Starting phenix.real_space_refine on Sun May 11 14:10:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k8j_36951/05_2025/8k8j_36951_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k8j_36951/05_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_36951/05_2025/8k8j_36951.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k8j_36951/05_2025/8k8j_36951.map" model { file = "/net/cci-nas-00/data/ceres_data/8k8j_36951/05_2025/8k8j_36951_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k8j_36951/05_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-5687/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: 5.23, per 1000 atoms: 0.64 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: 2.16 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.84 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: 2.33 Time building geometry restraints manager: 2.41 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: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.750 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:11.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.480 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.13257 ( 423) hydrogen bonds : angle 5.85791 ( 1203) SS BOND : bond 0.00368 ( 3) SS BOND : angle 1.76057 ( 6) covalent geometry : bond 0.00360 ( 8316) covalent geometry : angle 0.57657 (11258) *********************** 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 : 0.841 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: 1.3224 time to fit residues: 217.5180 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 : 0.909 ------------------------------------------------------------------------------- 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 = 44)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.136034 restraints weight = 9426.220| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.20 r_work: 0.3435 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 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 8319 Z= 0.149 Angle : 0.552 7.778 11264 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 Details of bonding type rmsd hydrogen bonds : bond 0.04042 ( 423) hydrogen bonds : angle 4.83641 ( 1203) SS BOND : bond 0.00368 ( 3) SS BOND : angle 1.38794 ( 6) covalent geometry : bond 0.00338 ( 8316) covalent geometry : angle 0.55139 (11258) *********************** 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 : 0.827 Fit side-chains REVERT: A 24 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7453 (mtmm) REVERT: A 31 GLN cc_start: 0.7796 (tp40) cc_final: 0.7530 (mp10) REVERT: B 17 GLN cc_start: 0.8263 (tm-30) cc_final: 0.8038 (tm-30) REVERT: B 105 TYR cc_start: 0.9027 (OUTLIER) cc_final: 0.8575 (t80) REVERT: B 195 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7505 (p0) REVERT: B 258 ASP cc_start: 0.7656 (t0) cc_final: 0.7342 (t0) REVERT: G 32 LYS cc_start: 0.7331 (tmmt) cc_final: 0.7116 (tttt) REVERT: N 43 LYS cc_start: 0.7574 (OUTLIER) cc_final: 0.7285 (mtmm) REVERT: N 120 GLN cc_start: 0.7753 (mm-40) cc_final: 0.7551 (mm-40) REVERT: R 371 MET cc_start: 0.2569 (mmt) cc_final: 0.2228 (mmm) outliers start: 14 outliers final: 4 residues processed: 135 average time/residue: 1.2594 time to fit residues: 180.0025 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 : 0.903 ------------------------------------------------------------------------------- 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: 0.8980 chunk 96 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 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: 1.7184 ------------------------------------------------------------------------------- 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 = 0.3984 r_free = 0.3984 target = 0.171161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.131535 restraints weight = 9723.214| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.22 r_work: 0.3379 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 8319 Z= 0.249 Angle : 0.609 7.193 11264 Z= 0.322 Chirality : 0.045 0.178 1279 Planarity : 0.004 0.049 1426 Dihedral : 10.324 164.354 1145 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.59 % Allowed : 13.30 % Favored : 84.10 % 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: 0.22 (0.26), residues: 1017 helix: 1.53 (0.26), residues: 387 sheet: -0.20 (0.34), residues: 224 loop : -0.96 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 339 HIS 0.005 0.001 HIS A 347 PHE 0.023 0.002 PHE N 108 TYR 0.017 0.002 TYR R 153 ARG 0.005 0.000 ARG R 186 Details of bonding type rmsd hydrogen bonds : bond 0.04385 ( 423) hydrogen bonds : angle 4.94682 ( 1203) SS BOND : bond 0.00351 ( 3) SS BOND : angle 1.63907 ( 6) covalent geometry : bond 0.00588 ( 8316) covalent geometry : angle 0.60820 (11258) *********************** 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 152 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.849 Fit side-chains REVERT: A 20 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.7317 (ttp-110) REVERT: A 24 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.7541 (mtmm) REVERT: A 31 GLN cc_start: 0.7866 (tp40) cc_final: 0.7634 (mp10) REVERT: B 46 ARG cc_start: 0.8153 (tpm170) cc_final: 0.7818 (tpp-160) REVERT: B 186 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7179 (m-30) REVERT: B 195 ASP cc_start: 0.7767 (OUTLIER) cc_final: 0.7471 (p0) REVERT: B 258 ASP cc_start: 0.7802 (t0) cc_final: 0.7460 (t0) REVERT: G 32 LYS cc_start: 0.7519 (tmmt) cc_final: 0.7277 (tttt) REVERT: N 43 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7469 (mtmm) REVERT: R 150 ARG cc_start: 0.6263 (mtm-85) cc_final: 0.5892 (ptt180) REVERT: R 276 LEU cc_start: 0.7887 (mt) cc_final: 0.7568 (mt) REVERT: R 353 ILE cc_start: 0.7486 (OUTLIER) cc_final: 0.7211 (mp) outliers start: 23 outliers final: 6 residues processed: 140 average time/residue: 1.2967 time to fit residues: 191.8496 Evaluate side-chains 135 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 95 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 82 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 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 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 = 0.4012 r_free = 0.4012 target = 0.173834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.134797 restraints weight = 9529.061| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.19 r_work: 0.3438 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1538 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= 0.148 Angle : 0.537 6.678 11264 Z= 0.285 Chirality : 0.042 0.137 1279 Planarity : 0.003 0.048 1426 Dihedral : 9.335 160.228 1145 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.14 % Allowed : 16.46 % Favored : 81.40 % 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: 0.42 (0.26), residues: 1017 helix: 1.79 (0.26), residues: 387 sheet: -0.23 (0.34), residues: 220 loop : -0.88 (0.31), 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 0.001 PHE R 189 TYR 0.012 0.001 TYR R 153 ARG 0.003 0.000 ARG R 186 Details of bonding type rmsd hydrogen bonds : bond 0.03853 ( 423) hydrogen bonds : angle 4.70153 ( 1203) SS BOND : bond 0.00282 ( 3) SS BOND : angle 0.99659 ( 6) covalent geometry : bond 0.00337 ( 8316) covalent geometry : angle 0.53692 (11258) *********************** 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 150 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.825 Fit side-chains REVERT: A 24 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7551 (mtmm) REVERT: A 31 GLN cc_start: 0.7820 (tp40) cc_final: 0.7565 (mp10) REVERT: B 195 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7515 (p0) REVERT: B 228 ASP cc_start: 0.8695 (OUTLIER) cc_final: 0.8416 (p0) REVERT: B 258 ASP cc_start: 0.7707 (t0) cc_final: 0.7443 (t0) REVERT: N 43 LYS cc_start: 0.7611 (OUTLIER) cc_final: 0.7355 (mtmm) REVERT: N 120 GLN cc_start: 0.7718 (mm-40) cc_final: 0.7502 (mm-40) REVERT: R 150 ARG cc_start: 0.6161 (mtm-85) cc_final: 0.5750 (ptt180) REVERT: R 253 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7337 (mt) REVERT: R 276 LEU cc_start: 0.7801 (mt) cc_final: 0.7437 (mt) REVERT: R 354 ILE cc_start: 0.8173 (tp) cc_final: 0.7866 (tt) REVERT: R 402 LYS cc_start: 0.7364 (mtpt) cc_final: 0.6793 (mttp) outliers start: 19 outliers final: 10 residues processed: 141 average time/residue: 1.2268 time to fit residues: 183.2109 Evaluate side-chains 139 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 380 GLU 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 B residue 228 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 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: 0.8980 chunk 36 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 8 optimal weight: 0.0060 chunk 7 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 88 ASN ** 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 = 0.4026 r_free = 0.4026 target = 0.175097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.136302 restraints weight = 9471.963| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.19 r_work: 0.3461 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8319 Z= 0.127 Angle : 0.510 5.990 11264 Z= 0.272 Chirality : 0.041 0.136 1279 Planarity : 0.003 0.047 1426 Dihedral : 8.490 154.081 1145 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.37 % Allowed : 17.70 % 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 (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 (0.27), residues: 1017 helix: 1.92 (0.26), residues: 387 sheet: -0.22 (0.34), residues: 221 loop : -0.80 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 339 HIS 0.003 0.000 HIS A 347 PHE 0.012 0.001 PHE A 212 TYR 0.011 0.001 TYR N 95 ARG 0.003 0.000 ARG A 337 Details of bonding type rmsd hydrogen bonds : bond 0.03652 ( 423) hydrogen bonds : angle 4.57694 ( 1203) SS BOND : bond 0.00272 ( 3) SS BOND : angle 0.71597 ( 6) covalent geometry : bond 0.00283 ( 8316) covalent geometry : angle 0.50955 (11258) *********************** 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 155 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.923 Fit side-chains REVERT: A 31 GLN cc_start: 0.7784 (tp40) cc_final: 0.7524 (mp10) REVERT: B 46 ARG cc_start: 0.8141 (tpm170) cc_final: 0.7800 (tpp-160) REVERT: B 195 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7540 (p0) REVERT: B 228 ASP cc_start: 0.8686 (OUTLIER) cc_final: 0.8113 (p0) REVERT: B 258 ASP cc_start: 0.7691 (t0) cc_final: 0.7399 (t0) REVERT: G 17 GLU cc_start: 0.7431 (tp30) cc_final: 0.7073 (mm-30) REVERT: G 41 CYS cc_start: 0.8641 (t) cc_final: 0.8279 (m) REVERT: N 43 LYS cc_start: 0.7615 (OUTLIER) cc_final: 0.7333 (mtmm) REVERT: R 132 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7511 (mm) REVERT: R 295 MET cc_start: 0.8277 (tpp) cc_final: 0.8032 (mmp) REVERT: R 354 ILE cc_start: 0.8243 (tp) cc_final: 0.7934 (tt) REVERT: R 402 LYS cc_start: 0.7464 (mtpt) cc_final: 0.6927 (mttp) outliers start: 21 outliers final: 8 residues processed: 143 average time/residue: 1.2265 time to fit residues: 186.0319 Evaluate side-chains 138 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 195 ASP Chi-restraints excluded: chain B residue 228 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 26 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 16 optimal weight: 0.0670 chunk 77 optimal weight: 0.8980 chunk 9 optimal weight: 0.0170 chunk 2 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- 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** 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 = 0.4041 r_free = 0.4041 target = 0.176302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.137561 restraints weight = 9437.180| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.21 r_work: 0.3450 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8319 Z= 0.115 Angle : 0.496 5.655 11264 Z= 0.265 Chirality : 0.040 0.135 1279 Planarity : 0.003 0.046 1426 Dihedral : 8.053 151.355 1145 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.59 % Allowed : 17.47 % 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 (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: 0.66 (0.27), residues: 1017 helix: 1.97 (0.26), residues: 389 sheet: -0.05 (0.34), residues: 213 loop : -0.75 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 339 HIS 0.003 0.000 HIS A 347 PHE 0.012 0.001 PHE A 212 TYR 0.010 0.001 TYR N 95 ARG 0.008 0.000 ARG A 337 Details of bonding type rmsd hydrogen bonds : bond 0.03507 ( 423) hydrogen bonds : angle 4.46270 ( 1203) SS BOND : bond 0.00262 ( 3) SS BOND : angle 0.64925 ( 6) covalent geometry : bond 0.00251 ( 8316) covalent geometry : angle 0.49542 (11258) *********************** 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 159 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.824 Fit side-chains REVERT: A 28 LYS cc_start: 0.8262 (mmtp) cc_final: 0.7483 (ptmm) REVERT: A 31 GLN cc_start: 0.7783 (tp40) cc_final: 0.7518 (tm-30) REVERT: B 46 ARG cc_start: 0.8128 (tpm170) cc_final: 0.7835 (tpp-160) REVERT: B 135 VAL cc_start: 0.8788 (p) cc_final: 0.8516 (t) REVERT: B 228 ASP cc_start: 0.8656 (OUTLIER) cc_final: 0.7682 (p0) REVERT: B 258 ASP cc_start: 0.7647 (t0) cc_final: 0.7356 (t0) REVERT: G 41 CYS cc_start: 0.8672 (t) cc_final: 0.8281 (m) REVERT: N 43 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7365 (mtmm) REVERT: R 132 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7513 (mm) REVERT: R 253 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7291 (mt) REVERT: R 295 MET cc_start: 0.8254 (tpp) cc_final: 0.8018 (mmp) REVERT: R 354 ILE cc_start: 0.8178 (tp) cc_final: 0.7892 (tt) REVERT: R 371 MET cc_start: 0.2505 (mmt) cc_final: 0.2202 (mmm) REVERT: R 402 LYS cc_start: 0.7450 (mtpt) cc_final: 0.6904 (mttp) outliers start: 23 outliers final: 10 residues processed: 149 average time/residue: 1.1185 time to fit residues: 177.2592 Evaluate side-chains 139 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 228 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 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: 5.9990 chunk 38 optimal weight: 0.4980 chunk 40 optimal weight: 0.3980 chunk 26 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 3 optimal weight: 0.4980 chunk 33 optimal weight: 3.9990 chunk 14 optimal weight: 0.0570 chunk 49 optimal weight: 0.0870 chunk 45 optimal weight: 3.9990 overall best weight: 0.3076 ------------------------------------------------------------------------------- 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** R 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.178429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.139857 restraints weight = 9545.841| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.21 r_work: 0.3505 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8319 Z= 0.102 Angle : 0.498 7.603 11264 Z= 0.263 Chirality : 0.040 0.146 1279 Planarity : 0.003 0.045 1426 Dihedral : 7.631 145.080 1145 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.03 % Allowed : 19.73 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.27), residues: 1017 helix: 2.12 (0.26), residues: 388 sheet: 0.06 (0.34), residues: 212 loop : -0.72 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 339 HIS 0.003 0.000 HIS A 347 PHE 0.013 0.001 PHE A 212 TYR 0.011 0.001 TYR R 153 ARG 0.009 0.000 ARG A 337 Details of bonding type rmsd hydrogen bonds : bond 0.03377 ( 423) hydrogen bonds : angle 4.35898 ( 1203) SS BOND : bond 0.00292 ( 3) SS BOND : angle 0.49054 ( 6) covalent geometry : bond 0.00219 ( 8316) covalent geometry : angle 0.49766 (11258) *********************** 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 156 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.894 Fit side-chains REVERT: A 31 GLN cc_start: 0.7679 (tp40) cc_final: 0.7460 (tm-30) REVERT: A 213 GLN cc_start: 0.8283 (mt0) cc_final: 0.8073 (tt0) REVERT: B 46 ARG cc_start: 0.8147 (tpm170) cc_final: 0.7844 (tpp-160) REVERT: B 135 VAL cc_start: 0.8662 (p) cc_final: 0.8438 (t) REVERT: B 228 ASP cc_start: 0.8650 (OUTLIER) cc_final: 0.7976 (p0) REVERT: B 258 ASP cc_start: 0.7658 (t0) cc_final: 0.7393 (t0) REVERT: G 41 CYS cc_start: 0.8644 (t) cc_final: 0.8278 (m) REVERT: N 43 LYS cc_start: 0.7617 (ptpt) cc_final: 0.7368 (mtmm) REVERT: R 129 PHE cc_start: 0.7054 (m-10) cc_final: 0.6790 (m-10) REVERT: R 132 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7463 (mm) outliers start: 18 outliers final: 12 residues processed: 145 average time/residue: 1.1131 time to fit residues: 171.9052 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 : 0.937 ------------------------------------------------------------------------------- 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 87 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 12 VAL 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: 2.9990 chunk 57 optimal weight: 0.0980 chunk 35 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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** R 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.175348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.136164 restraints weight = 9588.328| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.21 r_work: 0.3438 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1845 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 : 0.561 7.979 11264 Z= 0.291 Chirality : 0.042 0.188 1279 Planarity : 0.003 0.045 1426 Dihedral : 8.229 154.197 1145 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.37 % Allowed : 19.95 % Favored : 77.68 % 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: 0.67 (0.26), residues: 1017 helix: 2.10 (0.26), residues: 382 sheet: -0.19 (0.33), residues: 221 loop : -0.73 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 339 HIS 0.012 0.001 HIS A 220 PHE 0.017 0.002 PHE R 177 TYR 0.012 0.001 TYR R 153 ARG 0.004 0.000 ARG A 337 Details of bonding type rmsd hydrogen bonds : bond 0.03730 ( 423) hydrogen bonds : angle 4.52653 ( 1203) SS BOND : bond 0.00281 ( 3) SS BOND : angle 0.82126 ( 6) covalent geometry : bond 0.00355 ( 8316) covalent geometry : angle 0.56083 (11258) *********************** 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 148 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.855 Fit side-chains REVERT: A 31 GLN cc_start: 0.7768 (tp40) cc_final: 0.7492 (mp10) REVERT: B 46 ARG cc_start: 0.8182 (tpm170) cc_final: 0.7860 (tpp-160) REVERT: B 228 ASP cc_start: 0.8708 (OUTLIER) cc_final: 0.8317 (p0) REVERT: B 258 ASP cc_start: 0.7727 (t0) cc_final: 0.7442 (t0) REVERT: G 41 CYS cc_start: 0.8615 (t) cc_final: 0.8255 (m) REVERT: N 43 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7365 (mtmm) REVERT: R 132 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7495 (mm) REVERT: R 253 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7272 (mt) REVERT: R 371 MET cc_start: 0.2325 (mmt) cc_final: 0.2084 (mmm) REVERT: R 402 LYS cc_start: 0.7500 (mtpt) cc_final: 0.6917 (mttp) outliers start: 21 outliers final: 13 residues processed: 138 average time/residue: 1.1666 time to fit residues: 171.3071 Evaluate side-chains 138 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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 87 THR Chi-restraints excluded: chain B residue 228 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 7 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 44 optimal weight: 0.0980 chunk 4 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 14 optimal weight: 0.0170 chunk 1 optimal weight: 4.9990 overall best weight: 0.5820 ------------------------------------------------------------------------------- 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** 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 = 0.176614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.137520 restraints weight = 9646.380| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.21 r_work: 0.3466 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8319 Z= 0.125 Angle : 0.543 7.673 11264 Z= 0.282 Chirality : 0.042 0.203 1279 Planarity : 0.003 0.044 1426 Dihedral : 7.924 149.195 1145 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.25 % Allowed : 20.74 % 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 (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: 1.95 (0.26), residues: 394 sheet: -0.04 (0.34), residues: 213 loop : -0.82 (0.31), residues: 410 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 0.016 0.001 PHE R 129 TYR 0.011 0.001 TYR R 153 ARG 0.008 0.000 ARG A 337 Details of bonding type rmsd hydrogen bonds : bond 0.03578 ( 423) hydrogen bonds : angle 4.47614 ( 1203) SS BOND : bond 0.00288 ( 3) SS BOND : angle 0.60290 ( 6) covalent geometry : bond 0.00283 ( 8316) covalent geometry : angle 0.54283 (11258) *********************** 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 145 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.915 Fit side-chains REVERT: A 31 GLN cc_start: 0.7813 (tp40) cc_final: 0.7540 (mp10) REVERT: B 46 ARG cc_start: 0.8164 (tpm170) cc_final: 0.7803 (tpp-160) REVERT: B 135 VAL cc_start: 0.8572 (p) cc_final: 0.8336 (t) REVERT: B 228 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.8199 (p0) REVERT: B 258 ASP cc_start: 0.7695 (t0) cc_final: 0.7429 (t0) REVERT: G 26 ASP cc_start: 0.7684 (t70) cc_final: 0.7442 (t70) REVERT: G 41 CYS cc_start: 0.8601 (t) cc_final: 0.8236 (m) REVERT: N 31 ASN cc_start: 0.7682 (m110) cc_final: 0.7244 (p0) REVERT: N 43 LYS cc_start: 0.7597 (OUTLIER) cc_final: 0.7349 (mtmm) REVERT: R 129 PHE cc_start: 0.6996 (m-10) cc_final: 0.6783 (m-10) REVERT: R 132 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7484 (mm) REVERT: R 371 MET cc_start: 0.2255 (mmt) cc_final: 0.2044 (mmm) REVERT: R 402 LYS cc_start: 0.7505 (mtpt) cc_final: 0.6934 (mttp) outliers start: 20 outliers final: 16 residues processed: 134 average time/residue: 1.2313 time to fit residues: 174.9108 Evaluate side-chains 139 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 228 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 110 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 92 optimal weight: 0.0870 chunk 69 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.9360 ------------------------------------------------------------------------------- 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 = 0.4025 r_free = 0.4025 target = 0.174706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.135315 restraints weight = 9500.945| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.22 r_work: 0.3428 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 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 : 0.004 0.046 8319 Z= 0.160 Angle : 0.573 7.910 11264 Z= 0.298 Chirality : 0.043 0.187 1279 Planarity : 0.003 0.043 1426 Dihedral : 8.119 151.734 1145 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.37 % Allowed : 20.86 % 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: 0.53 (0.26), residues: 1017 helix: 1.89 (0.26), residues: 388 sheet: -0.18 (0.33), residues: 219 loop : -0.83 (0.31), residues: 410 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 0.016 0.002 PHE R 129 TYR 0.012 0.001 TYR R 153 ARG 0.009 0.000 ARG A 337 Details of bonding type rmsd hydrogen bonds : bond 0.03793 ( 423) hydrogen bonds : angle 4.59348 ( 1203) SS BOND : bond 0.00320 ( 3) SS BOND : angle 0.86759 ( 6) covalent geometry : bond 0.00370 ( 8316) covalent geometry : angle 0.57305 (11258) ********************** 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 146 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.861 Fit side-chains REVERT: A 31 GLN cc_start: 0.7802 (tp40) cc_final: 0.7531 (mp10) REVERT: B 46 ARG cc_start: 0.8202 (tpm170) cc_final: 0.7889 (tpp-160) REVERT: B 228 ASP cc_start: 0.8725 (OUTLIER) cc_final: 0.8366 (p0) REVERT: B 258 ASP cc_start: 0.7784 (t0) cc_final: 0.7406 (t0) REVERT: G 41 CYS cc_start: 0.8588 (t) cc_final: 0.8262 (m) REVERT: N 43 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7362 (mtmm) REVERT: R 132 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7476 (mm) REVERT: R 253 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7279 (mt) REVERT: R 284 SER cc_start: 0.8155 (m) cc_final: 0.7679 (p) REVERT: R 402 LYS cc_start: 0.7531 (mtpt) cc_final: 0.6981 (mttp) outliers start: 21 outliers final: 17 residues processed: 135 average time/residue: 1.1474 time to fit residues: 164.8148 Evaluate side-chains 143 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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 44 GLN 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 228 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 110 VAL 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 11 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 0.0670 chunk 29 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 116 GLN R 304 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.176926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.137637 restraints weight = 9629.786| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.23 r_work: 0.3460 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8319 Z= 0.122 Angle : 0.546 8.213 11264 Z= 0.284 Chirality : 0.042 0.183 1279 Planarity : 0.003 0.043 1426 Dihedral : 7.871 148.061 1145 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.37 % Allowed : 21.53 % 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: 0.60 (0.26), residues: 1017 helix: 1.91 (0.26), residues: 394 sheet: -0.05 (0.34), residues: 213 loop : -0.84 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 339 HIS 0.005 0.001 HIS A 220 PHE 0.015 0.001 PHE R 177 TYR 0.011 0.001 TYR R 153 ARG 0.010 0.000 ARG A 346 Details of bonding type rmsd hydrogen bonds : bond 0.03544 ( 423) hydrogen bonds : angle 4.46740 ( 1203) SS BOND : bond 0.00310 ( 3) SS BOND : angle 0.60142 ( 6) covalent geometry : bond 0.00273 ( 8316) covalent geometry : angle 0.54612 (11258) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6276.26 seconds wall clock time: 108 minutes 44.86 seconds (6524.86 seconds total)