Starting phenix.real_space_refine on Sun May 11 23:37:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jsp_36626/05_2025/8jsp_36626.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jsp_36626/05_2025/8jsp_36626.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jsp_36626/05_2025/8jsp_36626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jsp_36626/05_2025/8jsp_36626.map" model { file = "/net/cci-nas-00/data/ceres_data/8jsp_36626/05_2025/8jsp_36626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jsp_36626/05_2025/8jsp_36626.cif" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.032 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 5480 2.51 5 N 1470 2.21 5 O 1586 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8599 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1743 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Chain: "B" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2516 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 322} Chain: "E" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1717 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "G" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 347 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 4, 'TRANS': 40} Chain: "R" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2264 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 12, 'TRANS': 273} Chain breaks: 1 Chain: "R" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'UJL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.27, per 1000 atoms: 0.61 Number of scatterers: 8599 At special positions: 0 Unit cell: (103.96, 115.92, 129.72, 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 1586 8.00 N 1470 7.00 C 5480 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.07 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 187 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 1.0 seconds 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2058 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 13 sheets defined 39.2% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 6 through 30 Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 207 through 211 removed outlier: 3.509A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.503A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 4.055A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 232 " --> pdb=" O ASP A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 232' Processing helix chain 'A' and resid 243 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.960A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.517A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N CYS A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 26 removed outlier: 3.523A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.847A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.774A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 24 Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.961A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.806A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 36 through 63 removed outlier: 3.686A pdb=" N VAL R 58 " --> pdb=" O ASN R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 99 Proline residue: R 91 - end of helix Processing helix chain 'R' and resid 105 through 123 Processing helix chain 'R' and resid 124 through 140 removed outlier: 4.227A pdb=" N CYS R 128 " --> pdb=" O ILE R 124 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASP R 140 " --> pdb=" O TRP R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 147 removed outlier: 3.551A pdb=" N TYR R 144 " --> pdb=" O ASP R 140 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 174 removed outlier: 3.937A pdb=" N ALA R 154 " --> pdb=" O PRO R 150 " (cutoff:3.500A) Proline residue: R 170 - end of helix Processing helix chain 'R' and resid 192 through 228 removed outlier: 4.060A pdb=" N THR R 200 " --> pdb=" O THR R 196 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ILE R 206 " --> pdb=" O GLY R 202 " (cutoff:3.500A) Proline residue: R 207 - end of helix removed outlier: 3.661A pdb=" N ILE R 226 " --> pdb=" O ALA R 222 " (cutoff:3.500A) Processing helix chain 'R' and resid 325 through 357 removed outlier: 3.741A pdb=" N THR R 343 " --> pdb=" O ARG R 339 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL R 344 " --> pdb=" O GLU R 340 " (cutoff:3.500A) Processing helix chain 'R' and resid 358 through 368 Processing helix chain 'R' and resid 369 through 373 removed outlier: 4.324A pdb=" N GLU R 372 " --> pdb=" O PRO R 369 " (cutoff:3.500A) Processing helix chain 'R' and resid 378 through 401 removed outlier: 3.785A pdb=" N ILE R 384 " --> pdb=" O LEU R 380 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLY R 389 " --> pdb=" O ILE R 385 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TYR R 390 " --> pdb=" O ASN R 386 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N SER R 393 " --> pdb=" O GLY R 389 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU R 394 " --> pdb=" O TYR R 390 " (cutoff:3.500A) Proline residue: R 397 - end of helix removed outlier: 3.692A pdb=" N TYR R 400 " --> pdb=" O ASN R 396 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 415 Processing sheet with id=AA1, first strand: chain 'A' and resid 196 through 200 removed outlier: 4.142A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.556A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.811A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 111 through 112 removed outlier: 4.076A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.546A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.831A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.830A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.896A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.679A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET E 83 " --> pdb=" O ARG E 18 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE E 80 " --> pdb=" O SER E 71 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER E 71 " --> pdb=" O PHE E 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.481A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU E 117 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA E 92 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL E 37 " --> pdb=" O TYR E 95 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR E 50 " --> pdb=" O TYR E 59 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR E 59 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 142 removed outlier: 4.008A pdb=" N THR E 141 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG E 160 " --> pdb=" O THR E 141 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER E 206 " --> pdb=" O THR E 213 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.736A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 194 through 195 removed outlier: 3.702A pdb=" N LEU E 178 " --> pdb=" O GLN E 186 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU E 188 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) 373 hydrogen bonds defined for protein. 1065 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: 2.31 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1561 1.32 - 1.45: 2279 1.45 - 1.57: 4849 1.57 - 1.69: 0 1.69 - 1.82: 90 Bond restraints: 8779 Sorted by residual: bond pdb=" C VAL R 89 " pdb=" O VAL R 89 " ideal model delta sigma weight residual 1.236 1.279 -0.043 1.19e-02 7.06e+03 1.31e+01 bond pdb=" N LEU R 118 " pdb=" CA LEU R 118 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.19e-02 7.06e+03 1.16e+01 bond pdb=" N CYS B 149 " pdb=" CA CYS B 149 " ideal model delta sigma weight residual 1.462 1.500 -0.038 1.20e-02 6.94e+03 1.00e+01 bond pdb=" C VAL R 85 " pdb=" O VAL R 85 " ideal model delta sigma weight residual 1.237 1.202 0.035 1.12e-02 7.97e+03 9.49e+00 bond pdb=" N CYS R 120 " pdb=" CA CYS R 120 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.33e-02 5.65e+03 9.11e+00 ... (remaining 8774 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 11470 1.93 - 3.87: 356 3.87 - 5.80: 56 5.80 - 7.73: 8 7.73 - 9.67: 3 Bond angle restraints: 11893 Sorted by residual: angle pdb=" C GLU E 234 " pdb=" N TYR E 235 " pdb=" CA TYR E 235 " ideal model delta sigma weight residual 122.89 113.22 9.67 1.12e+00 7.97e-01 7.45e+01 angle pdb=" N VAL R 85 " pdb=" CA VAL R 85 " pdb=" CB VAL R 85 " ideal model delta sigma weight residual 110.62 116.10 -5.48 1.05e+00 9.07e-01 2.72e+01 angle pdb=" C CYS B 121 " pdb=" CA CYS B 121 " pdb=" CB CYS B 121 " ideal model delta sigma weight residual 111.23 118.17 -6.94 1.42e+00 4.96e-01 2.39e+01 angle pdb=" CA VAL R 85 " pdb=" C VAL R 85 " pdb=" O VAL R 85 " ideal model delta sigma weight residual 121.41 116.94 4.47 1.04e+00 9.25e-01 1.85e+01 angle pdb=" N MET R 84 " pdb=" CA MET R 84 " pdb=" C MET R 84 " ideal model delta sigma weight residual 111.02 105.89 5.13 1.22e+00 6.72e-01 1.77e+01 ... (remaining 11888 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 4688 17.31 - 34.62: 435 34.62 - 51.93: 78 51.93 - 69.24: 13 69.24 - 86.55: 9 Dihedral angle restraints: 5223 sinusoidal: 2031 harmonic: 3192 Sorted by residual: dihedral pdb=" CA LEU B 79 " pdb=" C LEU B 79 " pdb=" N ILE B 80 " pdb=" CA ILE B 80 " ideal model delta harmonic sigma weight residual -180.00 -158.54 -21.46 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA TYR E 235 " pdb=" C TYR E 235 " pdb=" N PRO E 236 " pdb=" CA PRO E 236 " ideal model delta harmonic sigma weight residual 180.00 159.20 20.80 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA ASP B 118 " pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta harmonic sigma weight residual -180.00 -159.37 -20.63 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 5220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 923 0.045 - 0.089: 318 0.089 - 0.134: 94 0.134 - 0.179: 16 0.179 - 0.223: 2 Chirality restraints: 1353 Sorted by residual: chirality pdb=" CB THR A 327 " pdb=" CA THR A 327 " pdb=" OG1 THR A 327 " pdb=" CG2 THR A 327 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CB VAL R 85 " pdb=" CA VAL R 85 " pdb=" CG1 VAL R 85 " pdb=" CG2 VAL R 85 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.99e-01 chirality pdb=" CB ILE B 157 " pdb=" CA ILE B 157 " pdb=" CG1 ILE B 157 " pdb=" CG2 ILE B 157 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.49e-01 ... (remaining 1350 not shown) Planarity restraints: 1497 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 120 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.01e+00 pdb=" C ILE B 120 " -0.046 2.00e-02 2.50e+03 pdb=" O ILE B 120 " 0.018 2.00e-02 2.50e+03 pdb=" N CYS B 121 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 407 " 0.022 2.00e-02 2.50e+03 1.86e-02 6.03e+00 pdb=" CG PHE R 407 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE R 407 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE R 407 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE R 407 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE R 407 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE R 407 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP R 140 " 0.038 5.00e-02 4.00e+02 5.78e-02 5.34e+00 pdb=" N PRO R 141 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO R 141 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO R 141 " 0.032 5.00e-02 4.00e+02 ... (remaining 1494 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 985 2.74 - 3.28: 8673 3.28 - 3.82: 13698 3.82 - 4.36: 15583 4.36 - 4.90: 27107 Nonbonded interactions: 66046 Sorted by model distance: nonbonded pdb=" NE1 TRP E 47 " pdb=" O ALA E 49 " model vdw 2.204 3.120 nonbonded pdb=" OG SER A 293 " pdb=" OE1 GLU A 298 " model vdw 2.211 3.040 nonbonded pdb=" O ARG E 98 " pdb=" OG SER E 99 " model vdw 2.234 3.040 nonbonded pdb=" O ILE B 37 " pdb=" NZ LYS B 301 " model vdw 2.237 3.120 nonbonded pdb=" O ASP E 90 " pdb=" OH TYR E 94 " model vdw 2.239 3.040 ... (remaining 66041 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue 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: 0.690 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 21.800 Find NCS groups from input model: 0.110 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: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 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 : 0.006 0.052 8783 Z= 0.291 Angle : 0.794 9.666 11901 Z= 0.461 Chirality : 0.049 0.223 1353 Planarity : 0.005 0.058 1497 Dihedral : 14.057 86.552 3153 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.86 % Allowed : 0.86 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.25), residues: 1084 helix: 0.72 (0.26), residues: 383 sheet: -0.93 (0.34), residues: 239 loop : -1.47 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 82 HIS 0.008 0.002 HIS B 91 PHE 0.042 0.003 PHE R 407 TYR 0.026 0.003 TYR R 96 ARG 0.004 0.001 ARG E 191 Details of bonding type rmsd hydrogen bonds : bond 0.20229 ( 373) hydrogen bonds : angle 7.46001 ( 1065) SS BOND : bond 0.01735 ( 4) SS BOND : angle 0.48708 ( 8) covalent geometry : bond 0.00605 ( 8779) covalent geometry : angle 0.79441 (11893) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 164 time to evaluate : 0.921 Fit side-chains REVERT: A 346 ASN cc_start: 0.7768 (m110) cc_final: 0.7446 (m-40) REVERT: E 93 MET cc_start: 0.7738 (mpp) cc_final: 0.6880 (mpp) REVERT: R 330 GLU cc_start: 0.8616 (tp30) cc_final: 0.8403 (tp30) REVERT: R 337 LEU cc_start: 0.8831 (mm) cc_final: 0.8514 (mm) outliers start: 8 outliers final: 3 residues processed: 172 average time/residue: 0.1907 time to fit residues: 45.5725 Evaluate side-chains 125 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 122 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 115 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 54 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 97 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS B 230 ASN E 231 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.217520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.174471 restraints weight = 10944.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.175888 restraints weight = 7555.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.179118 restraints weight = 6359.689| |-----------------------------------------------------------------------------| r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8783 Z= 0.129 Angle : 0.617 7.209 11901 Z= 0.325 Chirality : 0.043 0.181 1353 Planarity : 0.004 0.041 1497 Dihedral : 5.601 88.325 1212 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.37 % Allowed : 9.28 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.26), residues: 1084 helix: 1.17 (0.27), residues: 387 sheet: -0.81 (0.33), residues: 242 loop : -1.33 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 297 HIS 0.004 0.001 HIS E 232 PHE 0.015 0.001 PHE B 292 TYR 0.030 0.002 TYR E 235 ARG 0.004 0.000 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.04775 ( 373) hydrogen bonds : angle 5.10621 ( 1065) SS BOND : bond 0.00317 ( 4) SS BOND : angle 0.65561 ( 8) covalent geometry : bond 0.00281 ( 8779) covalent geometry : angle 0.61665 (11893) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.943 Fit side-chains REVERT: A 346 ASN cc_start: 0.7552 (m110) cc_final: 0.7235 (m110) REVERT: B 262 MET cc_start: 0.6722 (tpt) cc_final: 0.6187 (tpp) REVERT: B 266 HIS cc_start: 0.7396 (t-90) cc_final: 0.7190 (t-90) REVERT: E 230 MET cc_start: 0.5166 (ppp) cc_final: 0.4587 (ttp) REVERT: E 231 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.6707 (pp30) REVERT: R 113 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7712 (mm) REVERT: R 333 ARG cc_start: 0.8555 (ptp-170) cc_final: 0.8243 (ptp-170) REVERT: R 335 MET cc_start: 0.7476 (ttp) cc_final: 0.7190 (ttm) outliers start: 22 outliers final: 16 residues processed: 162 average time/residue: 0.2053 time to fit residues: 46.4213 Evaluate side-chains 146 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 231 GLN Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 133 ASP Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 344 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 28 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 42 optimal weight: 7.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 HIS ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.210568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.167014 restraints weight = 11203.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.168102 restraints weight = 8310.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.171127 restraints weight = 6813.675| |-----------------------------------------------------------------------------| r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8783 Z= 0.185 Angle : 0.646 8.350 11901 Z= 0.343 Chirality : 0.044 0.189 1353 Planarity : 0.004 0.046 1497 Dihedral : 5.279 81.299 1211 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.24 % Allowed : 13.48 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.26), residues: 1084 helix: 1.17 (0.27), residues: 385 sheet: -0.92 (0.32), residues: 249 loop : -1.40 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.007 0.001 HIS B 91 PHE 0.017 0.002 PHE B 234 TYR 0.029 0.002 TYR A 230 ARG 0.004 0.000 ARG E 180 Details of bonding type rmsd hydrogen bonds : bond 0.05365 ( 373) hydrogen bonds : angle 5.05135 ( 1065) SS BOND : bond 0.01124 ( 4) SS BOND : angle 0.59844 ( 8) covalent geometry : bond 0.00439 ( 8779) covalent geometry : angle 0.64555 (11893) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 0.854 Fit side-chains REVERT: A 346 ASN cc_start: 0.7694 (m110) cc_final: 0.7245 (m110) REVERT: B 266 HIS cc_start: 0.7572 (t-90) cc_final: 0.7259 (t-170) REVERT: E 98 ARG cc_start: 0.7376 (ttp-170) cc_final: 0.7154 (ttp-170) REVERT: E 110 PHE cc_start: 0.7061 (t80) cc_final: 0.6806 (m-80) REVERT: R 113 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7785 (mm) REVERT: R 333 ARG cc_start: 0.8567 (ptp-170) cc_final: 0.8352 (ptp-170) outliers start: 30 outliers final: 27 residues processed: 157 average time/residue: 0.2084 time to fit residues: 45.3770 Evaluate side-chains 160 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 133 ASP Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 344 VAL Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 386 ASN Chi-restraints excluded: chain R residue 414 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 45 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 2 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 21 optimal weight: 20.0000 chunk 103 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 HIS ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.211457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.168186 restraints weight = 11162.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.169055 restraints weight = 7988.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.171937 restraints weight = 6733.456| |-----------------------------------------------------------------------------| r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8783 Z= 0.156 Angle : 0.613 7.693 11901 Z= 0.323 Chirality : 0.043 0.158 1353 Planarity : 0.004 0.045 1497 Dihedral : 5.123 81.087 1209 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.56 % Allowed : 15.86 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -0.61 (0.26), residues: 1084 helix: 1.22 (0.27), residues: 386 sheet: -1.02 (0.31), residues: 265 loop : -1.45 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS B 91 PHE 0.014 0.002 PHE R 362 TYR 0.029 0.002 TYR E 235 ARG 0.003 0.000 ARG E 180 Details of bonding type rmsd hydrogen bonds : bond 0.04866 ( 373) hydrogen bonds : angle 4.87637 ( 1065) SS BOND : bond 0.00888 ( 4) SS BOND : angle 0.39309 ( 8) covalent geometry : bond 0.00368 ( 8779) covalent geometry : angle 0.61285 (11893) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 ASN cc_start: 0.7676 (m110) cc_final: 0.7176 (m110) REVERT: B 120 ILE cc_start: 0.6780 (OUTLIER) cc_final: 0.6547 (mt) REVERT: E 228 TYR cc_start: 0.6008 (m-80) cc_final: 0.5545 (m-80) REVERT: R 333 ARG cc_start: 0.8577 (ptp-170) cc_final: 0.8308 (ptp-170) REVERT: R 334 LYS cc_start: 0.8266 (mtmm) cc_final: 0.8027 (mtmm) outliers start: 33 outliers final: 24 residues processed: 158 average time/residue: 0.2007 time to fit residues: 43.9260 Evaluate side-chains 160 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 171 ASN Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain R residue 133 ASP Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 344 VAL Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 386 ASN Chi-restraints excluded: chain R residue 414 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 85 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 89 optimal weight: 0.0980 chunk 10 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.215873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.172968 restraints weight = 11091.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.174438 restraints weight = 7718.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.177643 restraints weight = 6397.148| |-----------------------------------------------------------------------------| r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8783 Z= 0.114 Angle : 0.565 7.570 11901 Z= 0.298 Chirality : 0.042 0.151 1353 Planarity : 0.003 0.045 1497 Dihedral : 4.988 85.988 1207 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.91 % Allowed : 17.58 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.26), residues: 1084 helix: 1.42 (0.28), residues: 386 sheet: -0.78 (0.32), residues: 257 loop : -1.32 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 176 HIS 0.003 0.001 HIS B 266 PHE 0.011 0.001 PHE E 68 TYR 0.031 0.001 TYR E 235 ARG 0.002 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03975 ( 373) hydrogen bonds : angle 4.57633 ( 1065) SS BOND : bond 0.00675 ( 4) SS BOND : angle 0.74921 ( 8) covalent geometry : bond 0.00249 ( 8779) covalent geometry : angle 0.56511 (11893) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 ASN cc_start: 0.7651 (m110) cc_final: 0.7136 (m110) REVERT: E 228 TYR cc_start: 0.5937 (m-80) cc_final: 0.5551 (m-80) REVERT: R 65 ARG cc_start: 0.7100 (ttp-110) cc_final: 0.6699 (tpt90) REVERT: R 333 ARG cc_start: 0.8527 (ptp-170) cc_final: 0.8308 (ptp-170) REVERT: R 334 LYS cc_start: 0.8309 (mtmm) cc_final: 0.8079 (mtmm) outliers start: 27 outliers final: 24 residues processed: 161 average time/residue: 0.2019 time to fit residues: 45.0604 Evaluate side-chains 165 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain R residue 133 ASP Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 330 GLU Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 414 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 88 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 76 optimal weight: 30.0000 chunk 87 optimal weight: 0.2980 chunk 103 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.216555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.174260 restraints weight = 11090.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.175021 restraints weight = 7812.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.177875 restraints weight = 6531.269| |-----------------------------------------------------------------------------| r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8783 Z= 0.113 Angle : 0.574 7.730 11901 Z= 0.300 Chirality : 0.041 0.153 1353 Planarity : 0.003 0.046 1497 Dihedral : 4.915 86.192 1207 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.34 % Allowed : 17.80 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.26), residues: 1084 helix: 1.50 (0.28), residues: 386 sheet: -0.78 (0.32), residues: 262 loop : -1.29 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 161 HIS 0.003 0.001 HIS B 266 PHE 0.012 0.001 PHE E 68 TYR 0.037 0.001 TYR E 235 ARG 0.003 0.000 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.03850 ( 373) hydrogen bonds : angle 4.47704 ( 1065) SS BOND : bond 0.00641 ( 4) SS BOND : angle 0.62731 ( 8) covalent geometry : bond 0.00254 ( 8779) covalent geometry : angle 0.57412 (11893) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.926 Fit side-chains revert: symmetry clash REVERT: A 346 ASN cc_start: 0.7682 (m110) cc_final: 0.7143 (m110) REVERT: B 266 HIS cc_start: 0.7103 (t70) cc_final: 0.6759 (t70) REVERT: E 228 TYR cc_start: 0.5927 (m-80) cc_final: 0.5515 (m-80) REVERT: R 65 ARG cc_start: 0.7078 (ttp-110) cc_final: 0.6700 (tpt90) REVERT: R 333 ARG cc_start: 0.8511 (ptp-170) cc_final: 0.8288 (ptp-170) REVERT: R 334 LYS cc_start: 0.8293 (mtmm) cc_final: 0.7980 (mtmm) outliers start: 31 outliers final: 25 residues processed: 159 average time/residue: 0.2115 time to fit residues: 45.8752 Evaluate side-chains 161 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 47 TRP Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain R residue 133 ASP Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 414 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 76 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 105 optimal weight: 0.4980 chunk 62 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 45 optimal weight: 0.0170 chunk 86 optimal weight: 1.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 322 HIS ** E 231 GLN ** 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 = 0.4604 r_free = 0.4604 target = 0.218377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.176041 restraints weight = 11157.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.177272 restraints weight = 7627.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.179981 restraints weight = 6539.671| |-----------------------------------------------------------------------------| r_work (final): 0.4239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8783 Z= 0.107 Angle : 0.566 7.858 11901 Z= 0.296 Chirality : 0.041 0.147 1353 Planarity : 0.003 0.046 1497 Dihedral : 4.857 87.694 1207 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.34 % Allowed : 18.66 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.26), residues: 1084 helix: 1.54 (0.28), residues: 387 sheet: -0.73 (0.31), residues: 267 loop : -1.29 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 82 HIS 0.002 0.001 HIS B 91 PHE 0.012 0.001 PHE E 68 TYR 0.036 0.001 TYR E 235 ARG 0.004 0.000 ARG R 327 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 373) hydrogen bonds : angle 4.38058 ( 1065) SS BOND : bond 0.00589 ( 4) SS BOND : angle 0.54500 ( 8) covalent geometry : bond 0.00234 ( 8779) covalent geometry : angle 0.56583 (11893) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 ASN cc_start: 0.7600 (m110) cc_final: 0.7085 (m110) REVERT: E 228 TYR cc_start: 0.5951 (m-80) cc_final: 0.5505 (m-80) REVERT: R 65 ARG cc_start: 0.7147 (ttp-110) cc_final: 0.6724 (tpt90) REVERT: R 333 ARG cc_start: 0.8519 (ptp-170) cc_final: 0.8283 (ptp-170) outliers start: 31 outliers final: 26 residues processed: 160 average time/residue: 0.2155 time to fit residues: 47.8357 Evaluate side-chains 167 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 47 TRP Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain R residue 133 ASP Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 414 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 10 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 chunk 29 optimal weight: 0.0570 chunk 97 optimal weight: 0.0570 chunk 99 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 91 optimal weight: 0.1980 chunk 0 optimal weight: 4.9990 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 392 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.221194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.177432 restraints weight = 11222.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.181725 restraints weight = 7435.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.184753 restraints weight = 5701.400| |-----------------------------------------------------------------------------| r_work (final): 0.4298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8783 Z= 0.103 Angle : 0.570 9.371 11901 Z= 0.296 Chirality : 0.041 0.168 1353 Planarity : 0.003 0.045 1497 Dihedral : 4.802 89.814 1207 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.80 % Allowed : 19.20 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.26), residues: 1084 helix: 1.59 (0.28), residues: 387 sheet: -0.62 (0.31), residues: 268 loop : -1.24 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 82 HIS 0.005 0.001 HIS B 266 PHE 0.014 0.001 PHE E 68 TYR 0.034 0.001 TYR E 235 ARG 0.004 0.000 ARG R 327 Details of bonding type rmsd hydrogen bonds : bond 0.03284 ( 373) hydrogen bonds : angle 4.24849 ( 1065) SS BOND : bond 0.00503 ( 4) SS BOND : angle 0.42532 ( 8) covalent geometry : bond 0.00224 ( 8779) covalent geometry : angle 0.57041 (11893) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 ASN cc_start: 0.7498 (m110) cc_final: 0.7007 (m110) REVERT: E 186 GLN cc_start: 0.7116 (mt0) cc_final: 0.6911 (tt0) REVERT: E 228 TYR cc_start: 0.5847 (m-80) cc_final: 0.5468 (m-80) REVERT: R 65 ARG cc_start: 0.7157 (ttp-110) cc_final: 0.6861 (tpt90) outliers start: 26 outliers final: 22 residues processed: 160 average time/residue: 0.2114 time to fit residues: 46.5338 Evaluate side-chains 159 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 47 TRP Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain R residue 92 MET Chi-restraints excluded: chain R residue 133 ASP Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 414 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 41 optimal weight: 6.9990 chunk 57 optimal weight: 0.0980 chunk 95 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.216321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.172960 restraints weight = 11201.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.174810 restraints weight = 7757.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.177589 restraints weight = 6507.006| |-----------------------------------------------------------------------------| r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8783 Z= 0.134 Angle : 0.615 9.229 11901 Z= 0.321 Chirality : 0.042 0.150 1353 Planarity : 0.004 0.049 1497 Dihedral : 4.841 84.290 1207 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.80 % Allowed : 20.06 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.26), residues: 1084 helix: 1.46 (0.28), residues: 387 sheet: -0.52 (0.31), residues: 252 loop : -1.29 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 387 HIS 0.004 0.001 HIS B 91 PHE 0.011 0.001 PHE B 234 TYR 0.031 0.002 TYR E 235 ARG 0.004 0.000 ARG R 327 Details of bonding type rmsd hydrogen bonds : bond 0.04095 ( 373) hydrogen bonds : angle 4.41289 ( 1065) SS BOND : bond 0.00774 ( 4) SS BOND : angle 0.68709 ( 8) covalent geometry : bond 0.00312 ( 8779) covalent geometry : angle 0.61459 (11893) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: E 186 GLN cc_start: 0.7184 (mt0) cc_final: 0.6924 (tt0) REVERT: E 228 TYR cc_start: 0.6039 (m-80) cc_final: 0.5556 (m-80) REVERT: R 65 ARG cc_start: 0.7117 (ttp-110) cc_final: 0.6718 (tpt90) REVERT: R 335 MET cc_start: 0.7236 (ttp) cc_final: 0.6966 (ttm) outliers start: 26 outliers final: 23 residues processed: 155 average time/residue: 0.2097 time to fit residues: 44.3850 Evaluate side-chains 155 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 47 TRP Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain R residue 133 ASP Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 414 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 13 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 66 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.217523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.172885 restraints weight = 11134.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.177060 restraints weight = 7569.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.180028 restraints weight = 5922.124| |-----------------------------------------------------------------------------| r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8783 Z= 0.123 Angle : 0.622 9.547 11901 Z= 0.324 Chirality : 0.042 0.170 1353 Planarity : 0.004 0.048 1497 Dihedral : 4.884 85.771 1207 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.37 % Allowed : 20.39 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.26), residues: 1084 helix: 1.42 (0.28), residues: 387 sheet: -0.73 (0.30), residues: 262 loop : -1.23 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 161 HIS 0.006 0.001 HIS B 266 PHE 0.012 0.001 PHE E 68 TYR 0.031 0.002 TYR E 235 ARG 0.004 0.000 ARG R 333 Details of bonding type rmsd hydrogen bonds : bond 0.03855 ( 373) hydrogen bonds : angle 4.41478 ( 1065) SS BOND : bond 0.00674 ( 4) SS BOND : angle 0.61739 ( 8) covalent geometry : bond 0.00281 ( 8779) covalent geometry : angle 0.62177 (11893) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: E 110 PHE cc_start: 0.7046 (m-80) cc_final: 0.6826 (m-80) REVERT: E 228 TYR cc_start: 0.5810 (m-80) cc_final: 0.5466 (m-80) REVERT: R 65 ARG cc_start: 0.7115 (ttp-110) cc_final: 0.6810 (tpt90) REVERT: R 335 MET cc_start: 0.7132 (ttp) cc_final: 0.6865 (ttp) outliers start: 22 outliers final: 22 residues processed: 146 average time/residue: 0.2150 time to fit residues: 42.8778 Evaluate side-chains 149 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 47 TRP Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain R residue 133 ASP Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 414 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 37 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 73 optimal weight: 0.0970 chunk 57 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 392 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.214025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.173079 restraints weight = 11313.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.172491 restraints weight = 9267.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.175476 restraints weight = 7562.261| |-----------------------------------------------------------------------------| r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8783 Z= 0.147 Angle : 0.647 9.577 11901 Z= 0.338 Chirality : 0.043 0.161 1353 Planarity : 0.004 0.049 1497 Dihedral : 4.946 80.610 1207 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.27 % Allowed : 20.93 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.26), residues: 1084 helix: 1.41 (0.28), residues: 380 sheet: -0.81 (0.30), residues: 257 loop : -1.31 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 387 HIS 0.008 0.001 HIS B 266 PHE 0.013 0.002 PHE B 234 TYR 0.029 0.002 TYR A 230 ARG 0.004 0.000 ARG R 327 Details of bonding type rmsd hydrogen bonds : bond 0.04453 ( 373) hydrogen bonds : angle 4.55967 ( 1065) SS BOND : bond 0.00850 ( 4) SS BOND : angle 0.76153 ( 8) covalent geometry : bond 0.00345 ( 8779) covalent geometry : angle 0.64739 (11893) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3007.96 seconds wall clock time: 53 minutes 28.44 seconds (3208.44 seconds total)