Starting phenix.real_space_refine on Thu Jul 2 06:42:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dye_47301/07_2026/9dye_47301_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dye_47301/07_2026/9dye_47301.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dye_47301/07_2026/9dye_47301.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dye_47301/07_2026/9dye_47301.map" model { file = "/net/cci-nas-00/data/ceres_data/9dye_47301/07_2026/9dye_47301_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dye_47301/07_2026/9dye_47301_neut.cif" } resolution = 2.9 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= 0.000 sd= 0.036 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 52 5.16 5 C 4539 2.51 5 N 1207 2.21 5 O 1306 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7106 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1704 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 4, 'TRANS': 210} Chain breaks: 2 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "R" Number of atoms: 2244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2244 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 272} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "R" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 141 Unusual residues: {'CLR': 2, 'J40': 1, 'YLX': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 1.56, per 1000 atoms: 0.22 Number of scatterers: 7106 At special positions: 0 Unit cell: (76.893, 102.885, 132.126, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 P 2 15.00 O 1306 8.00 N 1207 7.00 C 4539 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 187 " distance=2.04 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: 0.46 Conformation dependent library (CDL) restraints added in 387.9 milliseconds 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1680 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 8 sheets defined 48.5% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 6 through 30 Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.672A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.340A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.596A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 255 through 260 removed outlier: 6.033A pdb=" N PHE A 258 " --> pdb=" O ASN A 255 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.713A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.562A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.534A pdb=" N ALA A 300 " --> pdb=" O TYR A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 351 removed outlier: 3.633A pdb=" N VAL A 334 " --> pdb=" O ASN A 330 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.719A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'R' and resid 36 through 64 Processing helix chain 'R' and resid 69 through 100 removed outlier: 4.552A pdb=" N LEU R 90 " --> pdb=" O SER R 86 " (cutoff:3.500A) Proline residue: R 91 - end of helix Processing helix chain 'R' and resid 105 through 140 removed outlier: 3.517A pdb=" N LEU R 118 " --> pdb=" O ALA R 114 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N CYS R 119 " --> pdb=" O LEU R 115 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS R 120 " --> pdb=" O ASP R 116 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU R 127 " --> pdb=" O SER R 123 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS R 128 " --> pdb=" O ILE R 124 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA R 131 " --> pdb=" O LEU R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 147 removed outlier: 3.516A pdb=" N VAL R 145 " --> pdb=" O PRO R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 169 removed outlier: 3.686A pdb=" N ALA R 153 " --> pdb=" O THR R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 181 removed outlier: 4.081A pdb=" N ARG R 181 " --> pdb=" O PRO R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 192 through 204 Processing helix chain 'R' and resid 204 through 227 Processing helix chain 'R' and resid 326 through 368 removed outlier: 4.438A pdb=" N VAL R 344 " --> pdb=" O GLU R 340 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU R 347 " --> pdb=" O THR R 343 " (cutoff:3.500A) Proline residue: R 360 - end of helix removed outlier: 3.632A pdb=" N VAL R 364 " --> pdb=" O PRO R 360 " (cutoff:3.500A) Processing helix chain 'R' and resid 378 through 401 removed outlier: 3.966A pdb=" N ASN R 392 " --> pdb=" O LEU R 388 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N SER R 393 " --> pdb=" O GLY R 389 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU R 394 " --> pdb=" O TYR R 390 " (cutoff:3.500A) Proline residue: R 397 - end of helix Processing helix chain 'R' and resid 404 through 415 removed outlier: 3.574A pdb=" N GLN R 408 " --> pdb=" O ASN R 404 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.993A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.573A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.855A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.785A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.737A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.500A 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: 6.676A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.841A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 371 hydrogen bonds defined for protein. 1074 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: 0.96 Time building geometry restraints manager: 0.56 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: 1301 1.32 - 1.45: 1767 1.45 - 1.57: 4099 1.57 - 1.69: 9 1.69 - 1.81: 72 Bond restraints: 7248 Sorted by residual: bond pdb=" N LEU R 368 " pdb=" CA LEU R 368 " ideal model delta sigma weight residual 1.461 1.498 -0.037 9.20e-03 1.18e+04 1.62e+01 bond pdb=" O4 J40 R 504 " pdb=" P4 J40 R 504 " ideal model delta sigma weight residual 1.702 1.629 0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" N ILE G 25 " pdb=" CA ILE G 25 " ideal model delta sigma weight residual 1.455 1.496 -0.041 1.18e-02 7.18e+03 1.20e+01 bond pdb=" O42 J40 R 504 " pdb=" P4 J40 R 504 " ideal model delta sigma weight residual 1.548 1.484 0.064 2.00e-02 2.50e+03 1.04e+01 bond pdb=" N VAL B 112 " pdb=" CA VAL B 112 " ideal model delta sigma weight residual 1.456 1.492 -0.037 1.15e-02 7.56e+03 1.03e+01 ... (remaining 7243 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.94: 9788 3.94 - 7.89: 35 7.89 - 11.83: 1 11.83 - 15.77: 0 15.77 - 19.71: 1 Bond angle restraints: 9825 Sorted by residual: angle pdb=" O1 J40 R 504 " pdb=" P1 J40 R 504 " pdb=" O13 J40 R 504 " ideal model delta sigma weight residual 92.86 112.57 -19.71 3.00e+00 1.11e-01 4.32e+01 angle pdb=" CA GLY A 40 " pdb=" C GLY A 40 " pdb=" O GLY A 40 " ideal model delta sigma weight residual 122.45 118.46 3.99 7.20e-01 1.93e+00 3.07e+01 angle pdb=" CA PRO R 170 " pdb=" C PRO R 170 " pdb=" N PRO R 171 " ideal model delta sigma weight residual 117.93 123.00 -5.07 1.20e+00 6.94e-01 1.78e+01 angle pdb=" N PRO R 170 " pdb=" CA PRO R 170 " pdb=" C PRO R 170 " ideal model delta sigma weight residual 110.70 115.55 -4.85 1.22e+00 6.72e-01 1.58e+01 angle pdb=" CA VAL R 37 " pdb=" C VAL R 37 " pdb=" O VAL R 37 " ideal model delta sigma weight residual 121.29 117.47 3.82 1.07e+00 8.73e-01 1.27e+01 ... (remaining 9820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.74: 4381 31.74 - 63.49: 87 63.49 - 95.23: 20 95.23 - 126.97: 5 126.97 - 158.72: 2 Dihedral angle restraints: 4495 sinusoidal: 1904 harmonic: 2591 Sorted by residual: dihedral pdb=" C11 YLX R 501 " pdb=" C12 YLX R 501 " pdb=" N1 YLX R 501 " pdb=" C20 YLX R 501 " ideal model delta sinusoidal sigma weight residual 283.89 125.17 158.72 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" CA MET A 322 " pdb=" C MET A 322 " pdb=" N THR A 323 " pdb=" CA THR A 323 " ideal model delta harmonic sigma weight residual 180.00 -157.45 -22.55 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" C10 YLX R 501 " pdb=" C11 YLX R 501 " pdb=" C12 YLX R 501 " pdb=" N1 YLX R 501 " ideal model delta sinusoidal sigma weight residual -68.74 80.60 -149.34 1 3.00e+01 1.11e-03 1.98e+01 ... (remaining 4492 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 574 0.042 - 0.085: 268 0.085 - 0.127: 199 0.127 - 0.170: 79 0.170 - 0.212: 10 Chirality restraints: 1130 Sorted by residual: chirality pdb=" CB VAL G 54 " pdb=" CA VAL G 54 " pdb=" CG1 VAL G 54 " pdb=" CG2 VAL G 54 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CB VAL B 71 " pdb=" CA VAL B 71 " pdb=" CG1 VAL B 71 " pdb=" CG2 VAL B 71 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.93e-01 chirality pdb=" CA VAL A 225 " pdb=" N VAL A 225 " pdb=" C VAL A 225 " pdb=" CB VAL A 225 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.95e-01 ... (remaining 1127 not shown) Planarity restraints: 1227 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N YLX R 501 " 0.033 2.00e-02 2.50e+03 2.15e-01 6.92e+02 pdb=" C YLX R 501 " 0.028 2.00e-02 2.50e+03 pdb=" O YLX R 501 " 0.255 2.00e-02 2.50e+03 pdb=" C1 YLX R 501 " -0.274 2.00e-02 2.50e+03 pdb=" C8 YLX R 501 " 0.238 2.00e-02 2.50e+03 pdb=" C9 YLX R 501 " -0.280 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C15 YLX R 501 " 0.021 2.00e-02 2.50e+03 2.13e-02 7.93e+00 pdb=" C16 YLX R 501 " -0.002 2.00e-02 2.50e+03 pdb=" C17 YLX R 501 " -0.024 2.00e-02 2.50e+03 pdb=" C18 YLX R 501 " -0.003 2.00e-02 2.50e+03 pdb=" N2 YLX R 501 " -0.035 2.00e-02 2.50e+03 pdb=" N3 YLX R 501 " 0.021 2.00e-02 2.50e+03 pdb=" N4 YLX R 501 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 35 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.46e+00 pdb=" C LYS A 35 " 0.032 2.00e-02 2.50e+03 pdb=" O LYS A 35 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU A 36 " -0.011 2.00e-02 2.50e+03 ... (remaining 1224 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1902 2.84 - 3.35: 6566 3.35 - 3.87: 11133 3.87 - 4.38: 13250 4.38 - 4.90: 22777 Nonbonded interactions: 55628 Sorted by model distance: nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.322 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.345 3.040 nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.370 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.412 3.040 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.418 3.040 ... (remaining 55623 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.190 Find NCS groups from input model: 0.040 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:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 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 : 0.009 0.073 7249 Z= 0.663 Angle : 1.096 19.714 9827 Z= 0.801 Chirality : 0.069 0.212 1130 Planarity : 0.007 0.215 1227 Dihedral : 15.315 158.716 2812 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.40 % Allowed : 1.59 % Favored : 98.01 % 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: -1.68 (0.27), residues: 878 helix: -0.95 (0.23), residues: 398 sheet: -0.24 (0.42), residues: 158 loop : -1.57 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 339 TYR 0.010 0.001 TYR R 205 PHE 0.009 0.001 PHE B 199 TRP 0.011 0.001 TRP R 387 HIS 0.003 0.001 HIS R 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00904 / 0.66 ( 7248) covalent geometry : angle 1.09533 / 0.80 ( 9825) SS BOND : bond 0.00616 / 0.32 ( 1) SS BOND : angle 2.60971 / 1.50 ( 2) hydrogen bonds : bond 0.22616 / 15.69 ( 371) hydrogen bonds : angle 7.43890 / 5.21 ( 1074) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 114 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7850 (tttt) cc_final: 0.7620 (ttpt) REVERT: A 216 GLU cc_start: 0.8189 (tt0) cc_final: 0.7938 (tt0) REVERT: B 46 ARG cc_start: 0.7125 (mtt180) cc_final: 0.6850 (mtp85) REVERT: B 217 MET cc_start: 0.7298 (ptt) cc_final: 0.7062 (pmt) REVERT: B 226 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7946 (mt-10) REVERT: B 258 ASP cc_start: 0.8030 (t0) cc_final: 0.7785 (t70) outliers start: 3 outliers final: 0 residues processed: 116 average time/residue: 0.4527 time to fit residues: 55.7362 Evaluate side-chains 80 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 ASN B 293 ASN R 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.162706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.115764 restraints weight = 7721.993| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.65 r_work: 0.3103 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7249 Z= 0.143 Angle : 0.582 9.097 9827 Z= 0.299 Chirality : 0.042 0.196 1130 Planarity : 0.004 0.042 1227 Dihedral : 13.310 167.753 1208 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.46 % Allowed : 9.15 % Favored : 89.39 % 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: 0.51 (0.29), residues: 878 helix: 1.62 (0.25), residues: 411 sheet: 0.24 (0.41), residues: 174 loop : -1.45 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 197 TYR 0.012 0.001 TYR R 205 PHE 0.013 0.002 PHE R 112 TRP 0.012 0.001 TRP R 175 HIS 0.004 0.001 HIS R 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 7248) covalent geometry : angle 0.58183 / 0.30 ( 9825) SS BOND : bond 0.00212 / 0.11 ( 1) SS BOND : angle 0.32682 / 0.18 ( 2) hydrogen bonds : bond 0.05455 / 3.67 ( 371) hydrogen bonds : angle 4.40439 / 3.11 ( 1074) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7116 (tttt) cc_final: 0.6854 (tttm) REVERT: B 46 ARG cc_start: 0.7400 (mtt180) cc_final: 0.6780 (mtp85) REVERT: B 217 MET cc_start: 0.7742 (ptt) cc_final: 0.7171 (pmt) REVERT: B 226 GLU cc_start: 0.8604 (mt-10) cc_final: 0.7976 (mt-10) REVERT: G 21 MET cc_start: 0.6618 (mmm) cc_final: 0.6151 (ttt) REVERT: R 104 LEU cc_start: 0.8249 (mt) cc_final: 0.7972 (mm) REVERT: R 223 ARG cc_start: 0.6962 (mmm-85) cc_final: 0.6163 (mtp-110) REVERT: R 227 ARG cc_start: 0.6988 (mtm-85) cc_final: 0.6692 (mtt180) outliers start: 11 outliers final: 8 residues processed: 99 average time/residue: 0.4695 time to fit residues: 49.5179 Evaluate side-chains 81 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 335 MET Chi-restraints excluded: chain R residue 349 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 18 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 41 optimal weight: 0.0010 chunk 85 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 119 ASN R 100 ASN R 193 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.158345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.110594 restraints weight = 7735.673| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.61 r_work: 0.3050 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7249 Z= 0.130 Angle : 0.557 9.761 9827 Z= 0.279 Chirality : 0.042 0.169 1130 Planarity : 0.003 0.032 1227 Dihedral : 12.597 176.483 1208 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.72 % Allowed : 12.20 % Favored : 86.07 % 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: 1.28 (0.30), residues: 878 helix: 2.52 (0.26), residues: 411 sheet: 0.38 (0.41), residues: 171 loop : -1.34 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 197 TYR 0.010 0.001 TYR R 205 PHE 0.014 0.001 PHE R 112 TRP 0.011 0.001 TRP R 175 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 7248) covalent geometry : angle 0.55714 / 0.28 ( 9825) SS BOND : bond 0.00168 / 0.09 ( 1) SS BOND : angle 0.39734 / 0.23 ( 2) hydrogen bonds : bond 0.04858 / 3.25 ( 371) hydrogen bonds : angle 4.02736 / 2.85 ( 1074) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.6822 (tttt) cc_final: 0.6599 (tttm) REVERT: A 188 HIS cc_start: 0.8262 (p90) cc_final: 0.8057 (p-80) REVERT: A 216 GLU cc_start: 0.8476 (tt0) cc_final: 0.8047 (tt0) REVERT: A 322 MET cc_start: 0.6975 (OUTLIER) cc_final: 0.6621 (mmm) REVERT: B 46 ARG cc_start: 0.7237 (mtt180) cc_final: 0.6552 (mtp85) REVERT: B 212 ASP cc_start: 0.8029 (t0) cc_final: 0.7585 (t0) REVERT: B 226 GLU cc_start: 0.8572 (mt-10) cc_final: 0.7855 (mt-10) REVERT: G 21 MET cc_start: 0.6455 (mmm) cc_final: 0.6061 (tmm) REVERT: R 84 MET cc_start: 0.6528 (ttm) cc_final: 0.6282 (mtp) REVERT: R 86 SER cc_start: 0.8598 (m) cc_final: 0.7950 (p) REVERT: R 100 ASN cc_start: 0.7377 (t0) cc_final: 0.7046 (t0) REVERT: R 104 LEU cc_start: 0.7713 (mt) cc_final: 0.7486 (mm) REVERT: R 223 ARG cc_start: 0.6540 (mmm-85) cc_final: 0.5764 (ttp-170) REVERT: R 227 ARG cc_start: 0.6773 (mtm-85) cc_final: 0.6453 (mtm-85) outliers start: 13 outliers final: 7 residues processed: 91 average time/residue: 0.4419 time to fit residues: 42.8658 Evaluate side-chains 83 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 227 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 0 optimal weight: 7.9990 chunk 62 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 57 optimal weight: 0.0470 chunk 41 optimal weight: 0.7980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 44 GLN B 155 ASN R 386 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.155797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.107352 restraints weight = 7873.054| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.64 r_work: 0.3089 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7249 Z= 0.116 Angle : 0.503 7.507 9827 Z= 0.259 Chirality : 0.041 0.132 1130 Planarity : 0.003 0.033 1227 Dihedral : 11.591 135.549 1208 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.65 % Allowed : 12.20 % Favored : 85.15 % 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: 1.47 (0.30), residues: 878 helix: 2.88 (0.26), residues: 405 sheet: 0.01 (0.39), residues: 182 loop : -1.22 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 197 TYR 0.009 0.001 TYR R 205 PHE 0.014 0.001 PHE R 112 TRP 0.011 0.001 TRP R 175 HIS 0.002 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 7248) covalent geometry : angle 0.50294 / 0.26 ( 9825) SS BOND : bond 0.00137 / 0.07 ( 1) SS BOND : angle 0.27062 / 0.16 ( 2) hydrogen bonds : bond 0.04309 / 2.86 ( 371) hydrogen bonds : angle 3.84394 / 2.71 ( 1074) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.6882 (tttt) cc_final: 0.6662 (tttm) REVERT: A 216 GLU cc_start: 0.8487 (tt0) cc_final: 0.8017 (tt0) REVERT: B 46 ARG cc_start: 0.7282 (mtt180) cc_final: 0.6611 (mtp85) REVERT: B 124 TYR cc_start: 0.8407 (m-80) cc_final: 0.8188 (m-80) REVERT: B 212 ASP cc_start: 0.8043 (t0) cc_final: 0.7692 (t0) REVERT: B 217 MET cc_start: 0.7990 (ptt) cc_final: 0.7100 (pmt) REVERT: B 226 GLU cc_start: 0.8612 (mt-10) cc_final: 0.7938 (mt-10) REVERT: B 290 ASP cc_start: 0.7852 (m-30) cc_final: 0.7620 (m-30) REVERT: G 21 MET cc_start: 0.6718 (mmm) cc_final: 0.6207 (tmm) REVERT: R 68 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7841 (mt0) REVERT: R 84 MET cc_start: 0.6589 (ttm) cc_final: 0.6325 (mtp) REVERT: R 86 SER cc_start: 0.8368 (m) cc_final: 0.7760 (p) REVERT: R 223 ARG cc_start: 0.6610 (mmm-85) cc_final: 0.5794 (ttp-170) REVERT: R 227 ARG cc_start: 0.6796 (mtm-85) cc_final: 0.6500 (mtm-85) outliers start: 20 outliers final: 9 residues processed: 99 average time/residue: 0.4893 time to fit residues: 51.4560 Evaluate side-chains 88 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 68 GLN Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 169 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 42 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 33 optimal weight: 0.0050 chunk 44 optimal weight: 0.6980 chunk 27 optimal weight: 0.1980 chunk 40 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS B 44 GLN B 155 ASN R 386 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.158493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.110628 restraints weight = 7747.757| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.58 r_work: 0.3002 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7249 Z= 0.100 Angle : 0.495 8.145 9827 Z= 0.249 Chirality : 0.040 0.134 1130 Planarity : 0.003 0.033 1227 Dihedral : 9.926 142.047 1208 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.52 % Allowed : 13.93 % Favored : 83.55 % 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: 1.63 (0.30), residues: 878 helix: 3.05 (0.27), residues: 404 sheet: 0.07 (0.39), residues: 182 loop : -1.17 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 197 TYR 0.007 0.001 TYR R 205 PHE 0.011 0.001 PHE R 112 TRP 0.010 0.001 TRP R 387 HIS 0.009 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 ( 7248) covalent geometry : angle 0.49544 / 0.25 ( 9825) SS BOND : bond 0.00140 / 0.07 ( 1) SS BOND : angle 0.15529 / 0.09 ( 2) hydrogen bonds : bond 0.03908 / 2.59 ( 371) hydrogen bonds : angle 3.72956 / 2.63 ( 1074) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.6899 (tttt) cc_final: 0.6632 (ttmt) REVERT: A 53 MET cc_start: 0.7410 (mtt) cc_final: 0.7160 (mtm) REVERT: B 46 ARG cc_start: 0.7220 (mtt180) cc_final: 0.6555 (mtp85) REVERT: B 124 TYR cc_start: 0.8367 (m-80) cc_final: 0.8107 (m-80) REVERT: B 143 THR cc_start: 0.8152 (m) cc_final: 0.7924 (m) REVERT: B 212 ASP cc_start: 0.8020 (t0) cc_final: 0.7666 (t0) REVERT: B 226 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8013 (mt-10) REVERT: B 234 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.7592 (m-80) REVERT: B 247 ASP cc_start: 0.6734 (t0) cc_final: 0.6143 (t0) REVERT: B 290 ASP cc_start: 0.7770 (m-30) cc_final: 0.7511 (m-30) REVERT: G 21 MET cc_start: 0.6593 (mmm) cc_final: 0.6075 (tmm) REVERT: R 68 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7548 (mt0) REVERT: R 84 MET cc_start: 0.6388 (ttm) cc_final: 0.6146 (mtp) REVERT: R 86 SER cc_start: 0.8264 (m) cc_final: 0.7678 (p) REVERT: R 223 ARG cc_start: 0.6510 (mmm-85) cc_final: 0.5699 (ttp-170) outliers start: 19 outliers final: 8 residues processed: 96 average time/residue: 0.4769 time to fit residues: 48.5249 Evaluate side-chains 92 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 68 GLN Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 169 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 12 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 83 optimal weight: 0.4980 chunk 64 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 58 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS B 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.153775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.105883 restraints weight = 7855.988| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.58 r_work: 0.2962 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7249 Z= 0.120 Angle : 0.510 10.464 9827 Z= 0.259 Chirality : 0.041 0.134 1130 Planarity : 0.003 0.032 1227 Dihedral : 9.924 148.910 1208 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.05 % Allowed : 13.66 % Favored : 83.29 % 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: 1.56 (0.30), residues: 878 helix: 3.02 (0.26), residues: 404 sheet: 0.01 (0.39), residues: 179 loop : -1.22 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 197 TYR 0.009 0.001 TYR R 195 PHE 0.012 0.001 PHE R 112 TRP 0.012 0.001 TRP R 387 HIS 0.007 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 7248) covalent geometry : angle 0.51021 / 0.26 ( 9825) SS BOND : bond 0.00156 / 0.08 ( 1) SS BOND : angle 0.17666 / 0.10 ( 2) hydrogen bonds : bond 0.04406 / 2.94 ( 371) hydrogen bonds : angle 3.79476 / 2.68 ( 1074) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.6891 (tttt) cc_final: 0.6630 (ttmt) REVERT: B 46 ARG cc_start: 0.7209 (mtt180) cc_final: 0.6545 (mtp85) REVERT: B 124 TYR cc_start: 0.8385 (m-80) cc_final: 0.8104 (m-80) REVERT: B 212 ASP cc_start: 0.8022 (t0) cc_final: 0.7660 (t0) REVERT: B 226 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8029 (mt-10) REVERT: B 234 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.7630 (m-80) REVERT: B 247 ASP cc_start: 0.6724 (t0) cc_final: 0.6126 (t0) REVERT: G 21 MET cc_start: 0.6574 (mmm) cc_final: 0.6057 (tmm) REVERT: R 68 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7575 (mt0) REVERT: R 116 ASP cc_start: 0.8301 (t0) cc_final: 0.8093 (t0) REVERT: R 227 ARG cc_start: 0.6568 (mtm-85) cc_final: 0.6347 (mtm-85) outliers start: 23 outliers final: 13 residues processed: 95 average time/residue: 0.4189 time to fit residues: 42.5227 Evaluate side-chains 90 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 68 GLN Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 344 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 46 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS R 386 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.152593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.104664 restraints weight = 7788.455| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.57 r_work: 0.2983 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7249 Z= 0.136 Angle : 0.513 9.604 9827 Z= 0.264 Chirality : 0.042 0.136 1130 Planarity : 0.003 0.031 1227 Dihedral : 10.352 158.245 1208 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.92 % Allowed : 14.06 % Favored : 83.02 % 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: 1.51 (0.30), residues: 878 helix: 2.96 (0.27), residues: 404 sheet: 0.03 (0.40), residues: 177 loop : -1.24 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 197 TYR 0.009 0.001 TYR R 205 PHE 0.014 0.001 PHE R 112 TRP 0.012 0.001 TRP R 175 HIS 0.008 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 7248) covalent geometry : angle 0.51350 / 0.26 ( 9825) SS BOND : bond 0.00180 / 0.09 ( 1) SS BOND : angle 0.13831 / 0.07 ( 2) hydrogen bonds : bond 0.04725 / 3.16 ( 371) hydrogen bonds : angle 3.85001 / 2.71 ( 1074) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.6996 (tttt) cc_final: 0.6633 (ttmt) REVERT: B 46 ARG cc_start: 0.7295 (mtt180) cc_final: 0.6619 (mtp85) REVERT: B 212 ASP cc_start: 0.8162 (t0) cc_final: 0.7742 (t0) REVERT: B 226 GLU cc_start: 0.8590 (mt-10) cc_final: 0.7868 (mt-10) REVERT: B 234 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.7838 (m-80) REVERT: B 290 ASP cc_start: 0.7570 (m-30) cc_final: 0.7263 (m-30) REVERT: G 21 MET cc_start: 0.6624 (mmm) cc_final: 0.6117 (tmm) REVERT: R 68 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7666 (mt0) REVERT: R 116 ASP cc_start: 0.8345 (t0) cc_final: 0.8129 (t0) REVERT: R 227 ARG cc_start: 0.6668 (mtm-85) cc_final: 0.6406 (mtm-85) outliers start: 22 outliers final: 15 residues processed: 94 average time/residue: 0.4766 time to fit residues: 47.7628 Evaluate side-chains 96 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 68 GLN Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 228 LYS Chi-restraints excluded: chain R residue 344 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 21 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 44 optimal weight: 0.2980 chunk 52 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 57 optimal weight: 0.0060 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.157161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.108845 restraints weight = 7808.111| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.60 r_work: 0.3047 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7249 Z= 0.108 Angle : 0.493 8.589 9827 Z= 0.255 Chirality : 0.041 0.150 1130 Planarity : 0.003 0.030 1227 Dihedral : 10.381 161.394 1208 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.25 % Allowed : 15.38 % Favored : 82.36 % 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: 1.53 (0.30), residues: 878 helix: 2.95 (0.27), residues: 405 sheet: -0.01 (0.40), residues: 179 loop : -1.17 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.008 0.001 TYR R 205 PHE 0.014 0.001 PHE R 112 TRP 0.014 0.001 TRP R 387 HIS 0.007 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 7248) covalent geometry : angle 0.49312 / 0.25 ( 9825) SS BOND : bond 0.00122 / 0.06 ( 1) SS BOND : angle 0.01876 / 0.01 ( 2) hydrogen bonds : bond 0.04240 / 2.82 ( 371) hydrogen bonds : angle 3.80800 / 2.69 ( 1074) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7007 (tttt) cc_final: 0.6746 (ttmt) REVERT: B 46 ARG cc_start: 0.7300 (mtt180) cc_final: 0.6632 (mtp85) REVERT: B 124 TYR cc_start: 0.8458 (m-80) cc_final: 0.8187 (m-80) REVERT: B 212 ASP cc_start: 0.8125 (t0) cc_final: 0.7769 (t0) REVERT: B 226 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8046 (mt-10) REVERT: B 234 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.7884 (m-80) REVERT: B 247 ASP cc_start: 0.6774 (t0) cc_final: 0.6261 (t0) REVERT: G 21 MET cc_start: 0.6651 (mmm) cc_final: 0.6293 (tpp) REVERT: R 68 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7653 (mt0) REVERT: R 116 ASP cc_start: 0.8277 (t0) cc_final: 0.8047 (t0) REVERT: R 227 ARG cc_start: 0.6651 (mtm-85) cc_final: 0.6423 (mtm-85) outliers start: 17 outliers final: 14 residues processed: 93 average time/residue: 0.4521 time to fit residues: 44.9075 Evaluate side-chains 94 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 68 GLN Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 228 LYS Chi-restraints excluded: chain R residue 344 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 61 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 42 optimal weight: 0.0980 chunk 57 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 67 optimal weight: 0.0770 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.154992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.107381 restraints weight = 7740.387| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.50 r_work: 0.3025 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7249 Z= 0.109 Angle : 0.505 9.816 9827 Z= 0.259 Chirality : 0.042 0.209 1130 Planarity : 0.003 0.030 1227 Dihedral : 10.225 158.046 1208 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.39 % Allowed : 15.25 % Favored : 82.36 % 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: 1.55 (0.30), residues: 878 helix: 2.93 (0.26), residues: 405 sheet: 0.02 (0.40), residues: 179 loop : -1.12 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 197 TYR 0.008 0.001 TYR R 195 PHE 0.011 0.001 PHE B 199 TRP 0.015 0.001 TRP R 387 HIS 0.007 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 7248) covalent geometry : angle 0.50490 / 0.26 ( 9825) SS BOND : bond 0.00125 / 0.07 ( 1) SS BOND : angle 0.07487 / 0.04 ( 2) hydrogen bonds : bond 0.04204 / 2.81 ( 371) hydrogen bonds : angle 3.81676 / 2.71 ( 1074) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.6997 (tttt) cc_final: 0.6737 (ttmt) REVERT: A 46 LYS cc_start: 0.5748 (mtmm) cc_final: 0.5270 (mtmm) REVERT: B 46 ARG cc_start: 0.7309 (mtt180) cc_final: 0.6628 (mtp85) REVERT: B 124 TYR cc_start: 0.8434 (m-80) cc_final: 0.8174 (m-80) REVERT: B 212 ASP cc_start: 0.8115 (t0) cc_final: 0.7748 (t0) REVERT: B 226 GLU cc_start: 0.8578 (mt-10) cc_final: 0.7976 (mt-10) REVERT: B 234 PHE cc_start: 0.8596 (OUTLIER) cc_final: 0.7866 (m-80) REVERT: B 247 ASP cc_start: 0.6747 (t0) cc_final: 0.6130 (t0) REVERT: G 21 MET cc_start: 0.6613 (mmm) cc_final: 0.6242 (tpp) REVERT: G 58 GLU cc_start: 0.7543 (mm-30) cc_final: 0.6780 (pm20) REVERT: R 68 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7661 (mt0) REVERT: R 116 ASP cc_start: 0.8238 (t0) cc_final: 0.7988 (t0) REVERT: R 227 ARG cc_start: 0.6620 (mtm-85) cc_final: 0.6384 (mtm-85) outliers start: 18 outliers final: 15 residues processed: 97 average time/residue: 0.3954 time to fit residues: 40.9068 Evaluate side-chains 98 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 68 GLN Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 228 LYS Chi-restraints excluded: chain R residue 344 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 15 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.145366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.091709 restraints weight = 7722.243| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.80 r_work: 0.2818 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7249 Z= 0.134 Angle : 0.537 12.265 9827 Z= 0.272 Chirality : 0.042 0.146 1130 Planarity : 0.003 0.030 1227 Dihedral : 10.213 160.024 1208 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.25 % Allowed : 16.31 % Favored : 81.43 % 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: 1.50 (0.30), residues: 878 helix: 2.90 (0.26), residues: 404 sheet: 0.05 (0.39), residues: 180 loop : -1.18 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.009 0.001 TYR R 205 PHE 0.011 0.001 PHE B 199 TRP 0.011 0.001 TRP R 387 HIS 0.007 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 7248) covalent geometry : angle 0.53682 / 0.27 ( 9825) SS BOND : bond 0.00187 / 0.10 ( 1) SS BOND : angle 0.19920 / 0.11 ( 2) hydrogen bonds : bond 0.04614 / 3.09 ( 371) hydrogen bonds : angle 3.89541 / 2.77 ( 1074) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7121 (tttt) cc_final: 0.6795 (ttpt) REVERT: B 46 ARG cc_start: 0.7329 (mtt180) cc_final: 0.6581 (mtp85) REVERT: B 226 GLU cc_start: 0.8576 (mt-10) cc_final: 0.7999 (mt-10) REVERT: B 234 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.7829 (m-80) REVERT: B 247 ASP cc_start: 0.6966 (t0) cc_final: 0.6395 (t0) REVERT: B 290 ASP cc_start: 0.7647 (m-30) cc_final: 0.7396 (m-30) REVERT: G 21 MET cc_start: 0.6741 (mmm) cc_final: 0.6359 (tpp) REVERT: G 58 GLU cc_start: 0.7545 (mm-30) cc_final: 0.6826 (pm20) REVERT: R 68 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7765 (mt0) REVERT: R 116 ASP cc_start: 0.8309 (t0) cc_final: 0.8033 (t0) REVERT: R 227 ARG cc_start: 0.6709 (mtm-85) cc_final: 0.6462 (mtm-85) REVERT: R 335 MET cc_start: 0.5780 (tpt) cc_final: 0.5521 (tpp) outliers start: 17 outliers final: 15 residues processed: 91 average time/residue: 0.3948 time to fit residues: 38.2717 Evaluate side-chains 95 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 68 GLN Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 228 LYS Chi-restraints excluded: chain R residue 344 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 6 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 67 optimal weight: 0.2980 chunk 61 optimal weight: 0.3980 chunk 60 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.147225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.093679 restraints weight = 7656.270| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.78 r_work: 0.2845 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7249 Z= 0.112 Angle : 0.496 8.263 9827 Z= 0.258 Chirality : 0.041 0.152 1130 Planarity : 0.003 0.030 1227 Dihedral : 10.051 157.974 1208 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.25 % Allowed : 16.18 % Favored : 81.56 % 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: 1.55 (0.30), residues: 878 helix: 2.92 (0.26), residues: 405 sheet: 0.08 (0.39), residues: 180 loop : -1.14 (0.34), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 197 TYR 0.008 0.001 TYR R 195 PHE 0.011 0.001 PHE B 199 TRP 0.015 0.001 TRP R 387 HIS 0.007 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 7248) covalent geometry : angle 0.49591 / 0.26 ( 9825) SS BOND : bond 0.00153 / 0.08 ( 1) SS BOND : angle 0.13129 / 0.07 ( 2) hydrogen bonds : bond 0.04139 / 2.76 ( 371) hydrogen bonds : angle 3.84562 / 2.74 ( 1074) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2214.74 seconds wall clock time: 38 minutes 28.30 seconds (2308.30 seconds total)