier: 3.554A pdb=" N MET R 237 " --> pdb=" O ASN R 233 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU R 238 " --> pdb=" O TYR R 234 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU R 247 " --> pdb=" O TYR R 243 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE R 248 " --> pdb=" O LEU R 244 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 266 Processing helix chain 'R' and resid 269 through 282 Proline residue: R 273 - end of helix removed outlier: 3.602A pdb=" N ILE R 276 " --> pdb=" O PRO R 273 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS R 277 " --> pdb=" O THR R 274 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE R 279 " --> pdb=" O ILE R 276 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR R 280 " --> pdb=" O HIS R 277 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA R 282 " --> pdb=" O ILE R 279 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 290 No H-bonds generated for 'chain 'R' and resid 288 through 290' Processing helix chain 'R' and resid 296 through 329 removed outlier: 3.645A pdb=" N TYR R 299 " --> pdb=" O HIS R 296 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N HIS R 302 " --> pdb=" O TYR R 299 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLY R 303 " --> pdb=" O ILE R 300 " (cutoff:3.500A) Proline residue: R 304 - end of helix removed outlier: 3.524A pdb=" N ASN R 312 " --> pdb=" O LEU R 309 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL R 320 " --> pdb=" O LEU R 317 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR R 325 " --> pdb=" O VAL R 322 " (cutoff:3.500A) Processing helix chain 'R' and resid 334 through 352 Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 358 removed outlier: 4.030A pdb=" N VAL R 358 " --> pdb=" O GLN R 355 " (cutoff:3.500A) Processing helix chain 'R' and resid 366 through 391 removed outlier: 4.034A pdb=" N GLN R 383 " --> pdb=" O LEU R 379 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N GLY R 384 " --> pdb=" O ILE R 380 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N PHE R 385 " --> pdb=" O HIS R 381 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE R 386 " --> pdb=" O PHE R 382 " (cutoff:3.500A) Processing helix chain 'R' and resid 396 through 407 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 362 removed outlier: 7.425A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN A 292 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL A 224 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET A 221 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.779A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.352A 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: 6.509A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR B 124 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 178 through 180 removed outlier: 3.588A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.325A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.385A 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: 6.666A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 276 through 278 Processing sheet with id= H, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.637A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.573A 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 8 removed outlier: 3.567A pdb=" N SER N 7 " --> pdb=" O SER N 21 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 10 through 12 Processing sheet with id= K, first strand: chain 'N' and resid 92 through 98 removed outlier: 3.550A pdb=" N VAL N 93 " --> pdb=" O GLN N 39 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN N 35 " --> pdb=" O ALA N 97 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'R' and resid 92 through 94 348 hydrogen bonds defined for protein. 930 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: 2.78 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1463 1.32 - 1.44: 2561 1.44 - 1.57: 5064 1.57 - 1.69: 0 1.69 - 1.82: 88 Bond restraints: 9176 Sorted by residual: bond pdb=" N ASP R 215 " pdb=" CA ASP R 215 " ideal model delta sigma weight residual 1.458 1.492 -0.034 7.40e-03 1.83e+04 2.11e+01 bond pdb=" N THR A 285 " pdb=" CA THR A 285 " ideal model delta sigma weight residual 1.455 1.507 -0.052 1.21e-02 6.83e+03 1.82e+01 bond pdb=" C VAL A 287 " pdb=" O VAL A 287 " ideal model delta sigma weight residual 1.236 1.194 0.042 1.04e-02 9.25e+03 1.62e+01 bond pdb=" CA SER A 286 " pdb=" CB SER A 286 " ideal model delta sigma weight residual 1.529 1.463 0.066 1.65e-02 3.67e+03 1.58e+01 bond pdb=" N LYS A 271 " pdb=" CA LYS A 271 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.28e-02 6.10e+03 1.08e+01 ... (remaining 9171 not shown) Histogram of bond angle deviations from ideal: 100.51 - 107.27: 290 107.27 - 114.02: 5125 114.02 - 120.78: 3953 120.78 - 127.54: 2988 127.54 - 134.30: 95 Bond angle restraints: 12451 Sorted by residual: angle pdb=" N LEU R 222 " pdb=" CA LEU R 222 " pdb=" C LEU R 222 " ideal model delta sigma weight residual 112.54 105.16 7.38 1.22e+00 6.72e-01 3.66e+01 angle pdb=" N ARG A 283 " pdb=" CA ARG A 283 " pdb=" C ARG A 283 " ideal model delta sigma weight residual 110.53 102.88 7.65 1.29e+00 6.01e-01 3.52e+01 angle pdb=" CA ARG A 283 " pdb=" C ARG A 283 " pdb=" O ARG A 283 " ideal model delta sigma weight residual 121.94 117.25 4.69 1.15e+00 7.56e-01 1.66e+01 angle pdb=" CA ASP R 215 " pdb=" C ASP R 215 " pdb=" N PRO R 216 " ideal model delta sigma weight residual 118.09 121.28 -3.19 8.20e-01 1.49e+00 1.51e+01 angle pdb=" CA SER A 286 " pdb=" C SER A 286 " pdb=" O SER A 286 " ideal model delta sigma weight residual 121.89 117.44 4.45 1.17e+00 7.31e-01 1.45e+01 ... (remaining 12446 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 5021 17.73 - 35.47: 352 35.47 - 53.20: 62 53.20 - 70.94: 14 70.94 - 88.67: 7 Dihedral angle restraints: 5456 sinusoidal: 2093 harmonic: 3363 Sorted by residual: dihedral pdb=" CB CYS R 72 " pdb=" SG CYS R 72 " pdb=" SG CYS R 112 " pdb=" CB CYS R 112 " ideal model delta sinusoidal sigma weight residual -86.00 -167.34 81.34 1 1.00e+01 1.00e-02 8.15e+01 dihedral pdb=" CB CYS P 2 " pdb=" SG CYS P 2 " pdb=" SG CYS P 7 " pdb=" CB CYS P 7 " ideal model delta sinusoidal sigma weight residual 93.00 136.87 -43.87 1 1.00e+01 1.00e-02 2.68e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 131.46 -38.46 1 1.00e+01 1.00e-02 2.08e+01 ... (remaining 5453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1282 0.073 - 0.145: 100 0.145 - 0.218: 8 0.218 - 0.290: 2 0.290 - 0.363: 1 Chirality restraints: 1393 Sorted by residual: chirality pdb=" CA ARG A 283 " pdb=" N ARG A 283 " pdb=" C ARG A 283 " pdb=" CB ARG A 283 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CA ARG R 214 " pdb=" N ARG R 214 " pdb=" C ARG R 214 " pdb=" CB ARG R 214 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB ILE R 221 " pdb=" CA ILE R 221 " pdb=" CG1 ILE R 221 " pdb=" CG2 ILE R 221 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1390 not shown) Planarity restraints: 1601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG R 213 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.96e+00 pdb=" C ARG R 213 " 0.042 2.00e-02 2.50e+03 pdb=" O ARG R 213 " -0.016 2.00e-02 2.50e+03 pdb=" N ARG R 214 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 279 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.88e+00 pdb=" C ASN A 279 " -0.034 2.00e-02 2.50e+03 pdb=" O ASN A 279 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS A 280 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 282 " 0.006 2.00e-02 2.50e+03 1.32e-02 1.73e+00 pdb=" C LEU A 282 " -0.023 2.00e-02 2.50e+03 pdb=" O LEU A 282 " 0.008 2.00e-02 2.50e+03 pdb=" N ARG A 283 " 0.008 2.00e-02 2.50e+03 ... (remaining 1598 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2211 2.79 - 3.32: 8337 3.32 - 3.84: 14642 3.84 - 4.37: 17352 4.37 - 4.90: 30167 Nonbonded interactions: 72709 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.260 2.440 nonbonded pdb=" O GLN A 236 " pdb=" ND2 ASN A 239 " model vdw 2.262 2.520 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.290 2.440 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.309 2.440 nonbonded pdb=" O SER G 8 " pdb=" OG SER G 8 " model vdw 2.316 2.440 ... (remaining 72704 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: 1.480 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: 5.420 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 27.240 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6383 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9176 Z= 0.196 Angle : 0.591 7.649 12451 Z= 0.389 Chirality : 0.043 0.363 1393 Planarity : 0.003 0.032 1601 Dihedral : 12.732 88.670 3261 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.75 % Favored : 98.07 % Rotamer: Outliers : 0.43 % Allowed : 2.34 % Favored : 97.24 % 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: -2.52 (0.22), residues: 1140 helix: -1.93 (0.18), residues: 411 sheet: -1.17 (0.31), residues: 258 loop : -1.49 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 281 HIS 0.003 0.000 HIS R 121 PHE 0.008 0.001 PHE N 108 TYR 0.012 0.001 TYR N 60 ARG 0.004 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 141 time to evaluate : 0.890 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6237 (mt-10) cc_final: 0.6017 (mt-10) outliers start: 4 outliers final: 1 residues processed: 145 average time/residue: 0.2363 time to fit residues: 46.3726 Evaluate side-chains 115 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 221 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 0.0870 chunk 56 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 0.4980 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 31 GLN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 156 GLN B 340 ASN G 44 HIS P 22 ASN R 184 HIS R 296 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6523 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9176 Z= 0.179 Angle : 0.507 8.179 12451 Z= 0.267 Chirality : 0.040 0.146 1393 Planarity : 0.004 0.039 1601 Dihedral : 3.478 30.344 1256 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.59 % Allowed : 8.40 % Favored : 90.01 % 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: -0.86 (0.24), residues: 1140 helix: 0.33 (0.25), residues: 412 sheet: -0.72 (0.32), residues: 244 loop : -1.19 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 236 HIS 0.005 0.001 HIS A 357 PHE 0.014 0.001 PHE R 359 TYR 0.013 0.001 TYR N 95 ARG 0.008 0.000 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 128 time to evaluate : 0.904 Fit side-chains REVERT: R 55 CYS cc_start: -0.0209 (OUTLIER) cc_final: -0.0635 (p) outliers start: 15 outliers final: 8 residues processed: 138 average time/residue: 0.2347 time to fit residues: 44.5912 Evaluate side-chains 124 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 115 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 55 CYS Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 293 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 20.0000 chunk 68 optimal weight: 0.0370 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 340 ASN P 22 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9176 Z= 0.238 Angle : 0.528 8.872 12451 Z= 0.275 Chirality : 0.041 0.160 1393 Planarity : 0.004 0.037 1601 Dihedral : 3.789 24.881 1256 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.23 % Allowed : 12.11 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.25), residues: 1140 helix: 0.81 (0.26), residues: 413 sheet: -0.85 (0.32), residues: 246 loop : -1.17 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 236 HIS 0.006 0.001 HIS A 357 PHE 0.016 0.002 PHE B 151 TYR 0.014 0.001 TYR A 339 ARG 0.014 0.001 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 117 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: A 216 LYS cc_start: 0.6651 (mptt) cc_final: 0.6419 (pttt) REVERT: G 37 LEU cc_start: 0.6368 (OUTLIER) cc_final: 0.6103 (mp) outliers start: 21 outliers final: 13 residues processed: 133 average time/residue: 0.2291 time to fit residues: 42.7615 Evaluate side-chains 125 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 293 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 9.9990 chunk 52 optimal weight: 0.0970 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 96 optimal weight: 0.0070 chunk 28 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN ** P 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 201 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9176 Z= 0.151 Angle : 0.475 9.315 12451 Z= 0.246 Chirality : 0.039 0.147 1393 Planarity : 0.003 0.035 1601 Dihedral : 3.520 16.408 1254 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.13 % Allowed : 12.54 % Favored : 85.33 % 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: -0.36 (0.25), residues: 1140 helix: 1.09 (0.27), residues: 411 sheet: -0.75 (0.32), residues: 246 loop : -1.07 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 236 HIS 0.004 0.001 HIS A 357 PHE 0.012 0.001 PHE N 108 TYR 0.014 0.001 TYR N 95 ARG 0.013 0.000 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 0.966 Fit side-chains REVERT: A 216 LYS cc_start: 0.6624 (mptt) cc_final: 0.6408 (pttt) REVERT: G 37 LEU cc_start: 0.6275 (OUTLIER) cc_final: 0.6053 (mp) REVERT: R 55 CYS cc_start: -0.0081 (OUTLIER) cc_final: -0.0704 (p) outliers start: 20 outliers final: 11 residues processed: 131 average time/residue: 0.2464 time to fit residues: 43.8054 Evaluate side-chains 124 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain R residue 55 CYS Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 293 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 0.0000 chunk 44 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 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 : 0.003 0.039 9176 Z= 0.202 Angle : 0.494 8.202 12451 Z= 0.258 Chirality : 0.040 0.156 1393 Planarity : 0.004 0.035 1601 Dihedral : 3.634 17.832 1254 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.44 % Allowed : 13.82 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.25), residues: 1140 helix: 1.15 (0.27), residues: 414 sheet: -0.79 (0.32), residues: 246 loop : -1.09 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 236 HIS 0.005 0.001 HIS A 357 PHE 0.013 0.001 PHE B 151 TYR 0.014 0.001 TYR N 95 ARG 0.008 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 0.964 Fit side-chains REVERT: A 216 LYS cc_start: 0.6600 (mptt) cc_final: 0.6379 (pttt) REVERT: B 192 LEU cc_start: 0.6542 (OUTLIER) cc_final: 0.6177 (pt) outliers start: 23 outliers final: 16 residues processed: 130 average time/residue: 0.2273 time to fit residues: 40.4558 Evaluate side-chains 130 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 113 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 293 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 0.4980 chunk 103 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 0.2980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9176 Z= 0.163 Angle : 0.489 11.828 12451 Z= 0.250 Chirality : 0.040 0.213 1393 Planarity : 0.003 0.036 1601 Dihedral : 3.549 17.786 1254 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.34 % Allowed : 14.67 % Favored : 83.00 % 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: -0.26 (0.26), residues: 1140 helix: 1.23 (0.27), residues: 415 sheet: -0.83 (0.32), residues: 258 loop : -0.99 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 236 HIS 0.004 0.001 HIS A 357 PHE 0.010 0.001 PHE B 241 TYR 0.014 0.001 TYR N 95 ARG 0.008 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 117 time to evaluate : 0.967 Fit side-chains REVERT: A 216 LYS cc_start: 0.6577 (mptt) cc_final: 0.6356 (pttt) REVERT: R 284 TYR cc_start: 0.5107 (m-80) cc_final: 0.4733 (m-80) outliers start: 22 outliers final: 20 residues processed: 133 average time/residue: 0.2240 time to fit residues: 40.7858 Evaluate side-chains 131 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 111 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 293 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 40.0000 chunk 60 optimal weight: 6.9990 chunk 90 optimal weight: 0.5980 chunk 59 optimal weight: 0.0270 chunk 106 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 65 optimal weight: 0.0030 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 32 optimal weight: 0.2980 overall best weight: 0.3648 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 257 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9176 Z= 0.130 Angle : 0.468 11.218 12451 Z= 0.242 Chirality : 0.039 0.186 1393 Planarity : 0.003 0.035 1601 Dihedral : 3.423 16.648 1254 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.23 % Allowed : 14.88 % Favored : 82.89 % 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: -0.14 (0.26), residues: 1140 helix: 1.32 (0.27), residues: 415 sheet: -0.72 (0.32), residues: 258 loop : -0.95 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.003 0.001 HIS A 357 PHE 0.010 0.001 PHE B 241 TYR 0.014 0.001 TYR N 95 ARG 0.008 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 0.960 Fit side-chains REVERT: A 216 LYS cc_start: 0.6540 (mptt) cc_final: 0.6320 (pttt) REVERT: R 284 TYR cc_start: 0.5129 (m-80) cc_final: 0.4769 (m-80) outliers start: 21 outliers final: 18 residues processed: 132 average time/residue: 0.2295 time to fit residues: 41.4338 Evaluate side-chains 128 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 159 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 68 optimal weight: 0.4980 chunk 72 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 99 optimal weight: 0.0370 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 14 ASN ** P 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 296 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9176 Z= 0.167 Angle : 0.504 13.289 12451 Z= 0.255 Chirality : 0.040 0.160 1393 Planarity : 0.003 0.035 1601 Dihedral : 3.461 18.290 1254 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.44 % Allowed : 15.09 % Favored : 82.47 % 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: -0.09 (0.26), residues: 1140 helix: 1.36 (0.27), residues: 415 sheet: -0.67 (0.33), residues: 253 loop : -0.93 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 236 HIS 0.004 0.001 HIS A 357 PHE 0.011 0.001 PHE B 151 TYR 0.013 0.001 TYR N 95 ARG 0.004 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 113 time to evaluate : 0.952 Fit side-chains REVERT: A 216 LYS cc_start: 0.6560 (mptt) cc_final: 0.6308 (pttt) REVERT: R 284 TYR cc_start: 0.5156 (m-80) cc_final: 0.4813 (m-80) outliers start: 23 outliers final: 20 residues processed: 129 average time/residue: 0.2529 time to fit residues: 44.8474 Evaluate side-chains 130 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 110 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 159 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 78 optimal weight: 50.0000 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 chunk 65 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN P 22 ASN R 186 ASN R 296 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9176 Z= 0.219 Angle : 0.526 12.794 12451 Z= 0.270 Chirality : 0.041 0.159 1393 Planarity : 0.003 0.035 1601 Dihedral : 3.623 19.256 1254 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.34 % Allowed : 15.52 % Favored : 82.15 % 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: -0.19 (0.26), residues: 1140 helix: 1.22 (0.27), residues: 422 sheet: -0.70 (0.33), residues: 253 loop : -0.98 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 236 HIS 0.005 0.001 HIS A 357 PHE 0.015 0.001 PHE B 151 TYR 0.023 0.001 TYR N 95 ARG 0.004 0.000 ARG R 258 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 113 time to evaluate : 0.916 Fit side-chains REVERT: A 216 LYS cc_start: 0.6562 (mptt) cc_final: 0.6303 (pttt) REVERT: N 120 GLN cc_start: 0.7051 (mm-40) cc_final: 0.6804 (mm-40) REVERT: R 284 TYR cc_start: 0.5164 (m-80) cc_final: 0.4804 (m-80) outliers start: 22 outliers final: 21 residues processed: 128 average time/residue: 0.2389 time to fit residues: 41.3874 Evaluate side-chains 130 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 109 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 159 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 110 optimal weight: 0.2980 chunk 101 optimal weight: 1.9990 chunk 88 optimal weight: 0.1980 chunk 9 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 296 HIS R 405 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9176 Z= 0.152 Angle : 0.519 15.807 12451 Z= 0.261 Chirality : 0.039 0.164 1393 Planarity : 0.003 0.035 1601 Dihedral : 3.490 18.803 1254 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.02 % Allowed : 15.83 % Favored : 82.15 % 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: -0.06 (0.26), residues: 1140 helix: 1.39 (0.27), residues: 415 sheet: -0.67 (0.33), residues: 253 loop : -0.92 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 236 HIS 0.004 0.001 HIS A 357 PHE 0.012 0.001 PHE R 269 TYR 0.022 0.001 TYR N 95 ARG 0.004 0.000 ARG N 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 0.992 Fit side-chains REVERT: A 216 LYS cc_start: 0.6532 (mptt) cc_final: 0.6278 (pttt) REVERT: B 45 MET cc_start: 0.1936 (mmm) cc_final: 0.1557 (tpt) REVERT: B 234 PHE cc_start: 0.7472 (OUTLIER) cc_final: 0.6946 (t80) REVERT: R 284 TYR cc_start: 0.5250 (m-80) cc_final: 0.4899 (m-80) outliers start: 19 outliers final: 17 residues processed: 126 average time/residue: 0.2504 time to fit residues: 42.9223 Evaluate side-chains 128 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 159 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 24 optimal weight: 0.3980 chunk 88 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 90 optimal weight: 0.0970 chunk 11 optimal weight: 0.1980 chunk 16 optimal weight: 6.9990 chunk 77 optimal weight: 50.0000 chunk 5 optimal weight: 0.0030 chunk 63 optimal weight: 0.7980 overall best weight: 0.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** P 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 296 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.246427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.206934 restraints weight = 10255.943| |-----------------------------------------------------------------------------| r_work (start): 0.4269 rms_B_bonded: 2.00 r_work: 0.3997 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9176 Z= 0.131 Angle : 0.501 15.967 12451 Z= 0.253 Chirality : 0.039 0.162 1393 Planarity : 0.003 0.035 1601 Dihedral : 3.373 17.478 1254 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.91 % Allowed : 15.73 % Favored : 82.36 % 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: 0.02 (0.26), residues: 1140 helix: 1.46 (0.27), residues: 415 sheet: -0.58 (0.34), residues: 249 loop : -0.90 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.003 0.001 HIS A 357 PHE 0.009 0.001 PHE B 241 TYR 0.020 0.001 TYR N 95 ARG 0.008 0.000 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2172.42 seconds wall clock time: 40 minutes 20.26 seconds (2420.26 seconds total)