Starting phenix.real_space_refine on Sat Dec 28 12:58:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jsp_36626/12_2024/8jsp_36626.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jsp_36626/12_2024/8jsp_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_36626/12_2024/8jsp_36626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jsp_36626/12_2024/8jsp_36626.map" model { file = "/net/cci-nas-00/data/ceres_data/8jsp_36626/12_2024/8jsp_36626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jsp_36626/12_2024/8jsp_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 5.24, 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: 2.26 Conformation dependent library (CDL) restraints added in 981.8 milliseconds 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: 2.38 Time building geometry restraints manager: 2.58 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: 0.930 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: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.770 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.180 ------------------------------------------------------------------------------- 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 8779 Z= 0.406 Angle : 0.794 9.666 11893 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 *********************** 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 : 1.064 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: 0.2000 time to fit residues: 47.8565 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 : 0.974 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 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 8779 Z= 0.188 Angle : 0.617 7.209 11893 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 *********************** 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 : 1.008 Fit side-chains REVERT: A 346 ASN cc_start: 0.7682 (m110) cc_final: 0.7213 (m110) REVERT: B 221 THR cc_start: 0.8556 (p) cc_final: 0.8316 (p) REVERT: B 262 MET cc_start: 0.6774 (tpt) cc_final: 0.6160 (tpp) REVERT: B 266 HIS cc_start: 0.7502 (t-90) cc_final: 0.7091 (t-90) REVERT: E 34 MET cc_start: 0.6857 (mmm) cc_final: 0.6654 (tmm) REVERT: E 230 MET cc_start: 0.5039 (ppp) cc_final: 0.4670 (ttp) REVERT: E 231 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.6657 (pp30) REVERT: R 113 ILE cc_start: 0.7682 (OUTLIER) cc_final: 0.7356 (mm) REVERT: R 333 ARG cc_start: 0.8574 (ptp-170) cc_final: 0.8174 (ptp-170) REVERT: R 335 MET cc_start: 0.7397 (ttp) cc_final: 0.7063 (ttm) outliers start: 22 outliers final: 16 residues processed: 162 average time/residue: 0.2096 time to fit residues: 47.0199 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 : 0.912 ------------------------------------------------------------------------------- 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 54 optimal weight: 0.1980 chunk 30 optimal weight: 0.0980 chunk 80 optimal weight: 0.9980 chunk 66 optimal weight: 30.0000 chunk 26 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 105 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 78 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8779 Z= 0.156 Angle : 0.564 6.622 11893 Z= 0.299 Chirality : 0.041 0.158 1353 Planarity : 0.003 0.041 1497 Dihedral : 5.008 87.663 1211 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.83 % Allowed : 14.02 % Favored : 84.14 % 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: -0.29 (0.26), residues: 1084 helix: 1.42 (0.27), residues: 387 sheet: -0.76 (0.31), residues: 259 loop : -1.25 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.002 0.000 HIS B 91 PHE 0.009 0.001 PHE B 199 TYR 0.031 0.001 TYR E 235 ARG 0.002 0.000 ARG E 180 *********************** 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 164 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8849 (p0) cc_final: 0.8489 (p0) REVERT: A 346 ASN cc_start: 0.7765 (m110) cc_final: 0.7240 (m110) REVERT: B 221 THR cc_start: 0.8517 (p) cc_final: 0.8304 (p) REVERT: B 266 HIS cc_start: 0.7541 (t-90) cc_final: 0.7084 (t-170) REVERT: E 34 MET cc_start: 0.6635 (mmm) cc_final: 0.6404 (tmm) REVERT: E 110 PHE cc_start: 0.7134 (t80) cc_final: 0.6735 (m-80) REVERT: R 333 ARG cc_start: 0.8579 (ptp-170) cc_final: 0.8287 (ptp-170) REVERT: R 334 LYS cc_start: 0.8515 (mtmm) cc_final: 0.8287 (mtmm) REVERT: R 335 MET cc_start: 0.7379 (ttp) cc_final: 0.7032 (ttm) outliers start: 17 outliers final: 15 residues processed: 157 average time/residue: 0.2346 time to fit residues: 50.3164 Evaluate side-chains 151 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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 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 85 SER Chi-restraints excluded: chain R residue 133 ASP Chi-restraints excluded: chain R residue 162 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8779 Z= 0.208 Angle : 0.583 7.351 11893 Z= 0.306 Chirality : 0.042 0.153 1353 Planarity : 0.003 0.046 1497 Dihedral : 4.984 87.978 1207 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.48 % Allowed : 16.18 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.26), residues: 1084 helix: 1.38 (0.27), residues: 387 sheet: -0.74 (0.31), residues: 259 loop : -1.22 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.007 0.001 HIS B 183 PHE 0.013 0.001 PHE R 362 TYR 0.030 0.002 TYR E 235 ARG 0.002 0.000 ARG E 180 *********************** 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 165 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8957 (p0) cc_final: 0.8683 (p0) REVERT: A 346 ASN cc_start: 0.7799 (m110) cc_final: 0.7187 (m110) REVERT: B 221 THR cc_start: 0.8557 (p) cc_final: 0.8310 (p) REVERT: B 266 HIS cc_start: 0.7641 (t-90) cc_final: 0.7247 (t70) REVERT: E 34 MET cc_start: 0.6769 (mmm) cc_final: 0.6551 (tmm) REVERT: E 110 PHE cc_start: 0.7192 (t80) cc_final: 0.6734 (m-80) REVERT: E 228 TYR cc_start: 0.5995 (m-80) cc_final: 0.5590 (m-80) REVERT: G 58 GLU cc_start: 0.8270 (pm20) cc_final: 0.7937 (pm20) REVERT: R 333 ARG cc_start: 0.8613 (ptp-170) cc_final: 0.8282 (ptp-170) REVERT: R 334 LYS cc_start: 0.8455 (mtmm) cc_final: 0.8188 (mtmm) REVERT: R 335 MET cc_start: 0.7366 (ttp) cc_final: 0.7028 (ttm) outliers start: 23 outliers final: 21 residues processed: 157 average time/residue: 0.2107 time to fit residues: 45.2482 Evaluate side-chains 158 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 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 172 THR 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 355 ILE 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 86 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 42 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8779 Z= 0.227 Angle : 0.594 7.612 11893 Z= 0.313 Chirality : 0.043 0.155 1353 Planarity : 0.004 0.048 1497 Dihedral : 4.977 84.346 1207 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.34 % Allowed : 16.18 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.26), residues: 1084 helix: 1.34 (0.27), residues: 387 sheet: -0.74 (0.31), residues: 265 loop : -1.26 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS B 91 PHE 0.013 0.002 PHE R 362 TYR 0.031 0.002 TYR E 235 ARG 0.003 0.000 ARG E 180 *********************** 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 168 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.6526 (mtt) cc_final: 0.6255 (ptp) REVERT: A 346 ASN cc_start: 0.7827 (m110) cc_final: 0.7168 (m110) REVERT: B 120 ILE cc_start: 0.6726 (OUTLIER) cc_final: 0.6445 (mt) REVERT: B 127 LYS cc_start: 0.8614 (mttm) cc_final: 0.8262 (mmtm) REVERT: B 221 THR cc_start: 0.8565 (p) cc_final: 0.8309 (p) REVERT: B 266 HIS cc_start: 0.7748 (t-90) cc_final: 0.7341 (t70) REVERT: E 110 PHE cc_start: 0.7168 (t80) cc_final: 0.6732 (m-80) REVERT: E 228 TYR cc_start: 0.6243 (m-80) cc_final: 0.5762 (m-80) REVERT: R 65 ARG cc_start: 0.7146 (ttp-110) cc_final: 0.6618 (tpt90) REVERT: R 333 ARG cc_start: 0.8597 (ptp-170) cc_final: 0.8278 (ptp-170) REVERT: R 334 LYS cc_start: 0.8360 (mtmm) cc_final: 0.8113 (mtmm) outliers start: 31 outliers final: 26 residues processed: 157 average time/residue: 0.2095 time to fit residues: 45.3413 Evaluate side-chains 160 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 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 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 6 GLU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 233 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 Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 355 ILE 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 34 optimal weight: 3.9990 chunk 93 optimal weight: 40.0000 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 85 optimal weight: 0.4980 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN B 183 HIS ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8779 Z= 0.236 Angle : 0.603 9.018 11893 Z= 0.317 Chirality : 0.043 0.153 1353 Planarity : 0.004 0.049 1497 Dihedral : 5.015 81.387 1207 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.99 % Allowed : 16.50 % 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: -0.45 (0.26), residues: 1084 helix: 1.30 (0.27), residues: 386 sheet: -0.78 (0.31), residues: 253 loop : -1.40 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 47 HIS 0.005 0.001 HIS B 91 PHE 0.019 0.002 PHE E 68 TYR 0.036 0.002 TYR E 235 ARG 0.003 0.000 ARG B 197 *********************** 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 179 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 127 LYS cc_start: 0.8636 (mttm) cc_final: 0.8284 (mmtm) REVERT: B 221 THR cc_start: 0.8527 (p) cc_final: 0.8267 (p) REVERT: B 266 HIS cc_start: 0.7827 (t-90) cc_final: 0.7596 (t70) REVERT: E 110 PHE cc_start: 0.7220 (t80) cc_final: 0.6820 (m-80) REVERT: E 228 TYR cc_start: 0.6250 (m-80) cc_final: 0.5693 (m-80) REVERT: G 58 GLU cc_start: 0.8340 (pm20) cc_final: 0.8027 (pm20) REVERT: R 65 ARG cc_start: 0.7208 (ttp-110) cc_final: 0.6646 (tpt90) REVERT: R 333 ARG cc_start: 0.8611 (ptp-170) cc_final: 0.8311 (ptp-170) REVERT: R 334 LYS cc_start: 0.8374 (mtmm) cc_final: 0.8075 (mtmm) outliers start: 37 outliers final: 33 residues processed: 162 average time/residue: 0.2449 time to fit residues: 54.1323 Evaluate side-chains 168 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 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 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 321 THR 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 115 THR 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 E residue 233 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 Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 355 ILE 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 11 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 57 optimal weight: 0.4980 chunk 103 optimal weight: 0.0000 chunk 64 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.0990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8779 Z= 0.207 Angle : 0.597 8.002 11893 Z= 0.313 Chirality : 0.042 0.159 1353 Planarity : 0.004 0.049 1497 Dihedral : 4.963 82.880 1207 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.88 % Allowed : 17.91 % Favored : 78.21 % 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: -0.40 (0.26), residues: 1084 helix: 1.36 (0.27), residues: 386 sheet: -0.77 (0.31), residues: 259 loop : -1.39 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 176 HIS 0.005 0.001 HIS B 183 PHE 0.022 0.002 PHE B 292 TYR 0.030 0.002 TYR A 230 ARG 0.003 0.000 ARG R 327 *********************** 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 172 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.6270 (mtt) cc_final: 0.6059 (ptp) REVERT: B 127 LYS cc_start: 0.8607 (mttm) cc_final: 0.8251 (mmtm) REVERT: B 221 THR cc_start: 0.8464 (p) cc_final: 0.8196 (p) REVERT: B 266 HIS cc_start: 0.7928 (t-90) cc_final: 0.7488 (t70) REVERT: E 110 PHE cc_start: 0.7174 (t80) cc_final: 0.6803 (m-80) REVERT: E 228 TYR cc_start: 0.6228 (m-80) cc_final: 0.5644 (m-80) REVERT: R 65 ARG cc_start: 0.7220 (ttp-110) cc_final: 0.6661 (tpt90) REVERT: R 333 ARG cc_start: 0.8620 (ptp-170) cc_final: 0.8332 (ptp-170) REVERT: R 334 LYS cc_start: 0.8362 (mtmm) cc_final: 0.7951 (mtmm) outliers start: 36 outliers final: 33 residues processed: 157 average time/residue: 0.2317 time to fit residues: 49.3813 Evaluate side-chains 166 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 133 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 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 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 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 171 ASN Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 233 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 Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 355 ILE 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 61 optimal weight: 30.0000 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 93 optimal weight: 0.0970 chunk 98 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 183 HIS ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8779 Z= 0.184 Angle : 0.576 7.795 11893 Z= 0.302 Chirality : 0.042 0.154 1353 Planarity : 0.004 0.048 1497 Dihedral : 4.893 84.436 1207 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.88 % Allowed : 18.02 % Favored : 78.10 % 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: 1.44 (0.28), residues: 385 sheet: -0.77 (0.31), residues: 260 loop : -1.34 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 176 HIS 0.003 0.001 HIS B 91 PHE 0.020 0.001 PHE E 68 TYR 0.030 0.001 TYR A 230 ARG 0.003 0.000 ARG R 327 *********************** 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: 36 poor density : 136 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 127 LYS cc_start: 0.8623 (mttm) cc_final: 0.8253 (mmtm) REVERT: B 221 THR cc_start: 0.8402 (p) cc_final: 0.8134 (p) REVERT: B 266 HIS cc_start: 0.7970 (t-90) cc_final: 0.7593 (t70) REVERT: B 268 ASN cc_start: 0.8568 (m-40) cc_final: 0.8277 (t0) REVERT: E 110 PHE cc_start: 0.7151 (t80) cc_final: 0.6795 (m-80) REVERT: E 228 TYR cc_start: 0.6121 (m-80) cc_final: 0.5612 (m-80) REVERT: R 65 ARG cc_start: 0.7204 (ttp-110) cc_final: 0.6634 (tpt90) REVERT: R 333 ARG cc_start: 0.8603 (ptp-170) cc_final: 0.8308 (ptp-170) outliers start: 36 outliers final: 33 residues processed: 158 average time/residue: 0.2262 time to fit residues: 48.5653 Evaluate side-chains 164 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 52 GLN 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 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 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 218 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 321 THR 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 E residue 233 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 Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 355 ILE 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 90 optimal weight: 0.7980 chunk 96 optimal weight: 0.3980 chunk 98 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 75 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 0.4980 chunk 95 optimal weight: 2.9990 chunk 63 optimal weight: 0.0040 chunk 101 optimal weight: 0.4980 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 110 ASN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8779 Z= 0.152 Angle : 0.581 8.148 11893 Z= 0.303 Chirality : 0.041 0.147 1353 Planarity : 0.003 0.045 1497 Dihedral : 4.848 88.153 1207 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.13 % Allowed : 18.99 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.26), residues: 1084 helix: 1.55 (0.28), residues: 386 sheet: -0.60 (0.31), residues: 252 loop : -1.19 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 82 HIS 0.008 0.001 HIS B 183 PHE 0.016 0.001 PHE E 68 TYR 0.030 0.001 TYR A 230 ARG 0.004 0.000 ARG R 327 *********************** 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 176 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 127 LYS cc_start: 0.8569 (mttm) cc_final: 0.8233 (mmtm) REVERT: B 221 THR cc_start: 0.8308 (p) cc_final: 0.8031 (p) REVERT: B 266 HIS cc_start: 0.7974 (t-90) cc_final: 0.7579 (t70) REVERT: B 268 ASN cc_start: 0.8531 (m-40) cc_final: 0.8292 (t0) REVERT: E 110 PHE cc_start: 0.7019 (t80) cc_final: 0.6728 (m-80) REVERT: E 228 TYR cc_start: 0.6060 (m-80) cc_final: 0.5599 (m-80) REVERT: R 65 ARG cc_start: 0.7195 (ttp-110) cc_final: 0.6581 (tpt90) REVERT: R 333 ARG cc_start: 0.8576 (ptp-170) cc_final: 0.8287 (ptp-170) REVERT: R 334 LYS cc_start: 0.8443 (mtmm) cc_final: 0.8121 (mtmm) REVERT: R 335 MET cc_start: 0.7079 (ttp) cc_final: 0.6814 (ttm) outliers start: 29 outliers final: 28 residues processed: 162 average time/residue: 0.2139 time to fit residues: 48.1089 Evaluate side-chains 167 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 52 GLN 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 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 76 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 THR 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 186 GLN 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 355 ILE 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 62 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 70 optimal weight: 0.3980 chunk 106 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 chunk 84 optimal weight: 0.4980 chunk 8 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 52 optimal weight: 0.5980 chunk 67 optimal weight: 0.0980 chunk 90 optimal weight: 3.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8779 Z= 0.155 Angle : 0.584 8.212 11893 Z= 0.305 Chirality : 0.042 0.185 1353 Planarity : 0.003 0.045 1497 Dihedral : 4.822 89.127 1207 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.70 % Allowed : 20.06 % 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: -0.07 (0.26), residues: 1084 helix: 1.49 (0.28), residues: 388 sheet: -0.48 (0.30), residues: 257 loop : -1.14 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 82 HIS 0.002 0.000 HIS R 126 PHE 0.014 0.001 PHE E 68 TYR 0.030 0.001 TYR A 230 ARG 0.004 0.000 ARG R 327 ********************** 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 158 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 127 LYS cc_start: 0.8576 (mttm) cc_final: 0.8340 (mmtt) REVERT: B 221 THR cc_start: 0.8303 (p) cc_final: 0.8010 (p) REVERT: B 266 HIS cc_start: 0.8014 (t-90) cc_final: 0.7593 (t70) REVERT: B 268 ASN cc_start: 0.8316 (m-40) cc_final: 0.8087 (t0) REVERT: E 110 PHE cc_start: 0.7057 (t80) cc_final: 0.6723 (m-80) REVERT: E 228 TYR cc_start: 0.6016 (m-80) cc_final: 0.5564 (m-80) REVERT: R 65 ARG cc_start: 0.7256 (ttp-110) cc_final: 0.6655 (tpt90) REVERT: R 333 ARG cc_start: 0.8567 (ptp-170) cc_final: 0.8256 (ptp-170) REVERT: R 334 LYS cc_start: 0.8440 (mtmm) cc_final: 0.8084 (mtmm) outliers start: 25 outliers final: 25 residues processed: 145 average time/residue: 0.2114 time to fit residues: 42.1786 Evaluate side-chains 157 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 52 GLN 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 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 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 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 172 THR Chi-restraints excluded: chain E residue 186 GLN 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 355 ILE 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 26 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 10 optimal weight: 20.0000 chunk 15 optimal weight: 7.9990 chunk 74 optimal weight: 0.0270 chunk 4 optimal weight: 0.6980 overall best weight: 1.1444 ------------------------------------------------------------------------------- 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 = 0.4579 r_free = 0.4579 target = 0.215912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.172660 restraints weight = 11079.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.176332 restraints weight = 7534.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.176108 restraints weight = 5777.771| |-----------------------------------------------------------------------------| r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.117 8779 Z= 0.228 Angle : 0.625 11.323 11893 Z= 0.329 Chirality : 0.043 0.234 1353 Planarity : 0.004 0.049 1497 Dihedral : 4.850 84.247 1207 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.70 % Allowed : 20.39 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.26), residues: 1084 helix: 1.50 (0.28), residues: 381 sheet: -0.50 (0.31), residues: 253 loop : -1.13 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 387 HIS 0.004 0.001 HIS B 91 PHE 0.016 0.001 PHE E 68 TYR 0.032 0.002 TYR A 230 ARG 0.004 0.000 ARG R 327 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1984.04 seconds wall clock time: 36 minutes 59.32 seconds (2219.32 seconds total)