Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 05:10:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xw9_33494/04_2023/7xw9_33494_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xw9_33494/04_2023/7xw9_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_33494/04_2023/7xw9_33494.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xw9_33494/04_2023/7xw9_33494.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xw9_33494/04_2023/7xw9_33494_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xw9_33494/04_2023/7xw9_33494_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 5.52, 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: 3.73 Conformation dependent library (CDL) restraints added in 1.5 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: 0.84 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: 2.88 Time building geometry restraints manager: 4.02 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: 0.410 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: 0.000 Extract box with map and model: 2.210 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.260 Find NCS groups from input model: 0.300 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:15.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.350 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.094 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 242 average time/residue: 1.2062 time to fit residues: 311.2184 Evaluate side-chains 226 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 225 time to evaluate : 1.082 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.5070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 9177 Z= 0.206 Angle : 0.555 9.764 12436 Z= 0.295 Chirality : 0.043 0.262 1408 Planarity : 0.004 0.050 1574 Dihedral : 4.544 40.927 1252 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 1.73 % 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: 0.97 (0.26), residues: 1124 helix: 1.36 (0.27), residues: 379 sheet: 1.26 (0.31), residues: 299 loop : -0.35 (0.31), residues: 446 *********************** 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 248 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 231 time to evaluate : 1.154 Fit side-chains outliers start: 17 outliers final: 10 residues processed: 237 average time/residue: 1.3085 time to fit residues: 328.9803 Evaluate side-chains 230 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 220 time to evaluate : 0.948 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 4 residues processed: 8 average time/residue: 0.4723 time to fit residues: 5.7292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 83 optimal weight: 9.9990 chunk 68 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 0.0570 chunk 109 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- 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: 0.7396 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 9177 Z= 0.182 Angle : 0.530 11.285 12436 Z= 0.279 Chirality : 0.042 0.214 1408 Planarity : 0.004 0.047 1574 Dihedral : 4.445 42.223 1252 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer Outliers : 2.45 % 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: 1.16 (0.26), residues: 1124 helix: 1.68 (0.27), residues: 379 sheet: 1.19 (0.30), residues: 305 loop : -0.30 (0.31), residues: 440 *********************** 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 248 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 224 time to evaluate : 1.071 Fit side-chains outliers start: 24 outliers final: 13 residues processed: 235 average time/residue: 1.2729 time to fit residues: 318.3010 Evaluate side-chains 234 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 221 time to evaluate : 1.067 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 6 residues processed: 9 average time/residue: 0.5572 time to fit residues: 7.1537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 0.0970 chunk 67 optimal weight: 3.9990 chunk 101 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 89 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 0.7443 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 9177 Z= 0.338 Angle : 0.596 12.027 12436 Z= 0.316 Chirality : 0.045 0.200 1408 Planarity : 0.004 0.049 1574 Dihedral : 4.793 41.826 1252 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer Outliers : 3.16 % 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: 0.99 (0.26), residues: 1124 helix: 1.52 (0.27), residues: 382 sheet: 1.04 (0.30), residues: 309 loop : -0.34 (0.31), residues: 433 *********************** 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: 31 poor density : 223 time to evaluate : 1.028 Fit side-chains outliers start: 31 outliers final: 15 residues processed: 231 average time/residue: 1.3331 time to fit residues: 327.0586 Evaluate side-chains 227 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 212 time to evaluate : 1.116 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 6 residues processed: 9 average time/residue: 0.2533 time to fit residues: 4.4304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 44 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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: 0.7437 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 9177 Z= 0.291 Angle : 0.572 11.002 12436 Z= 0.305 Chirality : 0.044 0.193 1408 Planarity : 0.004 0.049 1574 Dihedral : 4.775 41.813 1252 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer Outliers : 2.35 % 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: 0.95 (0.26), residues: 1124 helix: 1.52 (0.27), residues: 382 sheet: 1.06 (0.31), residues: 302 loop : -0.42 (0.31), residues: 440 *********************** 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 244 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 221 time to evaluate : 1.143 Fit side-chains outliers start: 23 outliers final: 14 residues processed: 232 average time/residue: 1.2925 time to fit residues: 318.9062 Evaluate side-chains 231 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 217 time to evaluate : 1.104 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 8 residues processed: 7 average time/residue: 0.4498 time to fit residues: 5.1293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 107 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 9177 Z= 0.290 Angle : 0.579 10.922 12436 Z= 0.307 Chirality : 0.044 0.189 1408 Planarity : 0.004 0.048 1574 Dihedral : 4.773 41.508 1252 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer Outliers : 2.86 % 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: 0.92 (0.26), residues: 1124 helix: 1.47 (0.27), residues: 381 sheet: 0.97 (0.30), residues: 309 loop : -0.38 (0.31), residues: 434 *********************** 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: 28 poor density : 223 time to evaluate : 1.030 Fit side-chains outliers start: 28 outliers final: 22 residues processed: 233 average time/residue: 1.3788 time to fit residues: 340.8986 Evaluate side-chains 244 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 222 time to evaluate : 0.992 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 10 residues processed: 13 average time/residue: 0.5279 time to fit residues: 9.3937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 ASN A 402 ASN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 9177 Z= 0.250 Angle : 0.566 12.268 12436 Z= 0.299 Chirality : 0.044 0.181 1408 Planarity : 0.004 0.047 1574 Dihedral : 4.688 41.235 1252 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 2.65 % 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: 0.95 (0.26), residues: 1124 helix: 1.53 (0.27), residues: 381 sheet: 1.02 (0.30), residues: 304 loop : -0.40 (0.31), residues: 439 *********************** 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 252 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 226 time to evaluate : 1.028 Fit side-chains outliers start: 26 outliers final: 18 residues processed: 241 average time/residue: 1.2583 time to fit residues: 323.0546 Evaluate side-chains 243 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 225 time to evaluate : 1.036 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 11 residues processed: 8 average time/residue: 0.2698 time to fit residues: 4.2350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 chunk 68 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 9 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 ASN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 9177 Z= 0.194 Angle : 0.541 11.682 12436 Z= 0.286 Chirality : 0.043 0.199 1408 Planarity : 0.004 0.045 1574 Dihedral : 4.515 40.927 1252 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer Outliers : 2.76 % 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: 1.00 (0.26), residues: 1124 helix: 1.60 (0.28), residues: 381 sheet: 1.07 (0.31), residues: 301 loop : -0.41 (0.31), residues: 442 *********************** 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 249 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 222 time to evaluate : 1.014 Fit side-chains outliers start: 27 outliers final: 18 residues processed: 237 average time/residue: 1.2922 time to fit residues: 325.6873 Evaluate side-chains 244 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 226 time to evaluate : 1.153 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 11 residues processed: 7 average time/residue: 0.5252 time to fit residues: 5.7581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.0030 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 ASN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.1941 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= 0.228 Angle : 0.564 12.051 12436 Z= 0.296 Chirality : 0.044 0.376 1408 Planarity : 0.004 0.045 1574 Dihedral : 4.570 41.243 1252 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 2.55 % 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: 0.98 (0.26), residues: 1124 helix: 1.56 (0.27), residues: 382 sheet: 1.04 (0.31), residues: 304 loop : -0.39 (0.31), residues: 438 *********************** 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 249 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 224 time to evaluate : 1.181 Fit side-chains outliers start: 25 outliers final: 20 residues processed: 239 average time/residue: 1.2963 time to fit residues: 329.3768 Evaluate side-chains 244 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 224 time to evaluate : 1.060 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 13 residues processed: 8 average time/residue: 0.1637 time to fit residues: 3.4528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 4.9990 chunk 73 optimal weight: 0.0980 chunk 110 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 93 optimal weight: 0.1980 chunk 26 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN 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: 0.7392 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.048 9177 Z= 0.152 Angle : 0.536 11.819 12436 Z= 0.279 Chirality : 0.043 0.387 1408 Planarity : 0.004 0.044 1574 Dihedral : 4.331 40.312 1252 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 2.04 % 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 (0.28), residues: 381 sheet: 1.00 (0.31), residues: 307 loop : -0.35 (0.31), residues: 436 ********************** 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 249 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 229 time to evaluate : 1.116 Fit side-chains outliers start: 20 outliers final: 16 residues processed: 242 average time/residue: 1.2869 time to fit residues: 333.6292 Evaluate side-chains 241 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 225 time to evaluate : 1.086 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 4 average time/residue: 0.6350 time to fit residues: 4.3374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.2980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 77 optimal weight: 0.0980 chunk 5 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 ASN B 230 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.132852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.116206 restraints weight = 11848.474| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.73 r_work: 0.3379 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2006 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= 0.161 Angle : 0.542 12.652 12436 Z= 0.280 Chirality : 0.043 0.394 1408 Planarity : 0.004 0.044 1574 Dihedral : 4.295 40.274 1252 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer Outliers : 2.24 % 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: 1.10 (0.26), residues: 1124 helix: 1.75 (0.28), residues: 381 sheet: 1.00 (0.30), residues: 305 loop : -0.33 (0.31), residues: 438 =============================================================================== Job complete usr+sys time: 4939.96 seconds wall clock time: 87 minutes 45.71 seconds (5265.71 seconds total)