Starting phenix.real_space_refine on Wed Mar 12 16:58:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k8j_36951/03_2025/8k8j_36951_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k8j_36951/03_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_36951/03_2025/8k8j_36951.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k8j_36951/03_2025/8k8j_36951.map" model { file = "/net/cci-nas-00/data/ceres_data/8k8j_36951/03_2025/8k8j_36951_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k8j_36951/03_2025/8k8j_36951_neut.cif" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.76, per 1000 atoms: 0.71 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: 2.30 Conformation dependent library (CDL) restraints added in 959.9 milliseconds 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: 0.83 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: 2.35 Time building geometry restraints manager: 2.56 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: 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.390 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.820 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.020 ------------------------------------------------------------------------------- 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 8316 Z= 0.239 Angle : 0.577 12.552 11258 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (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 TRP 0.030 0.002 TRP B 339 HIS 0.004 0.001 HIS A 347 PHE 0.028 0.002 PHE R 177 TYR 0.011 0.001 TYR R 153 ARG 0.002 0.000 ARG A 364 *********************** 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 : 0.937 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: 1.4073 time to fit residues: 231.3850 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 : 0.887 ------------------------------------------------------------------------------- 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 83 optimal weight: 0.3980 chunk 75 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 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 19 GLN ** A 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 GLN ** B 44 GLN ** 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 = 0.4024 r_free = 0.4024 target = 0.175020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.136035 restraints weight = 9426.219| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.20 r_work: 0.3436 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8316 Z= 0.223 Angle : 0.551 7.778 11258 Z= 0.293 Chirality : 0.042 0.137 1279 Planarity : 0.004 0.064 1426 Dihedral : 10.874 170.717 1147 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.58 % Allowed : 10.26 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.27), residues: 1017 helix: 1.83 (0.26), residues: 384 sheet: -0.14 (0.35), residues: 217 loop : -0.79 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 339 HIS 0.003 0.001 HIS A 347 PHE 0.015 0.002 PHE R 189 TYR 0.029 0.002 TYR R 153 ARG 0.011 0.000 ARG R 186 *********************** 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: 14 poor density : 127 time to evaluate : 0.923 Fit side-chains REVERT: A 24 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7453 (mtmm) REVERT: A 31 GLN cc_start: 0.7793 (tp40) cc_final: 0.7528 (mp10) REVERT: B 17 GLN cc_start: 0.8259 (tm-30) cc_final: 0.8036 (tm-30) REVERT: B 105 TYR cc_start: 0.9028 (OUTLIER) cc_final: 0.8575 (t80) REVERT: B 195 ASP cc_start: 0.7889 (OUTLIER) cc_final: 0.7503 (p0) REVERT: B 258 ASP cc_start: 0.7659 (t0) cc_final: 0.7348 (t0) REVERT: G 32 LYS cc_start: 0.7340 (tmmt) cc_final: 0.7125 (tttt) REVERT: N 43 LYS cc_start: 0.7575 (OUTLIER) cc_final: 0.7286 (mtmm) REVERT: N 120 GLN cc_start: 0.7747 (mm-40) cc_final: 0.7546 (mm-40) REVERT: R 371 MET cc_start: 0.2570 (mmt) cc_final: 0.2229 (mmm) outliers start: 14 outliers final: 4 residues processed: 135 average time/residue: 1.3509 time to fit residues: 192.8630 Evaluate side-chains 124 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 5 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN 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 = 0.3974 r_free = 0.3974 target = 0.170216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.130226 restraints weight = 9737.089| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.26 r_work: 0.3378 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 8316 Z= 0.436 Angle : 0.637 7.361 11258 Z= 0.337 Chirality : 0.046 0.201 1279 Planarity : 0.004 0.050 1426 Dihedral : 10.243 164.154 1145 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.59 % Allowed : 14.09 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.26), residues: 1017 helix: 1.41 (0.26), residues: 387 sheet: -0.21 (0.34), residues: 229 loop : -0.98 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 339 HIS 0.005 0.001 HIS A 347 PHE 0.026 0.002 PHE N 108 TYR 0.018 0.002 TYR R 153 ARG 0.006 0.000 ARG R 186 *********************** 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 146 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.945 Fit side-chains REVERT: A 20 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.7256 (ttp-110) REVERT: A 24 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.7511 (mtmm) REVERT: A 31 GLN cc_start: 0.7865 (tp40) cc_final: 0.7624 (mp10) REVERT: A 334 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8357 (mm-30) REVERT: B 46 ARG cc_start: 0.8135 (tpm170) cc_final: 0.7799 (tpp-160) REVERT: B 186 ASP cc_start: 0.7855 (OUTLIER) cc_final: 0.7108 (m-30) REVERT: B 195 ASP cc_start: 0.7751 (OUTLIER) cc_final: 0.7455 (p0) REVERT: B 258 ASP cc_start: 0.7824 (t0) cc_final: 0.7504 (t0) REVERT: N 43 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7471 (mtmm) REVERT: R 150 ARG cc_start: 0.6274 (mtm-85) cc_final: 0.5885 (ptt180) REVERT: R 276 LEU cc_start: 0.7876 (mt) cc_final: 0.7553 (mt) REVERT: R 353 ILE cc_start: 0.7502 (OUTLIER) cc_final: 0.7250 (mp) REVERT: R 354 ILE cc_start: 0.8251 (tp) cc_final: 0.7995 (tt) REVERT: R 411 MET cc_start: 0.5621 (OUTLIER) cc_final: 0.5327 (mmm) outliers start: 23 outliers final: 6 residues processed: 135 average time/residue: 1.3223 time to fit residues: 188.9569 Evaluate side-chains 132 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain R residue 411 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 95 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 82 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.173608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.134564 restraints weight = 9518.091| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.20 r_work: 0.3437 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8316 Z= 0.223 Angle : 0.533 5.517 11258 Z= 0.284 Chirality : 0.042 0.136 1279 Planarity : 0.003 0.049 1426 Dihedral : 9.038 158.594 1145 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.14 % Allowed : 16.69 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.26), residues: 1017 helix: 1.74 (0.26), residues: 387 sheet: -0.23 (0.34), residues: 220 loop : -0.91 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 339 HIS 0.003 0.001 HIS A 347 PHE 0.012 0.002 PHE R 189 TYR 0.011 0.001 TYR R 153 ARG 0.003 0.000 ARG B 150 *********************** 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 154 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.886 Fit side-chains REVERT: A 24 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7553 (mtmm) REVERT: A 31 GLN cc_start: 0.7822 (tp40) cc_final: 0.7568 (mp10) REVERT: B 46 ARG cc_start: 0.8023 (tpm170) cc_final: 0.7710 (tpp-160) REVERT: B 195 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.7503 (p0) REVERT: B 228 ASP cc_start: 0.8681 (p0) cc_final: 0.8431 (p0) REVERT: B 258 ASP cc_start: 0.7727 (t0) cc_final: 0.7432 (t0) REVERT: N 43 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7363 (mtmm) REVERT: R 150 ARG cc_start: 0.6167 (mtm-85) cc_final: 0.5759 (ptt180) REVERT: R 253 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7298 (mt) REVERT: R 276 LEU cc_start: 0.7813 (mt) cc_final: 0.7463 (mt) REVERT: R 402 LYS cc_start: 0.7383 (mtpt) cc_final: 0.6832 (mttp) outliers start: 19 outliers final: 9 residues processed: 145 average time/residue: 1.3534 time to fit residues: 207.0009 Evaluate side-chains 137 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain R residue 253 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 70 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 50 optimal weight: 0.1980 chunk 97 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 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 = 0.4027 r_free = 0.4027 target = 0.175233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.136338 restraints weight = 9456.570| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.19 r_work: 0.3442 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8316 Z= 0.183 Angle : 0.504 5.633 11258 Z= 0.270 Chirality : 0.041 0.138 1279 Planarity : 0.003 0.047 1426 Dihedral : 8.602 158.943 1145 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.48 % Allowed : 17.70 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.27), residues: 1017 helix: 1.88 (0.26), residues: 387 sheet: -0.25 (0.34), residues: 221 loop : -0.80 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 339 HIS 0.002 0.000 HIS A 347 PHE 0.013 0.001 PHE A 212 TYR 0.012 0.001 TYR A 348 ARG 0.004 0.000 ARG A 337 *********************** 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 159 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.985 Fit side-chains REVERT: A 31 GLN cc_start: 0.7768 (tp40) cc_final: 0.7472 (tm-30) REVERT: A 213 GLN cc_start: 0.8313 (mt0) cc_final: 0.8104 (tt0) REVERT: B 46 ARG cc_start: 0.8131 (tpm170) cc_final: 0.7795 (tpp-160) REVERT: B 195 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.7508 (p0) REVERT: B 228 ASP cc_start: 0.8654 (p0) cc_final: 0.8098 (p0) REVERT: B 258 ASP cc_start: 0.7675 (t0) cc_final: 0.7386 (t0) REVERT: G 41 CYS cc_start: 0.8648 (t) cc_final: 0.8269 (m) REVERT: N 43 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7326 (mtmm) REVERT: R 132 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7509 (mm) REVERT: R 253 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7301 (mt) REVERT: R 354 ILE cc_start: 0.8116 (tp) cc_final: 0.7874 (tt) REVERT: R 402 LYS cc_start: 0.7467 (mtpt) cc_final: 0.6921 (mttp) outliers start: 22 outliers final: 11 residues processed: 148 average time/residue: 1.2456 time to fit residues: 195.4187 Evaluate side-chains 143 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ILE 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 26 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 16 optimal weight: 0.0040 chunk 77 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 2 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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 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 = 0.4031 r_free = 0.4031 target = 0.175330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.136415 restraints weight = 9455.020| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.20 r_work: 0.3456 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8316 Z= 0.185 Angle : 0.502 5.723 11258 Z= 0.269 Chirality : 0.041 0.136 1279 Planarity : 0.003 0.046 1426 Dihedral : 8.460 159.192 1145 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.48 % Allowed : 18.71 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.27), residues: 1017 helix: 2.00 (0.26), residues: 383 sheet: -0.25 (0.34), residues: 221 loop : -0.75 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 339 HIS 0.002 0.000 HIS A 347 PHE 0.013 0.001 PHE A 212 TYR 0.011 0.001 TYR R 153 ARG 0.003 0.000 ARG B 214 *********************** 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 157 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.937 Fit side-chains REVERT: A 28 LYS cc_start: 0.8266 (mmtp) cc_final: 0.7484 (ptmm) REVERT: A 31 GLN cc_start: 0.7735 (tp40) cc_final: 0.7479 (tm-30) REVERT: B 46 ARG cc_start: 0.8133 (tpm170) cc_final: 0.7848 (tpp-160) REVERT: B 135 VAL cc_start: 0.8773 (p) cc_final: 0.8513 (t) REVERT: B 228 ASP cc_start: 0.8666 (p0) cc_final: 0.7969 (p0) REVERT: B 258 ASP cc_start: 0.7701 (t0) cc_final: 0.7410 (t0) REVERT: G 17 GLU cc_start: 0.7490 (tp30) cc_final: 0.7120 (mm-30) REVERT: G 41 CYS cc_start: 0.8630 (t) cc_final: 0.8268 (m) REVERT: N 43 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7367 (mtmm) REVERT: R 132 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7469 (mm) REVERT: R 253 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7319 (mt) REVERT: R 295 MET cc_start: 0.8283 (tpp) cc_final: 0.8042 (mmp) REVERT: R 354 ILE cc_start: 0.8154 (tp) cc_final: 0.7856 (tt) REVERT: R 371 MET cc_start: 0.2623 (mmt) cc_final: 0.2314 (mmm) REVERT: R 402 LYS cc_start: 0.7484 (mtpt) cc_final: 0.6927 (mttm) outliers start: 22 outliers final: 11 residues processed: 148 average time/residue: 1.2672 time to fit residues: 198.8397 Evaluate side-chains 144 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ILE 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 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 59 optimal weight: 3.9990 chunk 38 optimal weight: 0.4980 chunk 40 optimal weight: 0.0770 chunk 26 optimal weight: 0.1980 chunk 82 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.177243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.138539 restraints weight = 9562.739| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.21 r_work: 0.3484 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8316 Z= 0.157 Angle : 0.498 5.768 11258 Z= 0.265 Chirality : 0.040 0.141 1279 Planarity : 0.003 0.045 1426 Dihedral : 8.205 155.251 1145 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.03 % Allowed : 19.62 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.27), residues: 1017 helix: 2.03 (0.26), residues: 389 sheet: -0.06 (0.34), residues: 213 loop : -0.73 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 339 HIS 0.002 0.000 HIS A 347 PHE 0.011 0.001 PHE A 212 TYR 0.010 0.001 TYR R 153 ARG 0.009 0.000 ARG A 337 *********************** 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 154 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.858 Fit side-chains REVERT: A 28 LYS cc_start: 0.8280 (mmtp) cc_final: 0.7508 (ptmm) REVERT: A 31 GLN cc_start: 0.7750 (tp40) cc_final: 0.7548 (tm-30) REVERT: B 46 ARG cc_start: 0.8162 (tpm170) cc_final: 0.7845 (tpp-160) REVERT: B 135 VAL cc_start: 0.8695 (p) cc_final: 0.8459 (t) REVERT: B 228 ASP cc_start: 0.8595 (p0) cc_final: 0.7733 (p0) REVERT: B 258 ASP cc_start: 0.7658 (t0) cc_final: 0.7360 (t0) REVERT: G 26 ASP cc_start: 0.7781 (t70) cc_final: 0.7530 (t70) REVERT: G 41 CYS cc_start: 0.8607 (t) cc_final: 0.8248 (m) REVERT: N 43 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7373 (mtmm) REVERT: R 132 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7502 (mm) REVERT: R 295 MET cc_start: 0.8253 (tpp) cc_final: 0.8019 (mmp) REVERT: R 354 ILE cc_start: 0.8133 (tp) cc_final: 0.7841 (tt) REVERT: R 371 MET cc_start: 0.2687 (mmt) cc_final: 0.2330 (mmm) outliers start: 18 outliers final: 13 residues processed: 144 average time/residue: 1.2892 time to fit residues: 197.1711 Evaluate side-chains 141 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ILE 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 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 62 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 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** A 375 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.173369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.133881 restraints weight = 9572.836| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.21 r_work: 0.3408 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8316 Z= 0.284 Angle : 0.564 6.046 11258 Z= 0.298 Chirality : 0.043 0.170 1279 Planarity : 0.003 0.045 1426 Dihedral : 8.549 158.972 1145 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.37 % Allowed : 20.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.26), residues: 1017 helix: 1.90 (0.26), residues: 383 sheet: -0.18 (0.33), residues: 219 loop : -0.78 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 339 HIS 0.011 0.001 HIS A 220 PHE 0.017 0.002 PHE N 108 TYR 0.013 0.001 TYR R 153 ARG 0.004 0.000 ARG A 337 *********************** 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 147 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.950 Fit side-chains REVERT: A 31 GLN cc_start: 0.7819 (tp40) cc_final: 0.7545 (mp10) REVERT: B 46 ARG cc_start: 0.8169 (tpm170) cc_final: 0.7826 (tpp-160) REVERT: B 228 ASP cc_start: 0.8719 (p0) cc_final: 0.8329 (p0) REVERT: B 258 ASP cc_start: 0.7583 (t0) cc_final: 0.7337 (t0) REVERT: G 41 CYS cc_start: 0.8630 (t) cc_final: 0.8278 (m) REVERT: N 43 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.7402 (mtmm) REVERT: R 132 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7467 (mm) REVERT: R 253 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7245 (mt) REVERT: R 284 SER cc_start: 0.8150 (m) cc_final: 0.7655 (p) REVERT: R 295 MET cc_start: 0.8309 (tpp) cc_final: 0.8074 (mmp) REVERT: R 371 MET cc_start: 0.2348 (mmt) cc_final: 0.2046 (mmm) REVERT: R 402 LYS cc_start: 0.7489 (mtpt) cc_final: 0.6900 (mttm) outliers start: 21 outliers final: 12 residues processed: 138 average time/residue: 1.6453 time to fit residues: 241.0828 Evaluate side-chains 134 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 1.568 ------------------------------------------------------------------------------- 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 70 LEU 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 7 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 14 optimal weight: 0.0770 chunk 1 optimal weight: 3.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.175221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.136045 restraints weight = 9643.112| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.21 r_work: 0.3446 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8316 Z= 0.206 Angle : 0.537 6.345 11258 Z= 0.285 Chirality : 0.042 0.181 1279 Planarity : 0.003 0.045 1426 Dihedral : 8.324 154.814 1145 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.92 % Allowed : 21.31 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.26), residues: 1017 helix: 1.90 (0.26), residues: 388 sheet: -0.07 (0.34), residues: 213 loop : -0.81 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 339 HIS 0.006 0.001 HIS A 220 PHE 0.015 0.002 PHE A 212 TYR 0.011 0.001 TYR R 153 ARG 0.008 0.000 ARG A 337 *********************** 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 142 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.884 Fit side-chains REVERT: A 31 GLN cc_start: 0.7781 (tp40) cc_final: 0.7516 (mp10) REVERT: A 334 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8373 (mm-30) REVERT: B 46 ARG cc_start: 0.8176 (tpm170) cc_final: 0.7870 (tpp-160) REVERT: B 135 VAL cc_start: 0.8610 (p) cc_final: 0.8355 (t) REVERT: B 228 ASP cc_start: 0.8711 (p0) cc_final: 0.8093 (p0) REVERT: B 258 ASP cc_start: 0.7582 (t0) cc_final: 0.7302 (t0) REVERT: G 41 CYS cc_start: 0.8625 (t) cc_final: 0.8280 (m) REVERT: N 43 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.7393 (mtmm) REVERT: R 129 PHE cc_start: 0.6987 (m-10) cc_final: 0.6728 (m-10) REVERT: R 132 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7478 (mm) REVERT: R 253 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7297 (mt) REVERT: R 295 MET cc_start: 0.8298 (tpp) cc_final: 0.8075 (mmp) REVERT: R 371 MET cc_start: 0.2309 (mmt) cc_final: 0.2059 (mmm) outliers start: 17 outliers final: 14 residues processed: 134 average time/residue: 1.2916 time to fit residues: 183.5144 Evaluate side-chains 137 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 70 LEU Chi-restraints excluded: chain B residue 87 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 69 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 50 optimal weight: 0.0470 chunk 22 optimal weight: 2.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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** R 304 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.175848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.136642 restraints weight = 9456.515| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.20 r_work: 0.3457 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8316 Z= 0.200 Angle : 0.532 6.752 11258 Z= 0.282 Chirality : 0.042 0.171 1279 Planarity : 0.003 0.045 1426 Dihedral : 8.156 152.942 1145 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.14 % Allowed : 21.76 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.26), residues: 1017 helix: 1.93 (0.26), residues: 388 sheet: -0.06 (0.34), residues: 213 loop : -0.79 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 339 HIS 0.006 0.001 HIS A 220 PHE 0.016 0.001 PHE A 212 TYR 0.011 0.001 TYR R 153 ARG 0.005 0.000 ARG A 337 ********************** 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 145 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.870 Fit side-chains REVERT: A 31 GLN cc_start: 0.7792 (tp40) cc_final: 0.7524 (mp10) REVERT: B 46 ARG cc_start: 0.8177 (tpm170) cc_final: 0.7873 (tpp-160) REVERT: B 228 ASP cc_start: 0.8692 (p0) cc_final: 0.8021 (p0) REVERT: B 258 ASP cc_start: 0.7649 (t0) cc_final: 0.7295 (t0) REVERT: G 26 ASP cc_start: 0.7764 (t70) cc_final: 0.7490 (t70) REVERT: G 41 CYS cc_start: 0.8632 (t) cc_final: 0.8271 (m) REVERT: N 31 ASN cc_start: 0.7719 (m110) cc_final: 0.7256 (p0) REVERT: N 43 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7372 (mtmm) REVERT: R 129 PHE cc_start: 0.7002 (m-10) cc_final: 0.6766 (m-10) REVERT: R 132 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7501 (mm) REVERT: R 276 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7616 (mt) REVERT: R 295 MET cc_start: 0.8321 (tpp) cc_final: 0.8096 (mmp) REVERT: R 371 MET cc_start: 0.2185 (mmt) cc_final: 0.1949 (mmm) outliers start: 19 outliers final: 15 residues processed: 136 average time/residue: 1.2322 time to fit residues: 177.7023 Evaluate side-chains 141 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 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 11 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 42 optimal weight: 0.0470 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.176190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.136701 restraints weight = 9592.796| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.22 r_work: 0.3458 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8316 Z= 0.199 Angle : 0.556 11.988 11258 Z= 0.293 Chirality : 0.042 0.165 1279 Planarity : 0.003 0.045 1426 Dihedral : 8.207 153.164 1145 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.03 % Allowed : 21.98 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.26), residues: 1017 helix: 1.96 (0.26), residues: 388 sheet: -0.04 (0.34), residues: 213 loop : -0.79 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 339 HIS 0.006 0.001 HIS A 220 PHE 0.018 0.001 PHE R 177 TYR 0.011 0.001 TYR N 95 ARG 0.009 0.000 ARG A 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6799.25 seconds wall clock time: 118 minutes 48.01 seconds (7128.01 seconds total)