Starting phenix.real_space_refine on Tue Mar 3 22:22:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wbj_32401/03_2026/7wbj_32401.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wbj_32401/03_2026/7wbj_32401.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wbj_32401/03_2026/7wbj_32401.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wbj_32401/03_2026/7wbj_32401.map" model { file = "/net/cci-nas-00/data/ceres_data/7wbj_32401/03_2026/7wbj_32401.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wbj_32401/03_2026/7wbj_32401.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.064 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 57 5.16 5 C 5704 2.51 5 N 1550 2.21 5 O 1678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8989 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2871 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 344} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 221 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "A" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1931 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2590 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 418 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 958 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 1.88, per 1000 atoms: 0.21 Number of scatterers: 8989 At special positions: 0 Unit cell: (87.822, 100.674, 167.076, 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 57 16.00 O 1678 8.00 N 1550 7.00 C 5704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 38 " - pdb=" SG CYS R 61 " distance=2.03 Simple disulfide: pdb=" SG CYS R 52 " - pdb=" SG CYS R 93 " distance=2.03 Simple disulfide: pdb=" SG CYS R 75 " - pdb=" SG CYS R 109 " distance=2.03 Simple disulfide: pdb=" SG CYS R 202 " - pdb=" SG CYS R 271 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 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: 0.63 Conformation dependent library (CDL) restraints added in 419.6 milliseconds 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 13 sheets defined 38.4% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'R' and resid 31 through 38 removed outlier: 3.518A pdb=" N CYS R 38 " --> pdb=" O GLU R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 110 Processing helix chain 'R' and resid 115 through 151 removed outlier: 4.092A pdb=" N THR R 121 " --> pdb=" O GLU R 117 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR R 143 " --> pdb=" O MET R 139 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE R 146 " --> pdb=" O ALA R 142 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU R 148 " --> pdb=" O GLY R 144 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE R 151 " --> pdb=" O ILE R 147 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 155 Processing helix chain 'R' and resid 156 through 182 removed outlier: 3.709A pdb=" N ASP R 180 " --> pdb=" O VAL R 176 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASP R 181 " --> pdb=" O LEU R 177 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL R 182 " --> pdb=" O VAL R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 196 through 219 Processing helix chain 'R' and resid 220 through 230 Processing helix chain 'R' and resid 239 through 261 removed outlier: 3.622A pdb=" N ALA R 243 " --> pdb=" O ARG R 239 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU R 251 " --> pdb=" O ILE R 247 " (cutoff:3.500A) Proline residue: R 252 - end of helix Processing helix chain 'R' and resid 278 through 311 removed outlier: 3.578A pdb=" N VAL R 283 " --> pdb=" O VAL R 279 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ILE R 284 " --> pdb=" O PRO R 280 " (cutoff:3.500A) Proline residue: R 287 - end of helix removed outlier: 4.092A pdb=" N SER R 291 " --> pdb=" O PRO R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 323 through 338 Proline residue: R 335 - end of helix Processing helix chain 'R' and resid 339 through 343 Processing helix chain 'R' and resid 354 through 362 Processing helix chain 'R' and resid 363 through 367 Processing helix chain 'R' and resid 368 through 376 removed outlier: 3.764A pdb=" N VAL R 373 " --> pdb=" O LEU R 369 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LEU R 374 " --> pdb=" O VAL R 370 " (cutoff:3.500A) Processing helix chain 'R' and resid 379 through 393 removed outlier: 4.502A pdb=" N GLU R 385 " --> pdb=" O GLU R 381 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ARG R 388 " --> pdb=" O CYS R 384 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 27 Processing helix chain 'A' and resid 10 through 40 removed outlier: 4.630A pdb=" N ASN A 14 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLU A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP A 33 " --> pdb=" O GLN A 29 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 301 removed outlier: 3.677A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.782A pdb=" N ARG A 317 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 4.114A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 391 removed outlier: 3.933A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.734A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 35 removed outlier: 3.789A pdb=" N ASN B 35 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.820A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA G 23 " --> pdb=" O LEU G 19 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 35 Processing helix chain 'G' and resid 36 through 44 removed outlier: 3.502A pdb=" N CYS G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 56 through 57 removed outlier: 4.037A pdb=" N ASP R 57 " --> pdb=" O THR R 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 91 through 93 removed outlier: 3.625A pdb=" N ASN R 92 " --> pdb=" O GLU R 100 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLU R 100 " --> pdb=" O ASN R 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 211 through 214 removed outlier: 6.865A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 207 through 208 Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.652A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.048A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.509A pdb=" N ALA B 104 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.834A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 189 removed outlier: 4.027A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 232 removed outlier: 3.715A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 277 Processing sheet with id=AB3, first strand: chain 'N' and resid 3 through 6 removed outlier: 3.661A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP N 73 " --> pdb=" O THR N 78 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.660A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) 364 hydrogen bonds defined for protein. 1032 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: 1.49 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2663 1.33 - 1.46: 1655 1.46 - 1.58: 4787 1.58 - 1.70: 0 1.70 - 1.82: 74 Bond restraints: 9179 Sorted by residual: bond pdb=" C ALA N 101 " pdb=" N PRO N 102 " ideal model delta sigma weight residual 1.329 1.385 -0.057 1.20e-02 6.94e+03 2.24e+01 bond pdb=" CA ALA N 101 " pdb=" C ALA N 101 " ideal model delta sigma weight residual 1.523 1.560 -0.037 1.19e-02 7.06e+03 9.79e+00 bond pdb=" CA PHE N 108 " pdb=" C PHE N 108 " ideal model delta sigma weight residual 1.526 1.507 0.019 9.20e-03 1.18e+04 4.34e+00 bond pdb=" C ILE R 286 " pdb=" N PRO R 287 " ideal model delta sigma weight residual 1.337 1.356 -0.019 9.80e-03 1.04e+04 3.84e+00 bond pdb=" CA CYS N 99 " pdb=" CB CYS N 99 " ideal model delta sigma weight residual 1.529 1.503 0.027 1.37e-02 5.33e+03 3.79e+00 ... (remaining 9174 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 12047 1.47 - 2.93: 316 2.93 - 4.40: 57 4.40 - 5.86: 15 5.86 - 7.33: 10 Bond angle restraints: 12445 Sorted by residual: angle pdb=" C ALA N 101 " pdb=" N PRO N 102 " pdb=" CA PRO N 102 " ideal model delta sigma weight residual 120.31 114.83 5.48 9.80e-01 1.04e+00 3.13e+01 angle pdb=" C VAL N 110 " pdb=" CA VAL N 110 " pdb=" CB VAL N 110 " ideal model delta sigma weight residual 111.29 117.65 -6.36 1.64e+00 3.72e-01 1.50e+01 angle pdb=" N PHE N 108 " pdb=" CA PHE N 108 " pdb=" C PHE N 108 " ideal model delta sigma weight residual 110.56 117.89 -7.33 1.94e+00 2.66e-01 1.43e+01 angle pdb=" N ILE R 31 " pdb=" CA ILE R 31 " pdb=" C ILE R 31 " ideal model delta sigma weight residual 113.42 109.12 4.30 1.17e+00 7.31e-01 1.35e+01 angle pdb=" N ALA N 101 " pdb=" CA ALA N 101 " pdb=" C ALA N 101 " ideal model delta sigma weight residual 109.44 115.67 -6.23 1.81e+00 3.05e-01 1.18e+01 ... (remaining 12440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 4886 17.89 - 35.79: 467 35.79 - 53.68: 84 53.68 - 71.57: 17 71.57 - 89.47: 9 Dihedral angle restraints: 5463 sinusoidal: 2129 harmonic: 3334 Sorted by residual: dihedral pdb=" CB CYS R 202 " pdb=" SG CYS R 202 " pdb=" SG CYS R 271 " pdb=" CB CYS R 271 " ideal model delta sinusoidal sigma weight residual 93.00 151.59 -58.59 1 1.00e+01 1.00e-02 4.60e+01 dihedral pdb=" CB CYS R 52 " pdb=" SG CYS R 52 " pdb=" SG CYS R 93 " pdb=" CB CYS R 93 " ideal model delta sinusoidal sigma weight residual 93.00 130.23 -37.23 1 1.00e+01 1.00e-02 1.96e+01 dihedral pdb=" SG CYS R 52 " pdb=" CB CYS R 93 " pdb=" SG CYS R 93 " pdb=" CA CYS R 93 " ideal model delta sinusoidal sigma weight residual -73.00 -12.21 -60.79 1 2.00e+01 2.50e-03 1.23e+01 ... (remaining 5460 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1192 0.062 - 0.125: 200 0.125 - 0.187: 8 0.187 - 0.250: 1 0.250 - 0.312: 2 Chirality restraints: 1403 Sorted by residual: chirality pdb=" CA ASP N 109 " pdb=" N ASP N 109 " pdb=" C ASP N 109 " pdb=" CB ASP N 109 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA ILE R 59 " pdb=" N ILE R 59 " pdb=" C ILE R 59 " pdb=" CB ILE R 59 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA CYS B 204 " pdb=" N CYS B 204 " pdb=" C CYS B 204 " pdb=" CB CYS B 204 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.29e-01 ... (remaining 1400 not shown) Planarity restraints: 1584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA N 101 " 0.027 5.00e-02 4.00e+02 4.18e-02 2.80e+00 pdb=" N PRO N 102 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO N 102 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO N 102 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS N 99 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO N 100 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO N 100 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO N 100 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 279 " -0.020 5.00e-02 4.00e+02 2.95e-02 1.39e+00 pdb=" N PRO R 280 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO R 280 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO R 280 " -0.017 5.00e-02 4.00e+02 ... (remaining 1581 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 6 1.99 - 2.72: 449 2.72 - 3.45: 13327 3.45 - 4.17: 20404 4.17 - 4.90: 37399 Nonbonded interactions: 71585 Sorted by model distance: nonbonded pdb=" C ASN A 278 " pdb=" OD2 ASP N 106 " model vdw 1.264 3.270 nonbonded pdb=" CA ASN A 278 " pdb=" OD2 ASP N 106 " model vdw 1.516 3.470 nonbonded pdb=" CB ASN A 278 " pdb=" OD2 ASP N 106 " model vdw 1.562 3.440 nonbonded pdb=" O ASN A 278 " pdb=" OD2 ASP N 106 " model vdw 1.659 3.040 nonbonded pdb=" CB ASN A 278 " pdb=" OD1 ASP N 106 " model vdw 1.844 3.440 ... (remaining 71580 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.260 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.410 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 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 : 0.004 0.057 9185 Z= 0.185 Angle : 0.610 7.326 12457 Z= 0.329 Chirality : 0.046 0.312 1403 Planarity : 0.004 0.042 1584 Dihedral : 14.592 89.466 3289 Min Nonbonded Distance : 1.264 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.21 % Allowed : 0.51 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.25), residues: 1128 helix: 0.78 (0.27), residues: 406 sheet: -1.84 (0.34), residues: 202 loop : -1.39 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 263 TYR 0.014 0.001 TYR B 264 PHE 0.018 0.001 PHE B 278 TRP 0.009 0.001 TRP R 281 HIS 0.003 0.001 HIS R 191 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 9179) covalent geometry : angle 0.60873 (12445) SS BOND : bond 0.00502 ( 6) SS BOND : angle 1.32353 ( 12) hydrogen bonds : bond 0.13281 ( 364) hydrogen bonds : angle 6.13044 ( 1032) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 154 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 82 GLN cc_start: 0.8121 (tm-30) cc_final: 0.7903 (tm-30) outliers start: 2 outliers final: 0 residues processed: 155 average time/residue: 0.0782 time to fit residues: 17.2806 Evaluate side-chains 121 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.0570 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 0.0030 chunk 106 optimal weight: 0.9990 overall best weight: 0.5308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** 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 = 0.4338 r_free = 0.4338 target = 0.190031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.152073 restraints weight = 12917.655| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 3.10 r_work: 0.3646 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9185 Z= 0.127 Angle : 0.549 6.917 12457 Z= 0.286 Chirality : 0.042 0.154 1403 Planarity : 0.004 0.030 1584 Dihedral : 4.324 17.912 1241 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.85 % Allowed : 9.15 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.25), residues: 1128 helix: 1.03 (0.27), residues: 403 sheet: -1.78 (0.34), residues: 198 loop : -1.35 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 263 TYR 0.020 0.001 TYR R 130 PHE 0.017 0.001 PHE R 151 TRP 0.010 0.001 TRP R 390 HIS 0.004 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9179) covalent geometry : angle 0.54839 (12445) SS BOND : bond 0.00400 ( 6) SS BOND : angle 0.99061 ( 12) hydrogen bonds : bond 0.03677 ( 364) hydrogen bonds : angle 4.98230 ( 1032) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 8 ASP cc_start: 0.7689 (OUTLIER) cc_final: 0.7444 (t0) REVERT: A 266 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8143 (mt) REVERT: A 391 TYR cc_start: 0.7439 (m-80) cc_final: 0.7211 (m-80) REVERT: G 38 MET cc_start: 0.8082 (pmm) cc_final: 0.7188 (pmm) REVERT: N 82 GLN cc_start: 0.8117 (tm-30) cc_final: 0.6940 (tm-30) REVERT: N 94 TYR cc_start: 0.7969 (m-80) cc_final: 0.7302 (m-80) REVERT: N 117 TYR cc_start: 0.6007 (m-80) cc_final: 0.5733 (m-80) outliers start: 18 outliers final: 13 residues processed: 146 average time/residue: 0.0816 time to fit residues: 17.2392 Evaluate side-chains 127 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 174 ILE Chi-restraints excluded: chain R residue 385 GLU Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 74 optimal weight: 0.1980 chunk 37 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 59 ASN ** N 35 ASN ** 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 = 0.4340 r_free = 0.4340 target = 0.190132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.152037 restraints weight = 12940.965| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.99 r_work: 0.3656 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9185 Z= 0.126 Angle : 0.524 6.341 12457 Z= 0.274 Chirality : 0.041 0.165 1403 Planarity : 0.003 0.031 1584 Dihedral : 4.182 18.073 1241 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.88 % Allowed : 12.54 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.25), residues: 1128 helix: 1.09 (0.27), residues: 408 sheet: -1.79 (0.34), residues: 194 loop : -1.28 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 263 TYR 0.018 0.001 TYR R 130 PHE 0.013 0.001 PHE B 241 TRP 0.022 0.001 TRP B 169 HIS 0.003 0.001 HIS R 191 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9179) covalent geometry : angle 0.52292 (12445) SS BOND : bond 0.00495 ( 6) SS BOND : angle 1.13446 ( 12) hydrogen bonds : bond 0.03409 ( 364) hydrogen bonds : angle 4.75624 ( 1032) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 8 ASP cc_start: 0.7577 (t0) cc_final: 0.7293 (t0) REVERT: A 266 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8118 (mt) REVERT: A 391 TYR cc_start: 0.7380 (m-80) cc_final: 0.7109 (m-80) REVERT: B 169 TRP cc_start: 0.8187 (m100) cc_final: 0.7818 (m100) REVERT: B 303 ASP cc_start: 0.7370 (OUTLIER) cc_final: 0.7106 (m-30) REVERT: G 38 MET cc_start: 0.8053 (pmm) cc_final: 0.7598 (pmm) REVERT: N 82 GLN cc_start: 0.8557 (tm-30) cc_final: 0.8160 (tm-30) REVERT: N 94 TYR cc_start: 0.7935 (m-80) cc_final: 0.7156 (m-80) REVERT: N 117 TYR cc_start: 0.6090 (m-80) cc_final: 0.5783 (m-80) outliers start: 28 outliers final: 16 residues processed: 138 average time/residue: 0.0767 time to fit residues: 15.6756 Evaluate side-chains 132 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 174 ILE Chi-restraints excluded: chain R residue 222 VAL Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 385 GLU Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 70 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 3 optimal weight: 0.1980 chunk 89 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** 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 = 0.4304 r_free = 0.4304 target = 0.186582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.147869 restraints weight = 13048.089| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 2.98 r_work: 0.3620 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9185 Z= 0.189 Angle : 0.562 6.909 12457 Z= 0.294 Chirality : 0.043 0.174 1403 Planarity : 0.004 0.032 1584 Dihedral : 4.298 18.952 1241 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 4.21 % Allowed : 13.26 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.26), residues: 1128 helix: 1.03 (0.27), residues: 409 sheet: -2.00 (0.33), residues: 204 loop : -1.23 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 12 TYR 0.018 0.002 TYR R 130 PHE 0.012 0.002 PHE B 241 TRP 0.017 0.001 TRP B 169 HIS 0.003 0.001 HIS R 191 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 9179) covalent geometry : angle 0.56130 (12445) SS BOND : bond 0.00509 ( 6) SS BOND : angle 1.17011 ( 12) hydrogen bonds : bond 0.03541 ( 364) hydrogen bonds : angle 4.78411 ( 1032) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 125 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 342 MET cc_start: 0.7768 (tpp) cc_final: 0.7558 (tpp) REVERT: L 8 ASP cc_start: 0.7600 (t70) cc_final: 0.7241 (t0) REVERT: L 12 ARG cc_start: 0.8455 (mmm-85) cc_final: 0.8110 (mtp-110) REVERT: B 169 TRP cc_start: 0.8324 (m100) cc_final: 0.7814 (m100) REVERT: B 234 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7769 (m-80) REVERT: B 269 ILE cc_start: 0.7619 (OUTLIER) cc_final: 0.7357 (pt) REVERT: B 278 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.8172 (m-80) REVERT: G 38 MET cc_start: 0.8222 (pmm) cc_final: 0.7738 (pmm) REVERT: N 82 GLN cc_start: 0.8547 (tm-30) cc_final: 0.8093 (tm-30) REVERT: N 94 TYR cc_start: 0.8151 (m-80) cc_final: 0.7573 (m-80) REVERT: N 117 TYR cc_start: 0.6369 (m-80) cc_final: 0.6054 (m-80) outliers start: 41 outliers final: 26 residues processed: 152 average time/residue: 0.0840 time to fit residues: 18.2532 Evaluate side-chains 142 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 174 ILE Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain R residue 222 VAL Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 385 GLU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 37 optimal weight: 0.2980 chunk 47 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 71 optimal weight: 0.0000 chunk 84 optimal weight: 0.0570 chunk 106 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 35 ASN ** 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 = 0.4289 r_free = 0.4289 target = 0.188915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.141943 restraints weight = 12783.720| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 3.23 r_work: 0.3566 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9185 Z= 0.106 Angle : 0.494 6.978 12457 Z= 0.260 Chirality : 0.041 0.164 1403 Planarity : 0.003 0.029 1584 Dihedral : 4.019 19.804 1241 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.67 % Allowed : 16.55 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.26), residues: 1128 helix: 1.30 (0.28), residues: 408 sheet: -1.77 (0.34), residues: 194 loop : -1.25 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 12 TYR 0.015 0.001 TYR R 130 PHE 0.013 0.001 PHE N 68 TRP 0.010 0.001 TRP B 169 HIS 0.003 0.001 HIS R 191 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 9179) covalent geometry : angle 0.49372 (12445) SS BOND : bond 0.00348 ( 6) SS BOND : angle 0.73013 ( 12) hydrogen bonds : bond 0.03054 ( 364) hydrogen bonds : angle 4.53541 ( 1032) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 342 MET cc_start: 0.7963 (tpp) cc_final: 0.7673 (tpp) REVERT: L 8 ASP cc_start: 0.7689 (t70) cc_final: 0.7400 (t0) REVERT: L 12 ARG cc_start: 0.8443 (mmm-85) cc_final: 0.8117 (mtp-110) REVERT: A 266 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8097 (mt) REVERT: A 391 TYR cc_start: 0.7281 (m-80) cc_final: 0.6984 (m-80) REVERT: B 169 TRP cc_start: 0.8355 (m100) cc_final: 0.7794 (m100) REVERT: B 234 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7671 (m-80) REVERT: B 269 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.7190 (pt) REVERT: B 339 TRP cc_start: 0.7826 (OUTLIER) cc_final: 0.7521 (m-90) REVERT: G 38 MET cc_start: 0.8206 (pmm) cc_final: 0.7684 (pmm) REVERT: N 82 GLN cc_start: 0.8548 (tm-30) cc_final: 0.8032 (tm-30) REVERT: N 94 TYR cc_start: 0.8110 (m-80) cc_final: 0.7346 (m-80) REVERT: N 117 TYR cc_start: 0.6143 (m-80) cc_final: 0.5863 (m-80) outliers start: 26 outliers final: 16 residues processed: 148 average time/residue: 0.0767 time to fit residues: 16.7086 Evaluate side-chains 138 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 222 VAL Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 385 GLU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 84 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 26 optimal weight: 0.3980 chunk 107 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 60 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** 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 = 0.4239 r_free = 0.4239 target = 0.183933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.131300 restraints weight = 12806.470| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 3.07 r_work: 0.3488 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9185 Z= 0.210 Angle : 0.569 7.036 12457 Z= 0.299 Chirality : 0.043 0.157 1403 Planarity : 0.004 0.035 1584 Dihedral : 4.319 19.725 1241 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.21 % Allowed : 16.65 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.26), residues: 1128 helix: 1.12 (0.27), residues: 407 sheet: -1.90 (0.34), residues: 198 loop : -1.21 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 317 TYR 0.018 0.002 TYR N 60 PHE 0.015 0.002 PHE N 68 TRP 0.013 0.002 TRP B 169 HIS 0.003 0.001 HIS R 191 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 9179) covalent geometry : angle 0.56878 (12445) SS BOND : bond 0.00490 ( 6) SS BOND : angle 0.97112 ( 12) hydrogen bonds : bond 0.03575 ( 364) hydrogen bonds : angle 4.70515 ( 1032) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 121 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 356 GLN cc_start: 0.7391 (pp30) cc_final: 0.6343 (pm20) REVERT: L 8 ASP cc_start: 0.7796 (t70) cc_final: 0.7486 (t0) REVERT: B 58 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8557 (mt) REVERT: B 169 TRP cc_start: 0.8503 (m100) cc_final: 0.7864 (m100) REVERT: B 234 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.7539 (m-80) REVERT: B 269 ILE cc_start: 0.7604 (OUTLIER) cc_final: 0.7282 (pt) REVERT: G 38 MET cc_start: 0.8114 (pmm) cc_final: 0.7653 (pmm) REVERT: N 82 GLN cc_start: 0.8535 (tm-30) cc_final: 0.8144 (tm-30) REVERT: N 94 TYR cc_start: 0.8326 (m-80) cc_final: 0.7759 (m-80) REVERT: N 117 TYR cc_start: 0.6272 (m-80) cc_final: 0.6028 (m-80) outliers start: 41 outliers final: 27 residues processed: 149 average time/residue: 0.0733 time to fit residues: 16.1170 Evaluate side-chains 146 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 174 ILE Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain R residue 222 VAL Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 385 GLU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 17 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 7 optimal weight: 8.9990 chunk 2 optimal weight: 50.0000 chunk 42 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 0.0980 chunk 18 optimal weight: 0.7980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN ** N 35 ASN ** 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 = 0.4268 r_free = 0.4268 target = 0.186762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.137332 restraints weight = 12786.902| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 3.53 r_work: 0.3516 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9185 Z= 0.132 Angle : 0.521 8.928 12457 Z= 0.271 Chirality : 0.041 0.147 1403 Planarity : 0.003 0.034 1584 Dihedral : 4.159 17.304 1241 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.88 % Allowed : 19.01 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.26), residues: 1128 helix: 1.26 (0.27), residues: 415 sheet: -1.80 (0.34), residues: 194 loop : -1.22 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 12 TYR 0.015 0.001 TYR R 130 PHE 0.017 0.001 PHE N 68 TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS R 191 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9179) covalent geometry : angle 0.52001 (12445) SS BOND : bond 0.00505 ( 6) SS BOND : angle 0.89498 ( 12) hydrogen bonds : bond 0.03211 ( 364) hydrogen bonds : angle 4.56986 ( 1032) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 333 LEU cc_start: 0.8221 (tp) cc_final: 0.7976 (mt) REVERT: R 356 GLN cc_start: 0.7333 (pp30) cc_final: 0.6264 (pm20) REVERT: L 8 ASP cc_start: 0.7847 (t70) cc_final: 0.7521 (t0) REVERT: L 12 ARG cc_start: 0.8485 (mmm-85) cc_final: 0.8163 (mtp-110) REVERT: A 311 TYR cc_start: 0.7980 (m-80) cc_final: 0.7743 (m-80) REVERT: B 169 TRP cc_start: 0.8493 (m100) cc_final: 0.8263 (m100) REVERT: B 234 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7601 (m-80) REVERT: B 269 ILE cc_start: 0.7605 (OUTLIER) cc_final: 0.7270 (pt) REVERT: B 339 TRP cc_start: 0.7809 (OUTLIER) cc_final: 0.7441 (m-90) REVERT: G 38 MET cc_start: 0.8178 (pmm) cc_final: 0.7629 (pmm) REVERT: N 82 GLN cc_start: 0.8576 (tm-30) cc_final: 0.8145 (tm-30) REVERT: N 94 TYR cc_start: 0.8259 (m-80) cc_final: 0.7638 (m-80) REVERT: N 117 TYR cc_start: 0.6303 (m-80) cc_final: 0.5975 (m-80) outliers start: 28 outliers final: 19 residues processed: 143 average time/residue: 0.0702 time to fit residues: 14.9412 Evaluate side-chains 137 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 174 ILE Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain R residue 222 VAL Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 385 GLU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 26 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 41 optimal weight: 0.0170 chunk 30 optimal weight: 0.6980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 35 ASN ** 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 = 0.4275 r_free = 0.4275 target = 0.187336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.138627 restraints weight = 12669.920| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 3.54 r_work: 0.3524 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9185 Z= 0.127 Angle : 0.517 8.209 12457 Z= 0.268 Chirality : 0.041 0.148 1403 Planarity : 0.003 0.031 1584 Dihedral : 4.071 18.374 1241 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.57 % Allowed : 20.35 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.26), residues: 1128 helix: 1.36 (0.27), residues: 415 sheet: -1.74 (0.34), residues: 194 loop : -1.20 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 12 TYR 0.015 0.001 TYR R 130 PHE 0.012 0.001 PHE B 241 TRP 0.009 0.001 TRP R 219 HIS 0.003 0.001 HIS R 191 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9179) covalent geometry : angle 0.51662 (12445) SS BOND : bond 0.00530 ( 6) SS BOND : angle 0.93070 ( 12) hydrogen bonds : bond 0.03151 ( 364) hydrogen bonds : angle 4.52343 ( 1032) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 333 LEU cc_start: 0.8207 (tp) cc_final: 0.7961 (mt) REVERT: L 8 ASP cc_start: 0.7831 (t70) cc_final: 0.7560 (t70) REVERT: L 12 ARG cc_start: 0.8472 (mmm-85) cc_final: 0.8142 (mtp-110) REVERT: A 311 TYR cc_start: 0.7986 (m-80) cc_final: 0.7735 (m-80) REVERT: B 169 TRP cc_start: 0.8460 (m100) cc_final: 0.7867 (m100) REVERT: B 234 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7571 (m-80) REVERT: B 269 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7260 (pt) REVERT: B 339 TRP cc_start: 0.7789 (OUTLIER) cc_final: 0.7430 (m-90) REVERT: G 38 MET cc_start: 0.8226 (pmm) cc_final: 0.7691 (pmm) REVERT: G 40 TYR cc_start: 0.7380 (t80) cc_final: 0.7153 (t80) REVERT: N 82 GLN cc_start: 0.8618 (tm-30) cc_final: 0.8001 (tm-30) REVERT: N 94 TYR cc_start: 0.8230 (m-80) cc_final: 0.7645 (m-80) REVERT: N 117 TYR cc_start: 0.6270 (m-80) cc_final: 0.5905 (m-80) outliers start: 25 outliers final: 19 residues processed: 141 average time/residue: 0.0759 time to fit residues: 15.8365 Evaluate side-chains 138 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain R residue 222 VAL Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 385 GLU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 11 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 99 optimal weight: 0.0870 chunk 44 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 35 ASN ** 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 = 0.4273 r_free = 0.4273 target = 0.187147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.135506 restraints weight = 12756.211| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 3.05 r_work: 0.3547 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9185 Z= 0.131 Angle : 0.523 7.934 12457 Z= 0.271 Chirality : 0.041 0.148 1403 Planarity : 0.004 0.061 1584 Dihedral : 4.082 18.826 1241 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.29 % Allowed : 19.84 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.26), residues: 1128 helix: 1.38 (0.27), residues: 415 sheet: -1.74 (0.34), residues: 194 loop : -1.18 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 12 TYR 0.015 0.001 TYR R 130 PHE 0.017 0.001 PHE N 68 TRP 0.010 0.001 TRP R 219 HIS 0.003 0.001 HIS R 191 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9179) covalent geometry : angle 0.52320 (12445) SS BOND : bond 0.00495 ( 6) SS BOND : angle 0.76849 ( 12) hydrogen bonds : bond 0.03135 ( 364) hydrogen bonds : angle 4.51912 ( 1032) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: R 333 LEU cc_start: 0.8202 (tp) cc_final: 0.7965 (mt) REVERT: L 8 ASP cc_start: 0.7771 (t70) cc_final: 0.7500 (t70) REVERT: L 12 ARG cc_start: 0.8460 (mmm-85) cc_final: 0.8128 (mtp-110) REVERT: B 55 LEU cc_start: 0.8975 (mm) cc_final: 0.8730 (mp) REVERT: B 169 TRP cc_start: 0.8463 (m100) cc_final: 0.8231 (m100) REVERT: B 234 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.7553 (m-80) REVERT: B 269 ILE cc_start: 0.7597 (OUTLIER) cc_final: 0.7273 (pt) REVERT: B 339 TRP cc_start: 0.7801 (OUTLIER) cc_final: 0.7372 (m-90) REVERT: G 38 MET cc_start: 0.8113 (pmm) cc_final: 0.7738 (pmm) REVERT: N 82 GLN cc_start: 0.8634 (tm-30) cc_final: 0.8279 (tm-30) REVERT: N 94 TYR cc_start: 0.8226 (m-80) cc_final: 0.7679 (m-80) REVERT: N 117 TYR cc_start: 0.6261 (m-80) cc_final: 0.5900 (m-80) outliers start: 32 outliers final: 22 residues processed: 139 average time/residue: 0.0741 time to fit residues: 15.3376 Evaluate side-chains 138 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 174 ILE Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain R residue 222 VAL Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 385 GLU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 40 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 28 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 105 optimal weight: 0.2980 chunk 11 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.187106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.145955 restraints weight = 12701.428| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 3.35 r_work: 0.3550 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9185 Z= 0.117 Angle : 0.520 8.655 12457 Z= 0.268 Chirality : 0.041 0.156 1403 Planarity : 0.003 0.053 1584 Dihedral : 4.032 19.836 1241 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.57 % Allowed : 20.55 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.26), residues: 1128 helix: 1.41 (0.27), residues: 415 sheet: -1.65 (0.35), residues: 185 loop : -1.20 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 12 TYR 0.014 0.001 TYR R 130 PHE 0.017 0.001 PHE B 241 TRP 0.012 0.001 TRP R 281 HIS 0.003 0.001 HIS R 191 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9179) covalent geometry : angle 0.51945 (12445) SS BOND : bond 0.00378 ( 6) SS BOND : angle 0.64239 ( 12) hydrogen bonds : bond 0.03057 ( 364) hydrogen bonds : angle 4.46928 ( 1032) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: R 333 LEU cc_start: 0.8224 (tp) cc_final: 0.7982 (mt) REVERT: L 8 ASP cc_start: 0.7741 (t70) cc_final: 0.7462 (t70) REVERT: L 12 ARG cc_start: 0.8451 (mmm-85) cc_final: 0.8093 (mtp-110) REVERT: A 311 TYR cc_start: 0.7834 (m-80) cc_final: 0.7619 (m-80) REVERT: B 169 TRP cc_start: 0.8475 (m100) cc_final: 0.7890 (m100) REVERT: B 269 ILE cc_start: 0.7632 (OUTLIER) cc_final: 0.7287 (pt) REVERT: B 339 TRP cc_start: 0.7800 (OUTLIER) cc_final: 0.7420 (m-90) REVERT: G 38 MET cc_start: 0.7981 (pmm) cc_final: 0.7589 (pmm) REVERT: N 35 ASN cc_start: 0.7535 (OUTLIER) cc_final: 0.7073 (p0) REVERT: N 82 GLN cc_start: 0.8598 (tm-30) cc_final: 0.8241 (tm-30) REVERT: N 94 TYR cc_start: 0.8176 (m-80) cc_final: 0.7557 (m-80) REVERT: N 117 TYR cc_start: 0.6214 (m-80) cc_final: 0.5865 (m-80) outliers start: 25 outliers final: 20 residues processed: 133 average time/residue: 0.0739 time to fit residues: 14.5082 Evaluate side-chains 134 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 385 GLU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 100 optimal weight: 0.0470 chunk 50 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 8 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 87 optimal weight: 0.4980 chunk 16 optimal weight: 0.6980 chunk 90 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 31 optimal weight: 0.0980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** 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 = 0.4273 r_free = 0.4273 target = 0.187139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.146005 restraints weight = 12544.755| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 3.44 r_work: 0.3557 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.168 9185 Z= 0.264 Angle : 0.887 59.161 12457 Z= 0.525 Chirality : 0.043 0.552 1403 Planarity : 0.004 0.051 1584 Dihedral : 4.037 19.872 1241 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.57 % Allowed : 20.97 % Favored : 76.46 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.26), residues: 1128 helix: 1.42 (0.27), residues: 415 sheet: -1.62 (0.36), residues: 185 loop : -1.20 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 12 TYR 0.015 0.001 TYR R 130 PHE 0.016 0.001 PHE B 241 TRP 0.011 0.001 TRP R 281 HIS 0.003 0.001 HIS R 191 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 9179) covalent geometry : angle 0.88738 (12445) SS BOND : bond 0.00531 ( 6) SS BOND : angle 0.76860 ( 12) hydrogen bonds : bond 0.03036 ( 364) hydrogen bonds : angle 4.50999 ( 1032) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2136.86 seconds wall clock time: 37 minutes 23.15 seconds (2243.15 seconds total)