Starting phenix.real_space_refine on Thu Mar 14 08:11:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xw9_33494/03_2024/7xw9_33494_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xw9_33494/03_2024/7xw9_33494.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xw9_33494/03_2024/7xw9_33494.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xw9_33494/03_2024/7xw9_33494.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xw9_33494/03_2024/7xw9_33494_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xw9_33494/03_2024/7xw9_33494_updated.pdb" } resolution = 2.7 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= 0.002 sd= 0.033 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 5729 2.51 5 N 1533 2.21 5 O 1663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8988 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2294 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 278} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1862 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "S" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "L" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Unusual residues: {'NH2': 1} Classifications: {'peptide': 3, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 1, 'TRANS': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.45, per 1000 atoms: 0.61 Number of scatterers: 8988 At special positions: 0 Unit cell: (116.61, 111.54, 123.708, 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 1663 8.00 N 1533 7.00 C 5729 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 179 " distance=2.04 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " 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: 3.31 Conformation dependent library (CDL) restraints added in 1.7 seconds 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 14 sheets defined 34.2% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'R' and resid 24 through 52 Processing helix chain 'R' and resid 59 through 78 Processing helix chain 'R' and resid 80 through 88 removed outlier: 3.692A pdb=" N THR R 84 " --> pdb=" O LEU R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 128 removed outlier: 4.031A pdb=" N SER R 113 " --> pdb=" O ILE R 109 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 136 Processing helix chain 'R' and resid 139 through 163 removed outlier: 3.837A pdb=" N TYR R 156 " --> pdb=" O PHE R 152 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU R 163 " --> pdb=" O LEU R 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 219 removed outlier: 4.095A pdb=" N SER R 189 " --> pdb=" O ASN R 186 " (cutoff:3.500A) Proline residue: R 190 - end of helix removed outlier: 3.503A pdb=" N MET R 194 " --> pdb=" O ILE R 191 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL R 198 " --> pdb=" O ASP R 195 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE R 199 " --> pdb=" O PHE R 196 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR R 200 " --> pdb=" O GLY R 197 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL R 201 " --> pdb=" O VAL R 198 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL R 202 " --> pdb=" O PHE R 199 " (cutoff:3.500A) Proline residue: R 203 - end of helix removed outlier: 3.562A pdb=" N LEU R 206 " --> pdb=" O PRO R 203 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL R 209 " --> pdb=" O LEU R 206 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU R 210 " --> pdb=" O ALA R 207 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR R 211 " --> pdb=" O THR R 208 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE R 219 " --> pdb=" O ARG R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 291 removed outlier: 4.051A pdb=" N GLN R 263 " --> pdb=" O SER R 259 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL R 264 " --> pdb=" O SER R 260 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR R 265 " --> pdb=" O ARG R 261 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS R 266 " --> pdb=" O LYS R 262 " (cutoff:3.500A) Proline residue: R 281 - end of helix removed outlier: 3.648A pdb=" N SER R 290 " --> pdb=" O VAL R 286 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE R 291 " --> pdb=" O VAL R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 301 through 320 Proline residue: R 317 - end of helix Processing helix chain 'R' and resid 326 through 334 Processing helix chain 'A' and resid 7 through 32 removed outlier: 4.143A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 281 through 292 Processing helix chain 'A' and resid 309 through 318 Processing helix chain 'A' and resid 323 through 326 No H-bonds generated for 'chain 'A' and resid 323 through 326' Processing helix chain 'A' and resid 347 through 365 removed outlier: 3.678A pdb=" N ALA A 352 " --> pdb=" O ARG A 348 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A 360 " --> pdb=" O ILE A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 405 removed outlier: 3.560A pdb=" N ARG A 404 " --> pdb=" O GLN A 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.042A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 23 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 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'R' and resid 164 through 168 Processing sheet with id= B, first strand: chain 'A' and resid 302 through 307 removed outlier: 6.218A pdb=" N ILE A 269 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N PHE A 305 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N PHE A 271 " --> pdb=" O PHE A 305 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ASN A 307 " --> pdb=" O PHE A 271 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A 273 " --> pdb=" O ASN A 307 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA A 268 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N VAL A 249 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.783A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.843A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.552A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.729A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.696A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.418A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.625A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.513A pdb=" N THR S 78 " --> pdb=" O ASP S 73 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.521A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.660A pdb=" N LYS S 232 " --> pdb=" O VAL S 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'S' and resid 143 through 148 removed outlier: 3.635A pdb=" N ALA S 199 " --> pdb=" O SER S 196 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'S' and resid 214 through 219 removed outlier: 5.873A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) 394 hydrogen bonds defined for protein. 1089 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: 2.75 Time building geometry restraints manager: 3.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 1449 1.30 - 1.43: 2505 1.43 - 1.57: 5132 1.57 - 1.70: 0 1.70 - 1.83: 91 Bond restraints: 9177 Sorted by residual: bond pdb=" CG PCA L 1 " pdb=" CD PCA L 1 " ideal model delta sigma weight residual 1.517 1.420 0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" CA HIS L 2 " pdb=" C HIS L 2 " ideal model delta sigma weight residual 1.525 1.424 0.101 2.10e-02 2.27e+03 2.29e+01 bond pdb=" N PCA L 1 " pdb=" CD PCA L 1 " ideal model delta sigma weight residual 1.345 1.253 0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" N PCA L 1 " pdb=" CA PCA L 1 " ideal model delta sigma weight residual 1.458 1.379 0.079 1.90e-02 2.77e+03 1.73e+01 bond pdb=" CA PCA L 1 " pdb=" CB PCA L 1 " ideal model delta sigma weight residual 1.530 1.456 0.074 2.00e-02 2.50e+03 1.37e+01 ... (remaining 9172 not shown) Histogram of bond angle deviations from ideal: 100.27 - 107.07: 224 107.07 - 113.87: 5133 113.87 - 120.67: 3749 120.67 - 127.47: 3245 127.47 - 134.27: 85 Bond angle restraints: 12436 Sorted by residual: angle pdb=" N SER A 44 " pdb=" CA SER A 44 " pdb=" C SER A 44 " ideal model delta sigma weight residual 111.28 126.08 -14.80 1.09e+00 8.42e-01 1.84e+02 angle pdb=" CA PRO L 3 " pdb=" C PRO L 3 " pdb=" N NH2 L 4 " ideal model delta sigma weight residual 116.20 126.12 -9.92 2.00e+00 2.50e-01 2.46e+01 angle pdb=" C VAL R 201 " pdb=" N VAL R 202 " pdb=" CA VAL R 202 " ideal model delta sigma weight residual 122.13 113.55 8.58 1.85e+00 2.92e-01 2.15e+01 angle pdb=" C GLU A 43 " pdb=" N SER A 44 " pdb=" CA SER A 44 " ideal model delta sigma weight residual 120.28 126.31 -6.03 1.34e+00 5.57e-01 2.02e+01 angle pdb=" N TRP R 300 " pdb=" CA TRP R 300 " pdb=" C TRP R 300 " ideal model delta sigma weight residual 114.56 109.00 5.56 1.27e+00 6.20e-01 1.92e+01 ... (remaining 12431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.42: 4916 15.42 - 30.85: 426 30.85 - 46.27: 85 46.27 - 61.70: 18 61.70 - 77.12: 6 Dihedral angle restraints: 5451 sinusoidal: 2129 harmonic: 3322 Sorted by residual: dihedral pdb=" CA LEU R 22 " pdb=" C LEU R 22 " pdb=" N GLU R 23 " pdb=" CA GLU R 23 " ideal model delta harmonic sigma weight residual 180.00 156.11 23.89 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA TYR S 101 " pdb=" C TYR S 101 " pdb=" N TYR S 102 " pdb=" CA TYR S 102 " ideal model delta harmonic sigma weight residual 180.00 159.82 20.18 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA GLU R 298 " pdb=" C GLU R 298 " pdb=" N ASN R 299 " pdb=" CA ASN R 299 " ideal model delta harmonic sigma weight residual 180.00 161.53 18.47 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 5448 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1300 0.092 - 0.184: 102 0.184 - 0.276: 3 0.276 - 0.369: 1 0.369 - 0.461: 2 Chirality restraints: 1408 Sorted by residual: chirality pdb=" CA SER A 44 " pdb=" N SER A 44 " pdb=" C SER A 44 " pdb=" CB SER A 44 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.31e+00 chirality pdb=" CA PRO L 3 " pdb=" N PRO L 3 " pdb=" C PRO L 3 " pdb=" CB PRO L 3 " both_signs ideal model delta sigma weight residual False 2.72 2.30 0.42 2.00e-01 2.50e+01 4.38e+00 chirality pdb=" CB VAL R 202 " pdb=" CA VAL R 202 " pdb=" CG1 VAL R 202 " pdb=" CG2 VAL R 202 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 1405 not shown) Planarity restraints: 1574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N PCA L 1 " -0.064 2.00e-02 2.50e+03 4.54e-02 2.58e+01 pdb=" CA PCA L 1 " 0.057 2.00e-02 2.50e+03 pdb=" CG PCA L 1 " -0.023 2.00e-02 2.50e+03 pdb=" CD PCA L 1 " -0.016 2.00e-02 2.50e+03 pdb=" OE PCA L 1 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 198 " 0.015 2.00e-02 2.50e+03 2.95e-02 8.69e+00 pdb=" C VAL R 198 " -0.051 2.00e-02 2.50e+03 pdb=" O VAL R 198 " 0.019 2.00e-02 2.50e+03 pdb=" N PHE R 199 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 40 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C GLY A 40 " -0.039 2.00e-02 2.50e+03 pdb=" O GLY A 40 " 0.015 2.00e-02 2.50e+03 pdb=" N THR A 41 " 0.013 2.00e-02 2.50e+03 ... (remaining 1571 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 328 2.71 - 3.26: 8509 3.26 - 3.81: 14286 3.81 - 4.35: 18249 4.35 - 4.90: 31425 Nonbonded interactions: 72797 Sorted by model distance: nonbonded pdb=" OD1 ASP A 274 " pdb=" NZ LYS A 308 " model vdw 2.167 2.520 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.214 2.440 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.264 2.440 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.266 2.440 nonbonded pdb=" OE1 GLU A 234 " pdb=" NE2 HIS A 245 " model vdw 2.326 2.520 ... (remaining 72792 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.380 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: 1.990 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 27.460 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:12.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 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 : 0.005 0.104 9177 Z= 0.354 Angle : 0.686 14.803 12436 Z= 0.392 Chirality : 0.050 0.461 1408 Planarity : 0.005 0.064 1574 Dihedral : 12.265 77.123 3305 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.37 (0.25), residues: 1124 helix: 0.43 (0.26), residues: 384 sheet: 1.23 (0.32), residues: 272 loop : -0.41 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 91 HIS 0.011 0.001 HIS L 2 PHE 0.021 0.002 PHE R 161 TYR 0.021 0.002 TYR R 24 ARG 0.016 0.001 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 0.939 Fit side-chains REVERT: R 139 PHE cc_start: 0.8130 (t80) cc_final: 0.7129 (t80) REVERT: R 147 ILE cc_start: 0.8123 (pt) cc_final: 0.7897 (mt) REVERT: A 32 ARG cc_start: 0.6777 (mmt90) cc_final: 0.6502 (mmt90) REVERT: A 314 GLU cc_start: 0.6772 (mp0) cc_final: 0.6408 (mp0) REVERT: A 329 GLU cc_start: 0.6658 (mp0) cc_final: 0.6429 (mp0) REVERT: A 396 ASP cc_start: 0.6708 (m-30) cc_final: 0.6473 (m-30) REVERT: B 175 GLN cc_start: 0.7519 (mm-40) cc_final: 0.7294 (mm-40) REVERT: B 258 ASP cc_start: 0.6670 (t70) cc_final: 0.6390 (t70) REVERT: S 57 THR cc_start: 0.8332 (p) cc_final: 0.8104 (t) outliers start: 0 outliers final: 1 residues processed: 242 average time/residue: 1.1347 time to fit residues: 293.1240 Evaluate side-chains 227 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 226 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 0.0170 chunk 52 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 0.0970 overall best weight: 0.8218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 61 ASN R 110 ASN A 402 ASN B 259 GLN B 293 ASN B 340 ASN S 167 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9177 Z= 0.208 Angle : 0.548 9.860 12436 Z= 0.291 Chirality : 0.043 0.266 1408 Planarity : 0.004 0.050 1574 Dihedral : 4.529 38.896 1254 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.94 % Allowed : 8.27 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.26), residues: 1124 helix: 1.43 (0.27), residues: 379 sheet: 1.26 (0.31), residues: 299 loop : -0.34 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.019 0.001 PHE R 161 TYR 0.013 0.002 TYR R 24 ARG 0.007 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 235 time to evaluate : 0.969 Fit side-chains revert: symmetry clash REVERT: R 315 ILE cc_start: 0.8192 (mt) cc_final: 0.7983 (mp) REVERT: A 32 ARG cc_start: 0.6837 (mmt90) cc_final: 0.6596 (mmt90) REVERT: A 243 ASN cc_start: 0.8577 (m-40) cc_final: 0.8154 (m110) REVERT: A 329 GLU cc_start: 0.6662 (mp0) cc_final: 0.6433 (mp0) REVERT: A 396 ASP cc_start: 0.6719 (m-30) cc_final: 0.6475 (m-30) REVERT: B 22 ARG cc_start: 0.7019 (mtt90) cc_final: 0.6557 (mmm-85) REVERT: B 175 GLN cc_start: 0.7521 (mm-40) cc_final: 0.7297 (mm-40) REVERT: B 258 ASP cc_start: 0.6645 (t70) cc_final: 0.5997 (t70) REVERT: S 180 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.7307 (ptp) outliers start: 19 outliers final: 9 residues processed: 242 average time/residue: 1.2174 time to fit residues: 312.7154 Evaluate side-chains 236 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 226 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 ASN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9177 Z= 0.216 Angle : 0.540 11.157 12436 Z= 0.284 Chirality : 0.043 0.270 1408 Planarity : 0.004 0.048 1574 Dihedral : 4.543 43.228 1254 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.45 % Allowed : 11.43 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.18 (0.26), residues: 1124 helix: 1.68 (0.27), residues: 380 sheet: 1.21 (0.31), residues: 305 loop : -0.29 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 82 HIS 0.003 0.001 HIS B 62 PHE 0.021 0.001 PHE R 139 TYR 0.012 0.001 TYR S 178 ARG 0.007 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 227 time to evaluate : 0.758 Fit side-chains revert: symmetry clash REVERT: R 152 PHE cc_start: 0.7271 (m-10) cc_final: 0.7049 (m-80) REVERT: A 243 ASN cc_start: 0.8530 (m-40) cc_final: 0.8110 (m110) REVERT: A 329 GLU cc_start: 0.6703 (mp0) cc_final: 0.6267 (mp0) REVERT: A 389 ARG cc_start: 0.7959 (mtm180) cc_final: 0.7728 (mtm180) REVERT: A 396 ASP cc_start: 0.6729 (m-30) cc_final: 0.6468 (m-30) REVERT: B 175 GLN cc_start: 0.7502 (mm-40) cc_final: 0.7297 (mm-40) REVERT: B 212 ASP cc_start: 0.7755 (p0) cc_final: 0.7473 (p0) REVERT: B 258 ASP cc_start: 0.6684 (t70) cc_final: 0.6170 (t70) REVERT: S 180 MET cc_start: 0.7585 (OUTLIER) cc_final: 0.7376 (ptp) outliers start: 24 outliers final: 14 residues processed: 237 average time/residue: 1.2002 time to fit residues: 302.3322 Evaluate side-chains 237 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 222 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 25 GLN A 402 ASN B 259 GLN B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 9177 Z= 0.372 Angle : 0.605 11.766 12436 Z= 0.321 Chirality : 0.046 0.261 1408 Planarity : 0.004 0.050 1574 Dihedral : 4.876 41.749 1254 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.86 % Allowed : 13.78 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.26), residues: 1124 helix: 1.55 (0.27), residues: 381 sheet: 1.04 (0.30), residues: 309 loop : -0.33 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 82 HIS 0.007 0.001 HIS B 62 PHE 0.016 0.002 PHE R 296 TYR 0.024 0.002 TYR B 105 ARG 0.009 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 226 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7140 (mt-10) REVERT: A 243 ASN cc_start: 0.8561 (m-40) cc_final: 0.8114 (m110) REVERT: A 329 GLU cc_start: 0.6780 (mp0) cc_final: 0.6541 (mp0) REVERT: A 396 ASP cc_start: 0.6762 (m-30) cc_final: 0.6502 (m-30) REVERT: B 175 GLN cc_start: 0.7507 (mm-40) cc_final: 0.7286 (mm-40) REVERT: B 258 ASP cc_start: 0.6806 (t70) cc_final: 0.6528 (t70) REVERT: S 180 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.7497 (ptp) outliers start: 28 outliers final: 16 residues processed: 233 average time/residue: 1.2748 time to fit residues: 315.2589 Evaluate side-chains 234 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 217 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 179 CYS Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 44 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 21 optimal weight: 0.1980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 ASN B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9177 Z= 0.207 Angle : 0.531 10.934 12436 Z= 0.281 Chirality : 0.043 0.227 1408 Planarity : 0.004 0.047 1574 Dihedral : 4.614 41.457 1254 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.65 % Allowed : 14.39 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.11 (0.26), residues: 1124 helix: 1.71 (0.27), residues: 381 sheet: 1.04 (0.30), residues: 307 loop : -0.32 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.014 0.001 PHE R 139 TYR 0.011 0.001 TYR R 24 ARG 0.008 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 221 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: R 196 PHE cc_start: 0.8066 (t80) cc_final: 0.7708 (t80) REVERT: A 243 ASN cc_start: 0.8549 (m-40) cc_final: 0.8128 (m-40) REVERT: A 329 GLU cc_start: 0.6749 (mp0) cc_final: 0.6261 (mp0) REVERT: A 379 THR cc_start: 0.8106 (p) cc_final: 0.7877 (m) REVERT: A 396 ASP cc_start: 0.6743 (m-30) cc_final: 0.6483 (m-30) REVERT: B 45 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8002 (mtm) REVERT: B 175 GLN cc_start: 0.7503 (mm-40) cc_final: 0.7297 (mm-40) REVERT: B 212 ASP cc_start: 0.7819 (p0) cc_final: 0.7442 (p0) REVERT: B 258 ASP cc_start: 0.6832 (t70) cc_final: 0.6537 (t70) REVERT: S 180 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.7410 (ptp) REVERT: S 201 THR cc_start: 0.8021 (t) cc_final: 0.7734 (m) outliers start: 26 outliers final: 15 residues processed: 231 average time/residue: 1.2434 time to fit residues: 304.6504 Evaluate side-chains 235 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 218 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 179 CYS Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 0.0040 chunk 56 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 ASN B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9177 Z= 0.221 Angle : 0.538 10.887 12436 Z= 0.284 Chirality : 0.042 0.210 1408 Planarity : 0.004 0.045 1574 Dihedral : 4.556 41.296 1252 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.96 % Allowed : 14.69 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.07 (0.26), residues: 1124 helix: 1.71 (0.27), residues: 382 sheet: 0.97 (0.30), residues: 303 loop : -0.32 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.012 0.001 PHE R 296 TYR 0.011 0.001 TYR R 24 ARG 0.009 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 222 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: A 243 ASN cc_start: 0.8544 (m-40) cc_final: 0.8094 (m110) REVERT: A 329 GLU cc_start: 0.6747 (mp0) cc_final: 0.6504 (mp0) REVERT: A 379 THR cc_start: 0.8132 (p) cc_final: 0.7898 (m) REVERT: A 396 ASP cc_start: 0.6742 (m-30) cc_final: 0.6480 (m-30) REVERT: B 45 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8011 (mtm) REVERT: B 175 GLN cc_start: 0.7504 (mm-40) cc_final: 0.7295 (mm-40) REVERT: B 212 ASP cc_start: 0.7824 (p0) cc_final: 0.7461 (p0) REVERT: B 258 ASP cc_start: 0.6797 (t70) cc_final: 0.6528 (t70) REVERT: S 18 ARG cc_start: 0.7917 (ttm-80) cc_final: 0.7591 (ttt180) REVERT: S 180 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7362 (ptp) REVERT: S 201 THR cc_start: 0.8018 (t) cc_final: 0.7719 (m) outliers start: 29 outliers final: 19 residues processed: 230 average time/residue: 1.2577 time to fit residues: 307.1189 Evaluate side-chains 245 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 224 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 179 CYS Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 0.0070 chunk 63 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 ASN B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9177 Z= 0.166 Angle : 0.513 11.097 12436 Z= 0.270 Chirality : 0.041 0.185 1408 Planarity : 0.004 0.044 1574 Dihedral : 4.378 40.828 1252 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.65 % Allowed : 15.61 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.20 (0.26), residues: 1124 helix: 1.84 (0.27), residues: 382 sheet: 1.06 (0.31), residues: 301 loop : -0.27 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.002 0.001 HIS B 62 PHE 0.012 0.001 PHE R 139 TYR 0.011 0.001 TYR R 24 ARG 0.009 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 223 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: R 196 PHE cc_start: 0.8067 (t80) cc_final: 0.7681 (t80) REVERT: A 243 ASN cc_start: 0.8536 (m-40) cc_final: 0.8079 (m110) REVERT: A 329 GLU cc_start: 0.6725 (mp0) cc_final: 0.6485 (mp0) REVERT: A 389 ARG cc_start: 0.7893 (mtm-85) cc_final: 0.7670 (mtm180) REVERT: A 396 ASP cc_start: 0.6717 (m-30) cc_final: 0.6449 (m-30) REVERT: B 212 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7334 (p0) REVERT: B 258 ASP cc_start: 0.6781 (t70) cc_final: 0.6548 (t70) REVERT: S 18 ARG cc_start: 0.7921 (ttm170) cc_final: 0.7597 (ttt180) outliers start: 26 outliers final: 15 residues processed: 234 average time/residue: 1.1655 time to fit residues: 290.5915 Evaluate side-chains 234 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 218 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 179 CYS Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 ASN B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9177 Z= 0.229 Angle : 0.544 10.797 12436 Z= 0.287 Chirality : 0.043 0.193 1408 Planarity : 0.004 0.044 1574 Dihedral : 4.499 41.086 1252 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.55 % Allowed : 16.12 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.12 (0.26), residues: 1124 helix: 1.73 (0.27), residues: 383 sheet: 1.05 (0.31), residues: 301 loop : -0.32 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.005 0.001 HIS B 62 PHE 0.012 0.001 PHE R 296 TYR 0.011 0.001 TYR S 178 ARG 0.008 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 222 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: A 243 ASN cc_start: 0.8539 (m-40) cc_final: 0.8084 (m110) REVERT: A 329 GLU cc_start: 0.6751 (mp0) cc_final: 0.6520 (mp0) REVERT: A 389 ARG cc_start: 0.7932 (mtm-85) cc_final: 0.7646 (mtm180) REVERT: A 396 ASP cc_start: 0.6737 (m-30) cc_final: 0.6482 (m-30) REVERT: B 212 ASP cc_start: 0.7804 (p0) cc_final: 0.7415 (p0) REVERT: B 258 ASP cc_start: 0.6779 (t70) cc_final: 0.6514 (t70) REVERT: S 18 ARG cc_start: 0.7933 (ttm170) cc_final: 0.7610 (ttt180) outliers start: 25 outliers final: 18 residues processed: 234 average time/residue: 1.1922 time to fit residues: 296.7794 Evaluate side-chains 240 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 222 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 179 CYS Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.0970 chunk 60 optimal weight: 0.5980 chunk 43 optimal weight: 0.0030 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 ASN B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9177 Z= 0.144 Angle : 0.512 11.201 12436 Z= 0.268 Chirality : 0.041 0.159 1408 Planarity : 0.004 0.043 1574 Dihedral : 4.258 40.077 1252 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.84 % Allowed : 17.65 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.25 (0.26), residues: 1124 helix: 1.90 (0.28), residues: 382 sheet: 1.10 (0.31), residues: 300 loop : -0.27 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 300 HIS 0.002 0.001 HIS S 35 PHE 0.010 0.001 PHE R 296 TYR 0.011 0.001 TYR R 24 ARG 0.009 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 226 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: R 196 PHE cc_start: 0.8048 (t80) cc_final: 0.7668 (t80) REVERT: R 315 ILE cc_start: 0.8168 (mt) cc_final: 0.7953 (mp) REVERT: A 243 ASN cc_start: 0.8529 (m-40) cc_final: 0.8070 (m110) REVERT: A 329 GLU cc_start: 0.6724 (mp0) cc_final: 0.6480 (mp0) REVERT: A 389 ARG cc_start: 0.7808 (mtm-85) cc_final: 0.7520 (mtm180) REVERT: A 396 ASP cc_start: 0.6705 (m-30) cc_final: 0.6432 (m-30) REVERT: B 212 ASP cc_start: 0.7796 (p0) cc_final: 0.7385 (p0) REVERT: B 258 ASP cc_start: 0.6785 (t70) cc_final: 0.6333 (t70) REVERT: S 18 ARG cc_start: 0.7929 (ttm170) cc_final: 0.7590 (ttt180) outliers start: 18 outliers final: 10 residues processed: 236 average time/residue: 1.1733 time to fit residues: 295.4398 Evaluate side-chains 229 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 219 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 179 CYS Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 53 optimal weight: 0.0270 chunk 69 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 ASN B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9177 Z= 0.177 Angle : 0.535 11.104 12436 Z= 0.280 Chirality : 0.042 0.171 1408 Planarity : 0.004 0.043 1574 Dihedral : 4.321 40.362 1252 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.73 % Allowed : 18.06 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.21 (0.26), residues: 1124 helix: 1.89 (0.27), residues: 382 sheet: 0.96 (0.30), residues: 305 loop : -0.23 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 300 HIS 0.003 0.001 HIS B 62 PHE 0.011 0.001 PHE R 296 TYR 0.011 0.001 TYR S 178 ARG 0.009 0.000 ARG B 22 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 223 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: A 243 ASN cc_start: 0.8531 (m-40) cc_final: 0.8101 (m-40) REVERT: A 329 GLU cc_start: 0.6728 (mp0) cc_final: 0.6491 (mp0) REVERT: A 389 ARG cc_start: 0.7823 (mtm-85) cc_final: 0.7527 (mtm180) REVERT: A 396 ASP cc_start: 0.6719 (m-30) cc_final: 0.6450 (m-30) REVERT: B 212 ASP cc_start: 0.7797 (p0) cc_final: 0.7390 (p0) REVERT: B 258 ASP cc_start: 0.6742 (t70) cc_final: 0.6273 (t70) REVERT: B 340 ASN cc_start: 0.7617 (t0) cc_final: 0.7383 (t0) REVERT: S 18 ARG cc_start: 0.7923 (ttm170) cc_final: 0.7584 (ttt180) outliers start: 17 outliers final: 14 residues processed: 232 average time/residue: 1.2078 time to fit residues: 298.1647 Evaluate side-chains 234 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 220 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 177 ILE Chi-restraints excluded: chain R residue 179 CYS Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 ASN B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.132784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.116170 restraints weight = 11852.645| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.74 r_work: 0.3378 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9177 Z= 0.184 Angle : 0.544 11.292 12436 Z= 0.285 Chirality : 0.042 0.170 1408 Planarity : 0.004 0.043 1574 Dihedral : 4.339 40.380 1252 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.84 % Allowed : 17.86 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.19 (0.26), residues: 1124 helix: 1.85 (0.27), residues: 382 sheet: 0.99 (0.30), residues: 305 loop : -0.26 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 300 HIS 0.003 0.001 HIS B 62 PHE 0.011 0.001 PHE R 296 TYR 0.011 0.001 TYR S 178 ARG 0.009 0.000 ARG B 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4699.27 seconds wall clock time: 389 minutes 44.26 seconds (23384.26 seconds total)