Starting phenix.real_space_refine on Fri Aug 22 21:42:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k8j_36951/08_2025/8k8j_36951_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k8j_36951/08_2025/8k8j_36951.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k8j_36951/08_2025/8k8j_36951.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k8j_36951/08_2025/8k8j_36951.map" model { file = "/net/cci-nas-00/data/ceres_data/8k8j_36951/08_2025/8k8j_36951_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k8j_36951/08_2025/8k8j_36951_neut.cif" } resolution = 2.88 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= 1.030 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 S 55 5.16 5 Cl 1 4.86 5 C 5184 2.51 5 N 1418 2.21 5 O 1497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8155 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1970 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 372 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 2227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2227 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 8, 'TRANS': 270} Chain breaks: 1 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'J3O': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.97, per 1000 atoms: 0.24 Number of scatterers: 8155 At special positions: 0 Unit cell: (72.384, 102.336, 133.952, 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) Cl 1 17.00 S 55 16.00 O 1497 8.00 N 1418 7.00 C 5184 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 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=2.03 Simple disulfide: pdb=" SG CYS R 257 " - pdb=" SG CYS R 264 " 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: 0.65 Conformation dependent library (CDL) restraints added in 410.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1940 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 10 sheets defined 43.0% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 9 through 38 removed outlier: 3.665A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 63 Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 255 through 269 Processing helix chain 'A' and resid 283 through 294 removed outlier: 3.581A pdb=" N GLY A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.600A pdb=" N ASP A 300 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 Processing helix chain 'A' and resid 321 through 340 removed outlier: 3.906A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 379 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 4.070A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 29 through 34' Processing helix chain 'G' and resid 7 through 20 Processing helix chain 'G' and resid 27 through 42 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.618A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 112 through 144 removed outlier: 4.006A pdb=" N SER R 144 " --> pdb=" O VAL R 140 " (cutoff:3.500A) Processing helix chain 'R' and resid 144 through 150 removed outlier: 3.575A pdb=" N ARG R 148 " --> pdb=" O SER R 144 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG R 150 " --> pdb=" O SER R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 179 removed outlier: 4.298A pdb=" N ILE R 175 " --> pdb=" O VAL R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 220 removed outlier: 3.578A pdb=" N LEU R 190 " --> pdb=" O ARG R 186 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE R 191 " --> pdb=" O ASN R 187 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER R 199 " --> pdb=" O GLY R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 228 removed outlier: 3.509A pdb=" N VAL R 228 " --> pdb=" O TYR R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 254 Proline residue: R 251 - end of helix Processing helix chain 'R' and resid 272 through 304 Processing helix chain 'R' and resid 305 through 310 Processing helix chain 'R' and resid 339 through 368 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 372 through 377 removed outlier: 4.096A pdb=" N LYS R 376 " --> pdb=" O ASN R 372 " (cutoff:3.500A) Processing helix chain 'R' and resid 378 through 398 removed outlier: 3.768A pdb=" N MET R 384 " --> pdb=" O ALA R 380 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU R 385 " --> pdb=" O PHE R 381 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N CYS R 386 " --> pdb=" O CYS R 382 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU R 387 " --> pdb=" O SER R 383 " (cutoff:3.500A) Proline residue: R 394 - end of helix Processing helix chain 'R' and resid 401 through 411 removed outlier: 3.519A pdb=" N MET R 411 " --> pdb=" O ALA R 407 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.106A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.359A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.744A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE B 93 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.051A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.287A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.037A 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: 3.584A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.449A 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: 6.582A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.450A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 59 through 60 removed outlier: 6.582A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1203 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: 1.05 Time building geometry restraints manager: 0.88 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: 1358 1.32 - 1.44: 2243 1.44 - 1.57: 4636 1.57 - 1.69: 0 1.69 - 1.81: 79 Bond restraints: 8316 Sorted by residual: bond pdb=" N PHE R 108 " pdb=" CA PHE R 108 " ideal model delta sigma weight residual 1.462 1.484 -0.022 1.36e-02 5.41e+03 2.59e+00 bond pdb=" C CYS R 149 " pdb=" N ARG R 150 " ideal model delta sigma weight residual 1.331 1.364 -0.033 2.83e-02 1.25e+03 1.34e+00 bond pdb=" N GLY B 330 " pdb=" CA GLY B 330 " ideal model delta sigma weight residual 1.456 1.442 0.014 1.32e-02 5.74e+03 1.19e+00 bond pdb=" CB VAL R 196 " pdb=" CG2 VAL R 196 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.10e+00 bond pdb=" CB CYS N 96 " pdb=" SG CYS N 96 " ideal model delta sigma weight residual 1.808 1.776 0.032 3.30e-02 9.18e+02 9.61e-01 ... (remaining 8311 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 11167 2.51 - 5.02: 81 5.02 - 7.53: 6 7.53 - 10.04: 3 10.04 - 12.55: 1 Bond angle restraints: 11258 Sorted by residual: angle pdb=" C PHE R 108 " pdb=" CA PHE R 108 " pdb=" CB PHE R 108 " ideal model delta sigma weight residual 111.22 101.84 9.38 1.24e+00 6.50e-01 5.72e+01 angle pdb=" C7 J3O R 501 " pdb=" C5 J3O R 501 " pdb=" O3 J3O R 501 " ideal model delta sigma weight residual 114.19 101.64 12.55 3.00e+00 1.11e-01 1.75e+01 angle pdb=" CA PHE R 108 " pdb=" C PHE R 108 " pdb=" O PHE R 108 " ideal model delta sigma weight residual 120.37 115.87 4.50 1.56e+00 4.11e-01 8.31e+00 angle pdb=" C10 J3O R 501 " pdb=" C11 J3O R 501 " pdb=" C12 J3O R 501 " ideal model delta sigma weight residual 118.95 126.82 -7.87 3.00e+00 1.11e-01 6.89e+00 angle pdb=" C6 J3O R 501 " pdb=" C5 J3O R 501 " pdb=" O3 J3O R 501 " ideal model delta sigma weight residual 107.59 115.22 -7.63 3.00e+00 1.11e-01 6.47e+00 ... (remaining 11253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.74: 4879 34.74 - 69.47: 79 69.47 - 104.21: 16 104.21 - 138.95: 0 138.95 - 173.69: 2 Dihedral angle restraints: 4976 sinusoidal: 1978 harmonic: 2998 Sorted by residual: dihedral pdb=" CB CYS R 257 " pdb=" SG CYS R 257 " pdb=" SG CYS R 264 " pdb=" CB CYS R 264 " ideal model delta sinusoidal sigma weight residual -86.00 -27.77 -58.23 1 1.00e+01 1.00e-02 4.55e+01 dihedral pdb=" O2 J3O R 501 " pdb=" C4 J3O R 501 " pdb=" C5 J3O R 501 " pdb=" O3 J3O R 501 " ideal model delta sinusoidal sigma weight residual 134.58 -39.11 173.69 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1 J3O R 501 " pdb=" C4 J3O R 501 " pdb=" C5 J3O R 501 " pdb=" O3 J3O R 501 " ideal model delta sinusoidal sigma weight residual 312.12 139.75 172.37 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 4973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 870 0.039 - 0.078: 302 0.078 - 0.117: 90 0.117 - 0.156: 15 0.156 - 0.195: 2 Chirality restraints: 1279 Sorted by residual: chirality pdb=" CG LEU B 210 " pdb=" CB LEU B 210 " pdb=" CD1 LEU B 210 " pdb=" CD2 LEU B 210 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.53e-01 chirality pdb=" CA PHE R 108 " pdb=" N PHE R 108 " pdb=" C PHE R 108 " pdb=" CB PHE R 108 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.97e-01 chirality pdb=" CA TRP B 339 " pdb=" N TRP B 339 " pdb=" C TRP B 339 " pdb=" CB TRP B 339 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.37e-01 ... (remaining 1276 not shown) Planarity restraints: 1426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 J3O R 501 " -0.021 2.00e-02 2.50e+03 3.83e-02 1.47e+01 pdb=" C12 J3O R 501 " 0.066 2.00e-02 2.50e+03 pdb=" C13 J3O R 501 " -0.021 2.00e-02 2.50e+03 pdb=" O4 J3O R 501 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 J3O R 501 " 0.023 2.00e-02 2.50e+03 2.19e-02 9.60e+00 pdb=" C11 J3O R 501 " -0.049 2.00e-02 2.50e+03 pdb=" C12 J3O R 501 " 0.019 2.00e-02 2.50e+03 pdb=" C19 J3O R 501 " 0.005 2.00e-02 2.50e+03 pdb=" C20 J3O R 501 " 0.001 2.00e-02 2.50e+03 pdb=" C8 J3O R 501 " 0.018 2.00e-02 2.50e+03 pdb=" C9 J3O R 501 " -0.015 2.00e-02 2.50e+03 pdb=" O3 J3O R 501 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO B 236 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.028 5.00e-02 4.00e+02 ... (remaining 1423 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 523 2.73 - 3.27: 8380 3.27 - 3.82: 13831 3.82 - 4.36: 17061 4.36 - 4.90: 29484 Nonbonded interactions: 69279 Sorted by model distance: nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.190 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.204 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.221 3.040 nonbonded pdb=" OG1 THR N 28 " pdb=" OD1 ASN N 31 " model vdw 2.222 3.040 nonbonded pdb=" OD1 ASP N 50 " pdb=" OG SER N 59 " model vdw 2.233 3.040 ... (remaining 69274 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: 3.060 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: 8.380 Find NCS groups from input model: 0.020 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:6.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 18.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 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 0.039 8319 Z= 0.161 Angle : 0.578 12.552 11264 Z= 0.310 Chirality : 0.043 0.195 1279 Planarity : 0.003 0.050 1426 Dihedral : 15.122 173.686 3027 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.11 % Allowed : 0.45 % Favored : 99.44 % 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 aren not related in a simple way. whole: 0.30 (0.26), residues: 1017 helix: 1.67 (0.26), residues: 380 sheet: -0.35 (0.34), residues: 229 loop : -0.83 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 364 TYR 0.011 0.001 TYR R 153 PHE 0.028 0.002 PHE R 177 TRP 0.030 0.002 TRP B 339 HIS 0.004 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 8316) covalent geometry : angle 0.57657 (11258) SS BOND : bond 0.00368 ( 3) SS BOND : angle 1.76057 ( 6) hydrogen bonds : bond 0.13257 ( 423) hydrogen bonds : angle 5.85791 ( 1203) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 0.327 Fit side-chains REVERT: B 78 LYS cc_start: 0.8613 (mmtp) cc_final: 0.8409 (tppp) REVERT: B 118 ASP cc_start: 0.8597 (p0) cc_final: 0.8340 (p0) REVERT: B 258 ASP cc_start: 0.7745 (t0) cc_final: 0.7408 (t0) REVERT: G 32 LYS cc_start: 0.7511 (tmmt) cc_final: 0.7268 (tttt) REVERT: R 129 PHE cc_start: 0.7164 (m-10) cc_final: 0.6918 (m-10) outliers start: 1 outliers final: 1 residues processed: 156 average time/residue: 0.6562 time to fit residues: 107.6160 Evaluate side-chains 122 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 108 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 GLN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 77 ASN R 116 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.175259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.136154 restraints weight = 9536.349| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.21 r_work: 0.3436 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8319 Z= 0.147 Angle : 0.548 7.927 11264 Z= 0.292 Chirality : 0.042 0.137 1279 Planarity : 0.004 0.064 1426 Dihedral : 10.869 170.391 1147 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.47 % Allowed : 10.48 % Favored : 88.05 % 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 aren not related in a simple way. whole: 0.53 (0.27), residues: 1017 helix: 1.85 (0.26), residues: 384 sheet: -0.14 (0.35), residues: 217 loop : -0.77 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG R 186 TYR 0.023 0.001 TYR R 153 PHE 0.014 0.001 PHE R 189 TRP 0.026 0.002 TRP B 339 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8316) covalent geometry : angle 0.54730 (11258) SS BOND : bond 0.00354 ( 3) SS BOND : angle 1.31850 ( 6) hydrogen bonds : bond 0.04095 ( 423) hydrogen bonds : angle 4.83159 ( 1203) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.347 Fit side-chains REVERT: A 24 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7509 (mtmm) REVERT: A 28 LYS cc_start: 0.8241 (mmtp) cc_final: 0.7470 (ptmm) REVERT: A 31 GLN cc_start: 0.7772 (tp40) cc_final: 0.7503 (mp10) REVERT: B 17 GLN cc_start: 0.8274 (tm-30) cc_final: 0.8056 (tm-30) REVERT: B 105 TYR cc_start: 0.9031 (OUTLIER) cc_final: 0.8573 (t80) REVERT: B 195 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.7516 (p0) REVERT: B 258 ASP cc_start: 0.7650 (t0) cc_final: 0.7337 (t0) REVERT: G 32 LYS cc_start: 0.7313 (tmmt) cc_final: 0.7080 (tttt) REVERT: N 43 LYS cc_start: 0.7566 (OUTLIER) cc_final: 0.7281 (mtmm) REVERT: N 120 GLN cc_start: 0.7764 (mm-40) cc_final: 0.7560 (mm-40) REVERT: R 150 ARG cc_start: 0.6214 (mtm-85) cc_final: 0.5809 (ptt180) outliers start: 13 outliers final: 4 residues processed: 135 average time/residue: 0.6753 time to fit residues: 96.1158 Evaluate side-chains 126 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain R residue 228 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 62 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 GLN B 88 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN R 116 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.171596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.132238 restraints weight = 9555.062| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.20 r_work: 0.3391 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 8319 Z= 0.237 Angle : 0.601 7.203 11264 Z= 0.318 Chirality : 0.044 0.173 1279 Planarity : 0.004 0.049 1426 Dihedral : 10.392 164.333 1145 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.37 % Allowed : 13.08 % Favored : 84.55 % 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 aren not related in a simple way. whole: 0.26 (0.26), residues: 1017 helix: 1.55 (0.26), residues: 387 sheet: -0.18 (0.34), residues: 224 loop : -0.93 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 186 TYR 0.017 0.002 TYR R 153 PHE 0.022 0.002 PHE N 108 TRP 0.023 0.002 TRP B 339 HIS 0.005 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00556 ( 8316) covalent geometry : angle 0.59949 (11258) SS BOND : bond 0.00345 ( 3) SS BOND : angle 1.65650 ( 6) hydrogen bonds : bond 0.04357 ( 423) hydrogen bonds : angle 4.92132 ( 1203) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.333 Fit side-chains REVERT: A 20 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.7305 (ttp-110) REVERT: A 24 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7435 (mtmm) REVERT: A 31 GLN cc_start: 0.7890 (tp40) cc_final: 0.7649 (mp10) REVERT: A 334 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8373 (mm-30) REVERT: B 46 ARG cc_start: 0.8123 (tpm170) cc_final: 0.7790 (tpp-160) REVERT: B 186 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7165 (m-30) REVERT: B 195 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7506 (p0) REVERT: B 258 ASP cc_start: 0.7807 (t0) cc_final: 0.7476 (t0) REVERT: G 32 LYS cc_start: 0.7479 (tmmt) cc_final: 0.7252 (tttt) REVERT: N 43 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7465 (mtmm) REVERT: R 150 ARG cc_start: 0.6232 (mtm-85) cc_final: 0.5852 (ptt180) REVERT: R 276 LEU cc_start: 0.7859 (mt) cc_final: 0.7542 (mt) REVERT: R 353 ILE cc_start: 0.7486 (OUTLIER) cc_final: 0.7161 (mp) outliers start: 21 outliers final: 6 residues processed: 136 average time/residue: 0.6086 time to fit residues: 87.5982 Evaluate side-chains 132 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 353 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 80 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN R 116 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.174304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.135033 restraints weight = 9721.597| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.23 r_work: 0.3441 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8319 Z= 0.146 Angle : 0.531 6.601 11264 Z= 0.282 Chirality : 0.042 0.137 1279 Planarity : 0.003 0.048 1426 Dihedral : 9.176 157.648 1145 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.92 % Allowed : 15.67 % Favored : 82.41 % 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 aren not related in a simple way. whole: 0.48 (0.26), residues: 1017 helix: 1.84 (0.26), residues: 387 sheet: -0.18 (0.34), residues: 220 loop : -0.86 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 337 TYR 0.011 0.001 TYR R 153 PHE 0.012 0.001 PHE R 189 TRP 0.018 0.002 TRP B 339 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 8316) covalent geometry : angle 0.53101 (11258) SS BOND : bond 0.00271 ( 3) SS BOND : angle 1.00263 ( 6) hydrogen bonds : bond 0.03803 ( 423) hydrogen bonds : angle 4.66188 ( 1203) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.232 Fit side-chains REVERT: A 24 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7514 (mtmm) REVERT: A 31 GLN cc_start: 0.7814 (tp40) cc_final: 0.7559 (mp10) REVERT: B 195 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7572 (p0) REVERT: B 258 ASP cc_start: 0.7709 (t0) cc_final: 0.7451 (t0) REVERT: N 43 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7372 (mtmm) REVERT: N 120 GLN cc_start: 0.7706 (mm-40) cc_final: 0.7493 (mm-40) REVERT: R 150 ARG cc_start: 0.6202 (mtm-85) cc_final: 0.5780 (ptt180) REVERT: R 354 ILE cc_start: 0.8185 (tp) cc_final: 0.7876 (tt) outliers start: 17 outliers final: 9 residues processed: 139 average time/residue: 0.6478 time to fit residues: 94.8596 Evaluate side-chains 136 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 237 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 63 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 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 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN R 116 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.171846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.132471 restraints weight = 9600.211| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.21 r_work: 0.3398 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8319 Z= 0.208 Angle : 0.574 6.094 11264 Z= 0.305 Chirality : 0.043 0.172 1279 Planarity : 0.004 0.048 1426 Dihedral : 9.340 166.482 1145 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.16 % Allowed : 16.91 % Favored : 79.93 % 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 aren not related in a simple way. whole: 0.26 (0.26), residues: 1017 helix: 1.63 (0.26), residues: 387 sheet: -0.27 (0.33), residues: 223 loop : -0.97 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 214 TYR 0.012 0.002 TYR R 153 PHE 0.019 0.002 PHE N 108 TRP 0.018 0.002 TRP B 339 HIS 0.004 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00486 ( 8316) covalent geometry : angle 0.57326 (11258) SS BOND : bond 0.00333 ( 3) SS BOND : angle 1.14315 ( 6) hydrogen bonds : bond 0.04109 ( 423) hydrogen bonds : angle 4.80551 ( 1203) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.338 Fit side-chains REVERT: A 20 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.7238 (ttp-110) REVERT: A 24 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7562 (mtmm) REVERT: A 31 GLN cc_start: 0.7845 (tp40) cc_final: 0.7596 (mp10) REVERT: A 334 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8458 (mm-30) REVERT: B 46 ARG cc_start: 0.8165 (tpm170) cc_final: 0.7821 (tpp-160) REVERT: B 195 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7444 (p0) REVERT: B 258 ASP cc_start: 0.7695 (t0) cc_final: 0.7435 (t0) REVERT: N 43 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7402 (mtmm) REVERT: R 132 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7502 (mm) REVERT: R 150 ARG cc_start: 0.6176 (mtm-85) cc_final: 0.5905 (mtt180) REVERT: R 253 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7292 (mt) REVERT: R 354 ILE cc_start: 0.8282 (tp) cc_final: 0.7977 (tt) REVERT: R 402 LYS cc_start: 0.7415 (mtpt) cc_final: 0.6836 (mttp) outliers start: 28 outliers final: 11 residues processed: 140 average time/residue: 0.5677 time to fit residues: 84.1420 Evaluate side-chains 136 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 253 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 8 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 GLN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN R 116 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.173402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.134229 restraints weight = 9552.606| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.21 r_work: 0.3428 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8319 Z= 0.154 Angle : 0.530 5.794 11264 Z= 0.283 Chirality : 0.042 0.139 1279 Planarity : 0.003 0.048 1426 Dihedral : 8.930 163.435 1145 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.71 % Allowed : 18.04 % Favored : 79.26 % 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 aren not related in a simple way. whole: 0.38 (0.26), residues: 1017 helix: 1.74 (0.26), residues: 387 sheet: -0.24 (0.34), residues: 220 loop : -0.88 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 214 TYR 0.011 0.001 TYR R 153 PHE 0.014 0.002 PHE N 108 TRP 0.015 0.002 TRP B 339 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8316) covalent geometry : angle 0.53019 (11258) SS BOND : bond 0.00319 ( 3) SS BOND : angle 0.86195 ( 6) hydrogen bonds : bond 0.03850 ( 423) hydrogen bonds : angle 4.67444 ( 1203) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.261 Fit side-chains REVERT: A 31 GLN cc_start: 0.7814 (tp40) cc_final: 0.7565 (mp10) REVERT: B 46 ARG cc_start: 0.8137 (tpm170) cc_final: 0.7799 (tpp-160) REVERT: B 195 ASP cc_start: 0.7752 (OUTLIER) cc_final: 0.7496 (p0) REVERT: G 41 CYS cc_start: 0.8628 (t) cc_final: 0.8269 (m) REVERT: N 43 LYS cc_start: 0.7662 (OUTLIER) cc_final: 0.7421 (mtmm) REVERT: R 132 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7525 (mm) REVERT: R 253 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7311 (mt) REVERT: R 295 MET cc_start: 0.8286 (tpp) cc_final: 0.8030 (mmp) REVERT: R 402 LYS cc_start: 0.7453 (mtpt) cc_final: 0.6909 (mttp) outliers start: 24 outliers final: 13 residues processed: 137 average time/residue: 0.5608 time to fit residues: 81.1473 Evaluate side-chains 136 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 253 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 17 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 60 optimal weight: 6.9990 chunk 70 optimal weight: 0.1980 chunk 9 optimal weight: 0.1980 chunk 22 optimal weight: 0.9990 chunk 72 optimal weight: 0.0770 chunk 28 optimal weight: 1.9990 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 GLN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN R 116 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.177125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.138459 restraints weight = 9613.657| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.22 r_work: 0.3485 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 8319 Z= 0.106 Angle : 0.493 5.535 11264 Z= 0.264 Chirality : 0.040 0.142 1279 Planarity : 0.003 0.047 1426 Dihedral : 8.121 153.538 1145 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.93 % Allowed : 18.38 % Favored : 78.69 % 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 aren not related in a simple way. whole: 0.62 (0.27), residues: 1017 helix: 1.93 (0.26), residues: 389 sheet: -0.04 (0.35), residues: 207 loop : -0.79 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 337 TYR 0.010 0.001 TYR R 153 PHE 0.015 0.001 PHE A 212 TRP 0.015 0.002 TRP B 339 HIS 0.002 0.000 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 8316) covalent geometry : angle 0.49337 (11258) SS BOND : bond 0.00282 ( 3) SS BOND : angle 0.51362 ( 6) hydrogen bonds : bond 0.03460 ( 423) hydrogen bonds : angle 4.42007 ( 1203) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.304 Fit side-chains REVERT: A 28 LYS cc_start: 0.7929 (mmmm) cc_final: 0.7373 (ptmm) REVERT: A 31 GLN cc_start: 0.7753 (tp40) cc_final: 0.7490 (tm-30) REVERT: B 46 ARG cc_start: 0.8131 (tpm170) cc_final: 0.7781 (tpp-160) REVERT: B 135 VAL cc_start: 0.8734 (p) cc_final: 0.8481 (t) REVERT: G 41 CYS cc_start: 0.8662 (t) cc_final: 0.8294 (m) REVERT: N 43 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7384 (mtmm) REVERT: R 129 PHE cc_start: 0.7039 (m-10) cc_final: 0.6818 (m-10) REVERT: R 132 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7498 (mm) REVERT: R 295 MET cc_start: 0.8238 (tpp) cc_final: 0.8013 (mmp) outliers start: 26 outliers final: 14 residues processed: 153 average time/residue: 0.5481 time to fit residues: 89.2363 Evaluate side-chains 138 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 237 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 28 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.173113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.133874 restraints weight = 9605.115| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.22 r_work: 0.3417 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8319 Z= 0.185 Angle : 0.564 6.059 11264 Z= 0.298 Chirality : 0.043 0.165 1279 Planarity : 0.004 0.047 1426 Dihedral : 8.479 157.768 1145 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.93 % Allowed : 19.73 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.26), residues: 1017 helix: 1.78 (0.26), residues: 387 sheet: -0.21 (0.33), residues: 221 loop : -0.82 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 337 TYR 0.012 0.001 TYR R 153 PHE 0.017 0.002 PHE N 108 TRP 0.017 0.002 TRP B 339 HIS 0.004 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 8316) covalent geometry : angle 0.56336 (11258) SS BOND : bond 0.00328 ( 3) SS BOND : angle 0.96309 ( 6) hydrogen bonds : bond 0.03929 ( 423) hydrogen bonds : angle 4.65702 ( 1203) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.366 Fit side-chains REVERT: A 20 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7277 (ttp-110) REVERT: A 28 LYS cc_start: 0.8009 (mmmm) cc_final: 0.7417 (ptmm) REVERT: A 31 GLN cc_start: 0.7802 (tp40) cc_final: 0.7527 (mp10) REVERT: B 46 ARG cc_start: 0.8205 (tpm170) cc_final: 0.7896 (tpp-160) REVERT: B 258 ASP cc_start: 0.7630 (t0) cc_final: 0.7384 (t0) REVERT: G 17 GLU cc_start: 0.7471 (tp30) cc_final: 0.7117 (mm-30) REVERT: G 41 CYS cc_start: 0.8591 (t) cc_final: 0.8246 (m) REVERT: N 43 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7432 (mtmm) REVERT: R 132 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7476 (mm) REVERT: R 253 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7273 (mt) REVERT: R 295 MET cc_start: 0.8309 (tpp) cc_final: 0.8077 (mmp) REVERT: R 371 MET cc_start: 0.2728 (mmt) cc_final: 0.2447 (mmm) REVERT: R 402 LYS cc_start: 0.7485 (mtpt) cc_final: 0.6927 (mttm) outliers start: 26 outliers final: 14 residues processed: 138 average time/residue: 0.6526 time to fit residues: 95.5565 Evaluate side-chains 138 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 253 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 61 optimal weight: 0.0020 chunk 21 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 96 optimal weight: 0.0040 overall best weight: 0.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN R 116 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.176673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.137635 restraints weight = 9561.476| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.22 r_work: 0.3467 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8319 Z= 0.115 Angle : 0.516 5.958 11264 Z= 0.275 Chirality : 0.041 0.191 1279 Planarity : 0.003 0.046 1426 Dihedral : 8.101 152.701 1145 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.14 % Allowed : 20.86 % Favored : 77.00 % 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 aren not related in a simple way. whole: 0.58 (0.26), residues: 1017 helix: 1.88 (0.26), residues: 391 sheet: 0.00 (0.34), residues: 207 loop : -0.84 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 337 TYR 0.010 0.001 TYR R 153 PHE 0.015 0.001 PHE R 177 TRP 0.014 0.002 TRP B 339 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 8316) covalent geometry : angle 0.51620 (11258) SS BOND : bond 0.00292 ( 3) SS BOND : angle 0.55789 ( 6) hydrogen bonds : bond 0.03538 ( 423) hydrogen bonds : angle 4.47224 ( 1203) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.362 Fit side-chains REVERT: A 28 LYS cc_start: 0.7931 (mmmm) cc_final: 0.7370 (ptmm) REVERT: A 31 GLN cc_start: 0.7759 (tp40) cc_final: 0.7504 (tm-30) REVERT: B 46 ARG cc_start: 0.8159 (tpm170) cc_final: 0.7814 (tpp-160) REVERT: B 135 VAL cc_start: 0.8592 (p) cc_final: 0.8367 (t) REVERT: B 258 ASP cc_start: 0.7538 (t0) cc_final: 0.7237 (t0) REVERT: G 26 ASP cc_start: 0.7774 (t70) cc_final: 0.7498 (t70) REVERT: N 43 LYS cc_start: 0.7597 (OUTLIER) cc_final: 0.7358 (mtmm) REVERT: N 120 GLN cc_start: 0.7647 (mm-40) cc_final: 0.7437 (mm-40) REVERT: R 132 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7455 (mm) REVERT: R 371 MET cc_start: 0.2641 (mmt) cc_final: 0.2343 (mmm) outliers start: 19 outliers final: 15 residues processed: 139 average time/residue: 0.6401 time to fit residues: 94.4064 Evaluate side-chains 139 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 276 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 90 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.175242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.135865 restraints weight = 9499.911| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.23 r_work: 0.3446 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8319 Z= 0.144 Angle : 0.555 7.730 11264 Z= 0.291 Chirality : 0.042 0.173 1279 Planarity : 0.003 0.046 1426 Dihedral : 8.215 153.944 1145 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.48 % Allowed : 20.86 % Favored : 76.66 % 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 aren not related in a simple way. whole: 0.50 (0.26), residues: 1017 helix: 1.76 (0.26), residues: 394 sheet: -0.04 (0.34), residues: 213 loop : -0.85 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 337 TYR 0.011 0.001 TYR N 95 PHE 0.017 0.002 PHE R 177 TRP 0.016 0.002 TRP B 339 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 8316) covalent geometry : angle 0.55448 (11258) SS BOND : bond 0.00315 ( 3) SS BOND : angle 0.78184 ( 6) hydrogen bonds : bond 0.03697 ( 423) hydrogen bonds : angle 4.54851 ( 1203) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.353 Fit side-chains REVERT: A 28 LYS cc_start: 0.7950 (mmmm) cc_final: 0.7388 (ptmm) REVERT: A 31 GLN cc_start: 0.7777 (tp40) cc_final: 0.7520 (tm-30) REVERT: B 46 ARG cc_start: 0.8181 (tpm170) cc_final: 0.7875 (tpp-160) REVERT: B 258 ASP cc_start: 0.7591 (t0) cc_final: 0.7341 (t0) REVERT: G 26 ASP cc_start: 0.7753 (t70) cc_final: 0.7469 (t70) REVERT: N 43 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7363 (mtmm) REVERT: R 132 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7460 (mm) REVERT: R 253 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7261 (mt) REVERT: R 354 ILE cc_start: 0.8080 (tp) cc_final: 0.7799 (tt) REVERT: R 371 MET cc_start: 0.2293 (mmt) cc_final: 0.2031 (mmm) outliers start: 22 outliers final: 17 residues processed: 135 average time/residue: 0.6238 time to fit residues: 89.3636 Evaluate side-chains 139 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 276 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 4 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 9 optimal weight: 0.0570 chunk 89 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.175487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.136252 restraints weight = 9526.204| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.21 r_work: 0.3446 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8319 Z= 0.139 Angle : 0.550 8.065 11264 Z= 0.288 Chirality : 0.042 0.162 1279 Planarity : 0.003 0.045 1426 Dihedral : 8.159 153.431 1145 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.25 % Allowed : 20.86 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.26), residues: 1017 helix: 1.78 (0.26), residues: 394 sheet: -0.04 (0.34), residues: 213 loop : -0.86 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 337 TYR 0.011 0.001 TYR R 153 PHE 0.013 0.001 PHE A 212 TRP 0.017 0.002 TRP B 339 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 8316) covalent geometry : angle 0.54947 (11258) SS BOND : bond 0.00316 ( 3) SS BOND : angle 0.69028 ( 6) hydrogen bonds : bond 0.03653 ( 423) hydrogen bonds : angle 4.52660 ( 1203) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3214.96 seconds wall clock time: 55 minutes 30.74 seconds (3330.74 seconds total)